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allianceauth/allianceauth | allianceauth/timerboard/views.py | AddUpdateMixin.get_form_kwargs | def get_form_kwargs(self):
"""
Inject the request user into the kwargs passed to the form
"""
kwargs = super(AddUpdateMixin, self).get_form_kwargs()
kwargs.update({'user': self.request.user})
return kwargs | python | def get_form_kwargs(self):
"""
Inject the request user into the kwargs passed to the form
"""
kwargs = super(AddUpdateMixin, self).get_form_kwargs()
kwargs.update({'user': self.request.user})
return kwargs | [
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allianceauth/allianceauth | allianceauth/services/abstract.py | ServicesCRUDMixin.get_object | def get_object(self, queryset=None):
"""
Returns the object the view is displaying.
"""
if queryset is None:
queryset = self.get_queryset()
try:
return queryset.get(user__pk=self.request.user.pk)
except ObjectDoesNotExist:
raise Http404 | python | def get_object(self, queryset=None):
"""
Returns the object the view is displaying.
"""
if queryset is None:
queryset = self.get_queryset()
try:
return queryset.get(user__pk=self.request.user.pk)
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allianceauth/allianceauth | allianceauth/groupmanagement/managers.py | GroupManager.can_manage_groups | def can_manage_groups(cls, user):
"""
For use with user_passes_test decorator.
Check if the user can manage groups. Either has the
auth.group_management permission or is a leader of at least one group
and is also a Member.
:param user: django.contrib.auth.models.User for the request
:return: bool True if user can manage groups, False otherwise
"""
if user.is_authenticated:
return cls.has_management_permission(user) or user.leads_groups.all()
return False | python | def can_manage_groups(cls, user):
"""
For use with user_passes_test decorator.
Check if the user can manage groups. Either has the
auth.group_management permission or is a leader of at least one group
and is also a Member.
:param user: django.contrib.auth.models.User for the request
:return: bool True if user can manage groups, False otherwise
"""
if user.is_authenticated:
return cls.has_management_permission(user) or user.leads_groups.all()
return False | [
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allianceauth/allianceauth | allianceauth/groupmanagement/managers.py | GroupManager.can_manage_group | def can_manage_group(cls, user, group):
"""
Check user has permission to manage the given group
:param user: User object to test permission of
:param group: Group object the user is attempting to manage
:return: True if the user can manage the group
"""
if user.is_authenticated:
return cls.has_management_permission(user) or user.leads_groups.filter(group=group).exists()
return False | python | def can_manage_group(cls, user, group):
"""
Check user has permission to manage the given group
:param user: User object to test permission of
:param group: Group object the user is attempting to manage
:return: True if the user can manage the group
"""
if user.is_authenticated:
return cls.has_management_permission(user) or user.leads_groups.filter(group=group).exists()
return False | [
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allianceauth/allianceauth | allianceauth/groupmanagement/models.py | create_auth_group | def create_auth_group(sender, instance, created, **kwargs):
"""
Creates the AuthGroup model when a group is created
"""
if created:
AuthGroup.objects.create(group=instance) | python | def create_auth_group(sender, instance, created, **kwargs):
"""
Creates the AuthGroup model when a group is created
"""
if created:
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Proto.construct_command | def construct_command(self, command, keys=None, opts=None):
"""
Constructs a TS3 formatted command string
Keys can have a single nested list to construct a nested parameter
@param command: Command list
@type command: string
@param keys: Key/Value pairs
@type keys: dict
@param opts: Options
@type opts: list
"""
cstr = [command]
# Add the keys and values, escape as needed
if keys:
for key in keys:
if isinstance(keys[key], list):
ncstr = []
for nest in keys[key]:
ncstr.append("%s=%s" % (key, self._escape_str(nest)))
cstr.append("|".join(ncstr))
else:
cstr.append("%s=%s" % (key, self._escape_str(keys[key])))
# Add in options
if opts:
for opt in opts:
cstr.append("-%s" % opt)
return " ".join(cstr) | python | def construct_command(self, command, keys=None, opts=None):
"""
Constructs a TS3 formatted command string
Keys can have a single nested list to construct a nested parameter
@param command: Command list
@type command: string
@param keys: Key/Value pairs
@type keys: dict
@param opts: Options
@type opts: list
"""
cstr = [command]
# Add the keys and values, escape as needed
if keys:
for key in keys:
if isinstance(keys[key], list):
ncstr = []
for nest in keys[key]:
ncstr.append("%s=%s" % (key, self._escape_str(nest)))
cstr.append("|".join(ncstr))
else:
cstr.append("%s=%s" % (key, self._escape_str(keys[key])))
# Add in options
if opts:
for opt in opts:
cstr.append("-%s" % opt)
return " ".join(cstr) | [
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Proto.parse_command | def parse_command(self, commandstr):
"""
Parses a TS3 command string into command/keys/opts tuple
@param commandstr: Command string
@type commandstr: string
"""
if len(commandstr.split('|')) > 1:
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for cmd in commandstr.split('|'):
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return vals
cmdlist = commandstr.strip().split(' ')
command = None
keys = {}
opts = []
for key in cmdlist:
v = key.strip().split('=')
if len(v) > 1:
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if len(v) > 2:
# Fix the stupidities in TS3 escaping
v = [v[0], '='.join(v[1:])]
key, value = v
keys[key] = self._unescape_str(value)
elif not v == ['']:
if v[0][0] and v[0][0] == '-':
# Option
opts.append(v[0][1:])
else:
command = v[0]
d = {'keys': keys, 'opts': opts}
if command:
d['command'] = command
return d | python | def parse_command(self, commandstr):
"""
Parses a TS3 command string into command/keys/opts tuple
@param commandstr: Command string
@type commandstr: string
"""
if len(commandstr.split('|')) > 1:
vals = []
for cmd in commandstr.split('|'):
vals.append(self.parse_command(cmd))
return vals
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command = None
keys = {}
opts = []
for key in cmdlist:
v = key.strip().split('=')
if len(v) > 1:
# Key
if len(v) > 2:
# Fix the stupidities in TS3 escaping
v = [v[0], '='.join(v[1:])]
key, value = v
keys[key] = self._unescape_str(value)
elif not v == ['']:
if v[0][0] and v[0][0] == '-':
# Option
opts.append(v[0][1:])
else:
command = v[0]
d = {'keys': keys, 'opts': opts}
if command:
d['command'] = command
return d | [
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Proto._escape_str | def _escape_str(value):
"""
Escape a value into a TS3 compatible string
@param value: Value
@type value: string/int
"""
if isinstance(value, int):
return "%d" % value
value = value.replace("\\", r'\\')
for i, j in ts3_escape.items():
value = value.replace(i, j)
return value | python | def _escape_str(value):
"""
Escape a value into a TS3 compatible string
@param value: Value
@type value: string/int
"""
if isinstance(value, int):
return "%d" % value
value = value.replace("\\", r'\\')
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Proto._unescape_str | def _unescape_str(value):
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@param value: Value
@type value: string/int
"""
if isinstance(value, int):
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for i, j in ts3_escape.items():
value = value.replace(j, i)
return value | python | def _unescape_str(value):
"""
Unescape a TS3 compatible string into a normal string
@param value: Value
@type value: string/int
"""
if isinstance(value, int):
return "%d" % value
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Server.login | def login(self, username, password):
"""
Login to the TS3 Server
@param username: Username
@type username: str
@param password: Password
@type password: str
"""
d = self.send_command('login', keys={'client_login_name': username, 'client_login_password': password})
if d == 0:
self._log.info('Login Successful')
return True
return False | python | def login(self, username, password):
"""
Login to the TS3 Server
@param username: Username
@type username: str
@param password: Password
@type password: str
"""
d = self.send_command('login', keys={'client_login_name': username, 'client_login_password': password})
if d == 0:
self._log.info('Login Successful')
return True
return False | [
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Server.use | def use(self, id):
"""
Use a particular Virtual Server instance
@param id: Virtual Server ID
@type id: int
"""
if self._connected and id > 0:
self.send_command('use', keys={'sid': id}) | python | def use(self, id):
"""
Use a particular Virtual Server instance
@param id: Virtual Server ID
@type id: int
"""
if self._connected and id > 0:
self.send_command('use', keys={'sid': id}) | [
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allianceauth/allianceauth | allianceauth/services/modules/example/auth_hooks.py | ExampleService.render_services_ctrl | def render_services_ctrl(self, request):
"""
Example for rendering the service control panel row
You can override the default template and create a
custom one if you wish.
:param request:
:return:
"""
urls = self.Urls()
urls.auth_activate = 'auth_example_activate'
urls.auth_deactivate = 'auth_example_deactivate'
urls.auth_reset_password = 'auth_example_reset_password'
urls.auth_set_password = 'auth_example_set_password'
return render_to_string(self.service_ctrl_template, {
'service_name': self.title,
'urls': urls,
'service_url': self.service_url,
'username': 'example username'
}, request=request) | python | def render_services_ctrl(self, request):
"""
Example for rendering the service control panel row
You can override the default template and create a
custom one if you wish.
:param request:
:return:
"""
urls = self.Urls()
urls.auth_activate = 'auth_example_activate'
urls.auth_deactivate = 'auth_example_deactivate'
urls.auth_reset_password = 'auth_example_reset_password'
urls.auth_set_password = 'auth_example_set_password'
return render_to_string(self.service_ctrl_template, {
'service_name': self.title,
'urls': urls,
'service_url': self.service_url,
'username': 'example username'
}, request=request) | [
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allianceauth/allianceauth | allianceauth/eveonline/models.py | EveCharacter.alliance | def alliance(self) -> Union[EveAllianceInfo, None]:
"""
Pseudo foreign key from alliance_id to EveAllianceInfo
:raises: EveAllianceInfo.DoesNotExist
:return: EveAllianceInfo or None
"""
if self.alliance_id is None:
return None
return EveAllianceInfo.objects.get(alliance_id=self.alliance_id) | python | def alliance(self) -> Union[EveAllianceInfo, None]:
"""
Pseudo foreign key from alliance_id to EveAllianceInfo
:raises: EveAllianceInfo.DoesNotExist
:return: EveAllianceInfo or None
"""
if self.alliance_id is None:
return None
return EveAllianceInfo.objects.get(alliance_id=self.alliance_id) | [
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/signals.py | pre_save_config | def pre_save_config(sender, instance, *args, **kwargs):
"""
Checks if enable was toggled on group config and
deletes groups if necessary.
"""
logger.debug("Received pre_save from {}".format(instance))
if not instance.pk:
# new model being created
return
try:
old_instance = AutogroupsConfig.objects.get(pk=instance.pk)
# Check if enable was toggled, delete groups?
if old_instance.alliance_groups is True and instance.alliance_groups is False:
instance.delete_alliance_managed_groups()
if old_instance.corp_groups is True and instance.corp_groups is False:
instance.delete_corp_managed_groups()
except AutogroupsConfig.DoesNotExist:
pass | python | def pre_save_config(sender, instance, *args, **kwargs):
"""
Checks if enable was toggled on group config and
deletes groups if necessary.
"""
logger.debug("Received pre_save from {}".format(instance))
if not instance.pk:
# new model being created
return
try:
old_instance = AutogroupsConfig.objects.get(pk=instance.pk)
# Check if enable was toggled, delete groups?
if old_instance.alliance_groups is True and instance.alliance_groups is False:
instance.delete_alliance_managed_groups()
if old_instance.corp_groups is True and instance.corp_groups is False:
instance.delete_corp_managed_groups()
except AutogroupsConfig.DoesNotExist:
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/signals.py | check_groups_on_profile_update | def check_groups_on_profile_update(sender, instance, created, *args, **kwargs):
"""
Trigger check when main character or state changes.
"""
AutogroupsConfig.objects.update_groups_for_user(instance.user) | python | def check_groups_on_profile_update(sender, instance, created, *args, **kwargs):
"""
Trigger check when main character or state changes.
"""
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/signals.py | autogroups_states_changed | def autogroups_states_changed(sender, instance, action, reverse, model, pk_set, *args, **kwargs):
"""
Trigger group membership update when a state is added or removed from
an autogroup config.
"""
if action.startswith('post_'):
for pk in pk_set:
try:
state = State.objects.get(pk=pk)
instance.update_group_membership_for_state(state)
except State.DoesNotExist:
# Deleted States handled by the profile state change
pass | python | def autogroups_states_changed(sender, instance, action, reverse, model, pk_set, *args, **kwargs):
"""
Trigger group membership update when a state is added or removed from
an autogroup config.
"""
if action.startswith('post_'):
for pk in pk_set:
try:
state = State.objects.get(pk=pk)
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except State.DoesNotExist:
# Deleted States handled by the profile state change
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allianceauth/allianceauth | allianceauth/authentication/admin.py | make_service_hooks_update_groups_action | def make_service_hooks_update_groups_action(service):
"""
Make a admin action for the given service
:param service: services.hooks.ServicesHook
:return: fn to update services groups for the selected users
"""
def update_service_groups(modeladmin, request, queryset):
for user in queryset: # queryset filtering doesn't work here?
service.update_groups(user)
update_service_groups.__name__ = str('update_{}_groups'.format(slugify(service.name)))
update_service_groups.short_description = "Sync groups for selected {} accounts".format(service.title)
return update_service_groups | python | def make_service_hooks_update_groups_action(service):
"""
Make a admin action for the given service
:param service: services.hooks.ServicesHook
:return: fn to update services groups for the selected users
"""
def update_service_groups(modeladmin, request, queryset):
for user in queryset: # queryset filtering doesn't work here?
service.update_groups(user)
update_service_groups.__name__ = str('update_{}_groups'.format(slugify(service.name)))
update_service_groups.short_description = "Sync groups for selected {} accounts".format(service.title)
return update_service_groups | [
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allianceauth/allianceauth | allianceauth/authentication/admin.py | make_service_hooks_sync_nickname_action | def make_service_hooks_sync_nickname_action(service):
"""
Make a sync_nickname admin action for the given service
:param service: services.hooks.ServicesHook
:return: fn to sync nickname for the selected users
"""
def sync_nickname(modeladmin, request, queryset):
for user in queryset: # queryset filtering doesn't work here?
service.sync_nickname(user)
sync_nickname.__name__ = str('sync_{}_nickname'.format(slugify(service.name)))
sync_nickname.short_description = "Sync nicknames for selected {} accounts".format(service.title)
return sync_nickname | python | def make_service_hooks_sync_nickname_action(service):
"""
Make a sync_nickname admin action for the given service
:param service: services.hooks.ServicesHook
:return: fn to sync nickname for the selected users
"""
def sync_nickname(modeladmin, request, queryset):
for user in queryset: # queryset filtering doesn't work here?
service.sync_nickname(user)
sync_nickname.__name__ = str('sync_{}_nickname'.format(slugify(service.name)))
sync_nickname.short_description = "Sync nicknames for selected {} accounts".format(service.title)
return sync_nickname | [
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allianceauth/allianceauth | allianceauth/thirdparty/navhelper/templatetags/navactive.py | renavactive | def renavactive(request, pattern):
"""
{% renavactive request "^/a_regex" %}
"""
if re.search(pattern, request.path):
return getattr(settings, "NAVHELPER_ACTIVE_CLASS", "active")
return getattr(settings, "NAVHELPER_NOT_ACTIVE_CLASS", "") | python | def renavactive(request, pattern):
"""
{% renavactive request "^/a_regex" %}
"""
if re.search(pattern, request.path):
return getattr(settings, "NAVHELPER_ACTIVE_CLASS", "active")
return getattr(settings, "NAVHELPER_NOT_ACTIVE_CLASS", "") | [
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allianceauth/allianceauth | allianceauth/thirdparty/navhelper/templatetags/navactive.py | navactive | def navactive(request, urls):
"""
{% navactive request "view_name another_view_name" %}
"""
url_list = set(urls.split())
resolved = resolve(request.path)
resolved_urls = set()
if resolved.url_name:
resolved_urls.add(resolved.url_name)
if resolved.namespaces:
resolved_urls = resolved_urls.union(["{}:{}".format(namespace, resolved.url_name) for namespace in resolved.namespaces])
resolved_urls = resolved_urls.union(["{}:".format(namespace) for namespace in resolved.namespaces])
if getattr(resolved, 'app_name', None):
resolved_urls = resolved_urls.union(["{}:{}".format(resolved.app_name, resolved.url_name), "{}:".format(resolved.app_name)])
if getattr(resolved, 'app_names', []):
resolved_urls = resolved_urls.union(["{}:{}".format(app_name, resolved.url_name) for app_name in resolved.app_names])
resolved_urls = resolved_urls.union(["{}:".format(app_name) for app_name in resolved.app_names])
if url_list and resolved_urls and bool(resolved_urls & url_list):
return getattr(settings, "NAVHELPER_ACTIVE_CLASS", "active")
return getattr(settings, "NAVHELPER_NOT_ACTIVE_CLASS", "") | python | def navactive(request, urls):
"""
{% navactive request "view_name another_view_name" %}
"""
url_list = set(urls.split())
resolved = resolve(request.path)
resolved_urls = set()
if resolved.url_name:
resolved_urls.add(resolved.url_name)
if resolved.namespaces:
resolved_urls = resolved_urls.union(["{}:{}".format(namespace, resolved.url_name) for namespace in resolved.namespaces])
resolved_urls = resolved_urls.union(["{}:".format(namespace) for namespace in resolved.namespaces])
if getattr(resolved, 'app_name', None):
resolved_urls = resolved_urls.union(["{}:{}".format(resolved.app_name, resolved.url_name), "{}:".format(resolved.app_name)])
if getattr(resolved, 'app_names', []):
resolved_urls = resolved_urls.union(["{}:{}".format(app_name, resolved.url_name) for app_name in resolved.app_names])
resolved_urls = resolved_urls.union(["{}:".format(app_name) for app_name in resolved.app_names])
if url_list and resolved_urls and bool(resolved_urls & url_list):
return getattr(settings, "NAVHELPER_ACTIVE_CLASS", "active")
return getattr(settings, "NAVHELPER_NOT_ACTIVE_CLASS", "") | [
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/models.py | AutogroupsConfigManager.update_groups_for_state | def update_groups_for_state(self, state: State):
"""
Update all the Group memberships for the users
who have State
:param state: State to update for
:return:
"""
users = get_users_for_state(state)
for config in self.filter(states=state):
logger.debug("in state loop")
for user in users:
logger.debug("in user loop for {}".format(user))
config.update_group_membership_for_user(user) | python | def update_groups_for_state(self, state: State):
"""
Update all the Group memberships for the users
who have State
:param state: State to update for
:return:
"""
users = get_users_for_state(state)
for config in self.filter(states=state):
logger.debug("in state loop")
for user in users:
logger.debug("in user loop for {}".format(user))
config.update_group_membership_for_user(user) | [
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/models.py | AutogroupsConfigManager.update_groups_for_user | def update_groups_for_user(self, user: User, state: State = None):
"""
Update the Group memberships for the given users state
:param user: User to update for
:param state: State to update user for
:return:
"""
if state is None:
state = user.profile.state
for config in self.filter(states=state):
# grant user new groups for their state
config.update_group_membership_for_user(user)
for config in self.exclude(states=state):
# ensure user does not have groups from previous state
config.remove_user_from_alliance_groups(user)
config.remove_user_from_corp_groups(user) | python | def update_groups_for_user(self, user: User, state: State = None):
"""
Update the Group memberships for the given users state
:param user: User to update for
:param state: State to update user for
:return:
"""
if state is None:
state = user.profile.state
for config in self.filter(states=state):
# grant user new groups for their state
config.update_group_membership_for_user(user)
for config in self.exclude(states=state):
# ensure user does not have groups from previous state
config.remove_user_from_alliance_groups(user)
config.remove_user_from_corp_groups(user) | [
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/models.py | AutogroupsConfig._replace_spaces | def _replace_spaces(self, name: str) -> str:
"""
Replace the spaces in the given name based on the config
:param name: name to replace spaces in
:return: name with spaces replaced with the configured character(s) or unchanged if configured
"""
if self.replace_spaces:
return name.strip().replace(' ', str(self.replace_spaces_with))
return name | python | def _replace_spaces(self, name: str) -> str:
"""
Replace the spaces in the given name based on the config
:param name: name to replace spaces in
:return: name with spaces replaced with the configured character(s) or unchanged if configured
"""
if self.replace_spaces:
return name.strip().replace(' ', str(self.replace_spaces_with))
return name | [
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allianceauth/allianceauth | allianceauth/services/modules/discord/manager.py | api_backoff | def api_backoff(func):
"""
Decorator, Handles HTTP 429 "Too Many Requests" messages from the Discord API
If blocking=True is specified, this function will block and retry
the function up to max_retries=n times, or 3 if retries is not specified.
If the API call still recieves a backoff timer this function will raise
a <DiscordApiTooBusy> exception.
If the caller chooses blocking=False, the decorator will raise a DiscordApiBackoff
exception and the caller can choose to retry after the given timespan available in
the retry_after property in seconds.
"""
class PerformBackoff(Exception):
def __init__(self, retry_after, retry_datetime, global_ratelimit):
super(Exception, self).__init__()
self.retry_after = int(retry_after)
self.retry_datetime = retry_datetime
self.global_ratelimit = global_ratelimit
@wraps(func)
def decorated(*args, **kwargs):
blocking = kwargs.get('blocking', False)
retries = kwargs.get('max_retries', 3)
# Strip our parameters
if 'max_retries' in kwargs:
del kwargs['max_retries']
if 'blocking' in kwargs:
del kwargs['blocking']
cache_key = 'DISCORD_BACKOFF_' + func.__name__
cache_global_key = 'DISCORD_BACKOFF_GLOBAL'
while retries > 0:
try:
try:
# Check global backoff first, then route backoff
existing_global_backoff = cache.get(cache_global_key)
existing_backoff = existing_global_backoff or cache.get(cache_key)
if existing_backoff:
backoff_timer = datetime.datetime.strptime(existing_backoff, cache_time_format)
if backoff_timer > datetime.datetime.utcnow():
backoff_seconds = (backoff_timer - datetime.datetime.utcnow()).total_seconds()
logger.debug("Still under backoff for %s seconds, backing off" % backoff_seconds)
# Still under backoff
raise PerformBackoff(
retry_after=backoff_seconds,
retry_datetime=backoff_timer,
global_ratelimit=bool(existing_global_backoff)
)
logger.debug("Calling API calling function")
return func(*args, **kwargs)
except requests.HTTPError as e:
if e.response.status_code == 429:
try:
retry_after = int(e.response.headers['Retry-After'])
except (TypeError, KeyError):
# Pick some random time
retry_after = 5000
logger.info("Received backoff from API of %s seconds, handling" % retry_after)
# Store value in redis
backoff_until = (datetime.datetime.utcnow() +
datetime.timedelta(milliseconds=retry_after))
global_backoff = bool(e.response.headers.get('X-RateLimit-Global', False))
if global_backoff:
logger.info("Global backoff!!")
cache.set(cache_global_key, backoff_until.strftime(cache_time_format), retry_after)
else:
cache.set(cache_key, backoff_until.strftime(cache_time_format), retry_after)
raise PerformBackoff(retry_after=retry_after, retry_datetime=backoff_until,
global_ratelimit=global_backoff)
else:
# Not 429, re-raise
raise e
except PerformBackoff as bo:
# Sleep if we're blocking
if blocking:
logger.info("Blocking Back off from API calls for %s seconds" % bo.retry_after)
time.sleep((10 if bo.retry_after > 10 else bo.retry_after) / 1000)
else:
# Otherwise raise exception and let caller handle the backoff
raise DiscordApiBackoff(retry_after=bo.retry_after, global_ratelimit=bo.global_ratelimit)
finally:
retries -= 1
if retries == 0:
raise DiscordApiTooBusy()
return decorated | python | def api_backoff(func):
"""
Decorator, Handles HTTP 429 "Too Many Requests" messages from the Discord API
If blocking=True is specified, this function will block and retry
the function up to max_retries=n times, or 3 if retries is not specified.
If the API call still recieves a backoff timer this function will raise
a <DiscordApiTooBusy> exception.
If the caller chooses blocking=False, the decorator will raise a DiscordApiBackoff
exception and the caller can choose to retry after the given timespan available in
the retry_after property in seconds.
"""
class PerformBackoff(Exception):
def __init__(self, retry_after, retry_datetime, global_ratelimit):
super(Exception, self).__init__()
self.retry_after = int(retry_after)
self.retry_datetime = retry_datetime
self.global_ratelimit = global_ratelimit
@wraps(func)
def decorated(*args, **kwargs):
blocking = kwargs.get('blocking', False)
retries = kwargs.get('max_retries', 3)
# Strip our parameters
if 'max_retries' in kwargs:
del kwargs['max_retries']
if 'blocking' in kwargs:
del kwargs['blocking']
cache_key = 'DISCORD_BACKOFF_' + func.__name__
cache_global_key = 'DISCORD_BACKOFF_GLOBAL'
while retries > 0:
try:
try:
# Check global backoff first, then route backoff
existing_global_backoff = cache.get(cache_global_key)
existing_backoff = existing_global_backoff or cache.get(cache_key)
if existing_backoff:
backoff_timer = datetime.datetime.strptime(existing_backoff, cache_time_format)
if backoff_timer > datetime.datetime.utcnow():
backoff_seconds = (backoff_timer - datetime.datetime.utcnow()).total_seconds()
logger.debug("Still under backoff for %s seconds, backing off" % backoff_seconds)
# Still under backoff
raise PerformBackoff(
retry_after=backoff_seconds,
retry_datetime=backoff_timer,
global_ratelimit=bool(existing_global_backoff)
)
logger.debug("Calling API calling function")
return func(*args, **kwargs)
except requests.HTTPError as e:
if e.response.status_code == 429:
try:
retry_after = int(e.response.headers['Retry-After'])
except (TypeError, KeyError):
# Pick some random time
retry_after = 5000
logger.info("Received backoff from API of %s seconds, handling" % retry_after)
# Store value in redis
backoff_until = (datetime.datetime.utcnow() +
datetime.timedelta(milliseconds=retry_after))
global_backoff = bool(e.response.headers.get('X-RateLimit-Global', False))
if global_backoff:
logger.info("Global backoff!!")
cache.set(cache_global_key, backoff_until.strftime(cache_time_format), retry_after)
else:
cache.set(cache_key, backoff_until.strftime(cache_time_format), retry_after)
raise PerformBackoff(retry_after=retry_after, retry_datetime=backoff_until,
global_ratelimit=global_backoff)
else:
# Not 429, re-raise
raise e
except PerformBackoff as bo:
# Sleep if we're blocking
if blocking:
logger.info("Blocking Back off from API calls for %s seconds" % bo.retry_after)
time.sleep((10 if bo.retry_after > 10 else bo.retry_after) / 1000)
else:
# Otherwise raise exception and let caller handle the backoff
raise DiscordApiBackoff(retry_after=bo.retry_after, global_ratelimit=bo.global_ratelimit)
finally:
retries -= 1
if retries == 0:
raise DiscordApiTooBusy()
return decorated | [
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allianceauth/allianceauth | allianceauth/srp/views.py | random_string | def random_string(string_length=10):
"""Returns a random string of length string_length."""
random = str(uuid.uuid4()) # Convert UUID format to a Python string.
random = random.upper() # Make all characters uppercase.
random = random.replace("-", "") # Remove the UUID '-'.
return random[0:string_length] | python | def random_string(string_length=10):
"""Returns a random string of length string_length."""
random = str(uuid.uuid4()) # Convert UUID format to a Python string.
random = random.upper() # Make all characters uppercase.
random = random.replace("-", "") # Remove the UUID '-'.
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"""Return the names of all imported genomes"""
import rabaDB.filters as rfilt
f = rfilt.RabaQuery(Genome_Raba)
names = []
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"""Return the names of all imported genomes"""
import rabaDB.filters as rfilt
f = rfilt.RabaQuery(Genome_Raba)
names = []
for g in f.iterRun() :
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tariqdaouda/pyGeno | pyGeno/Transcript.py | Transcript.iterCodons | def iterCodons(self) :
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yield self.getCodon(i) | python | def iterCodons(self) :
"""iterates through the codons"""
for i in range(len(self.cDNA)/3) :
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | removeDuplicates | def removeDuplicates(inFileName, outFileName) :
"""removes duplicated lines from a 'inFileName' CSV file, the results are witten in 'outFileName'"""
f = open(inFileName)
legend = f.readline()
data = ''
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f.flush()
f.close()
f = open(outFileName, 'w')
f.write(legend+data)
f.flush()
f.close() | python | def removeDuplicates(inFileName, outFileName) :
"""removes duplicated lines from a 'inFileName' CSV file, the results are witten in 'outFileName'"""
f = open(inFileName)
legend = f.readline()
data = ''
h = {}
h[legend] = 0
lines = f.readlines()
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if not h.has_key(l) :
h[l] = 0
data += l
f.flush()
f.close()
f = open(outFileName, 'w')
f.write(legend+data)
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | catCSVs | def catCSVs(folder, ouputFileName, removeDups = False) :
"""Concatenates all csv in 'folder' and wites the results in 'ouputFileName'. My not work on non Unix systems"""
strCmd = r"""cat %s/*.csv > %s""" %(folder, ouputFileName)
os.system(strCmd)
if removeDups :
removeDuplicates(ouputFileName, ouputFileName) | python | def catCSVs(folder, ouputFileName, removeDups = False) :
"""Concatenates all csv in 'folder' and wites the results in 'ouputFileName'. My not work on non Unix systems"""
strCmd = r"""cat %s/*.csv > %s""" %(folder, ouputFileName)
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"""csvFilePaths should be an iterable. Joins all CSVs according to the values in the column 'column'. Write the results in a new file 'ouputFileName' """
res = ''
legend = []
csvs = []
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csvs.append(c)
legend.append(separator.join(c.legend.keys()))
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val = csvs[0].get(i, column)
line = separator.join(csvs[0][i])
for c in csvs[1:] :
for j in range(len(c)) :
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lines.append( line )
res = legend + '\n' + '\n'.join(lines)
f = open(ouputFileName, 'w')
f.write(res)
f.flush()
f.close()
return res | python | def joinCSVs(csvFilePaths, column, ouputFileName, separator = ',') :
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res = ''
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.addField | def addField(self, field) :
"""add a filed to the legend"""
if field.lower() in self.legend :
raise ValueError("%s is already in the legend" % field.lower())
self.legend[field.lower()] = len(self.legend)
if len(self.strLegend) > 0 :
self.strLegend += self.separator + field
else :
self.strLegend += field | python | def addField(self, field) :
"""add a filed to the legend"""
if field.lower() in self.legend :
raise ValueError("%s is already in the legend" % field.lower())
self.legend[field.lower()] = len(self.legend)
if len(self.strLegend) > 0 :
self.strLegend += self.separator + field
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"""Loads a CSV file"""
self.filename = filePath
f = open(filePath)
if lineSeparator == '\n' :
lines = f.readlines()
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lines = f.read().split(lineSeparator)
f.flush()
f.close()
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legendElement = c.strip()
if legendElement not in self.legend :
self.legend[legendElement] = i
i+=1
self.strLegend = self.lines[0].replace('\r', '\n').replace('\n', '')
self.lines = self.lines[1:] | python | def parse(self, filePath, skipLines=0, separator = ',', stringSeparator = '"', lineSeparator = '\n') :
"""Loads a CSV file"""
self.filename = filePath
f = open(filePath)
if lineSeparator == '\n' :
lines = f.readlines()
else :
lines = f.read().split(lineSeparator)
f.flush()
f.close()
lines = lines[skipLines:]
self.lines = []
self.comments = []
for l in lines :
# print l
if len(l) != 0 and l[0] != "#" :
self.lines.append(l)
elif l[0] == "#" :
self.comments.append(l)
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self.lineSeparator = lineSeparator
self.stringSeparator = stringSeparator
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legendElement = c.strip()
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.streamToFile | def streamToFile(self, filename, keepInMemory = False, writeRate = 1) :
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If keepInMemory is set to True, the parser will keep a version of the whole CSV in memory, writeRate is the number
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raise ValueError("There's no legend defined")
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pass
self.streamFile = open(filename, "a")
self.writeRate = writeRate
self.streamBuffer = []
self.keepInMemory = keepInMemory
self.streamFile.write(self.strLegend + "\n") | python | def streamToFile(self, filename, keepInMemory = False, writeRate = 1) :
"""Starts a stream to a file. Every line must be committed (l.commit()) to be appended in to the file.
If keepInMemory is set to True, the parser will keep a version of the whole CSV in memory, writeRate is the number
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"""
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raise ValueError("There's no legend defined")
try :
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except :
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self.streamFile = open(filename, "a")
self.writeRate = writeRate
self.streamBuffer = []
self.keepInMemory = keepInMemory
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"""Commits a line making it ready to be streamed to a file and saves the current buffer if needed. If no stream is active, raises a ValueError"""
if self.streamBuffer is None :
raise ValueError("Commit lines is only for when you are streaming to a file")
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self.streamFile.write("%s\n" % ('\n'.join(self.streamBuffer)))
self.streamFile.flush()
self.streamBuffer = [] | python | def commitLine(self, line) :
"""Commits a line making it ready to be streamed to a file and saves the current buffer if needed. If no stream is active, raises a ValueError"""
if self.streamBuffer is None :
raise ValueError("Commit lines is only for when you are streaming to a file")
self.streamBuffer.append(line)
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for i in xrange(len(self.streamBuffer)) :
self.streamBuffer[i] = str(self.streamBuffer[i])
self.streamFile.write("%s\n" % ('\n'.join(self.streamBuffer)))
self.streamFile.flush()
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.closeStreamToFile | def closeStreamToFile(self) :
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self.keepInMemory = True | python | def closeStreamToFile(self) :
"""Appends the remaining commited lines and closes the stream. If no stream is active, raises a ValueError"""
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raise ValueError("Commit lines is only for when you are streaming to a file")
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.newLine | def newLine(self) :
"""Appends an empty line at the end of the CSV and returns it"""
l = CSVEntry(self)
if self.keepInMemory :
self.lines.append(l)
return l | python | def newLine(self) :
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l = CSVEntry(self)
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.insertLine | def insertLine(self, i) :
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self.data.insert(i, CSVEntry(self))
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self.data.insert(i, CSVEntry(self))
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.save | def save(self, filePath) :
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f = open(filePath, 'w')
f.write(self.toStr())
f.flush()
f.close() | python | def save(self, filePath) :
"""save the CSV to a file"""
self.filename = filePath
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.toStr | def toStr(self) :
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return self.lineSeparator.join(s) | python | def toStr(self) :
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tariqdaouda/pyGeno | pyGeno/pyGenoObjectBases.py | pyGenoRabaObjectWrapper.count | def count(self, objectType, *args, **coolArgs) :
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tariqdaouda/pyGeno | pyGeno/pyGenoObjectBases.py | pyGenoRabaObjectWrapper.get | def get(self, objectType, *args, **coolArgs) :
"""Raba Magic inside. This is th function that you use for
querying pyGeno's DB.
Usage examples:
* myGenome.get("Gene", name = 'TPST2')
* myGene.get(Protein, id = 'ENSID...')
* myGenome.get(Transcript, {'start >' : x, 'end <' : y})"""
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"""Raba Magic inside. This is th function that you use for
querying pyGeno's DB.
Usage examples:
* myGenome.get("Gene", name = 'TPST2')
* myGene.get(Protein, id = 'ENSID...')
* myGenome.get(Transcript, {'start >' : x, 'end <' : y})"""
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"""Same as get. But retuns the elements one by one, much more efficient for large outputs"""
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | importSNPs | def importSNPs(packageFile) :
"""The big wrapper, this function should detect the SNP type by the package manifest and then launch the corresponding function.
Here's an example of a SNP manifest file for Casava SNPs::
[package_infos]
description = Casava SNPs for testing purposes
maintainer = Tariq Daouda
maintainer_contact = tariq.daouda [at] umontreal
version = 1
[set_infos]
species = human
name = dummySRY
type = Agnostic
source = my place at the IRIC
[snps]
filename = snps.txt # as with genomes you can either include de file at the root of the package or specify an URL from where it must be downloaded
"""
printf("Importing polymorphism set: %s... (This may take a while)" % packageFile)
isDir = False
if not os.path.isdir(packageFile) :
packageDir = _decompressPackage(packageFile)
else :
isDir = True
packageDir = packageFile
fpMan = os.path.normpath(packageDir+'/manifest.ini')
if not os.path.isfile(fpMan) :
raise ValueError("Not file named manifest.ini! Mais quel SCANDALE!!!!")
parser = SafeConfigParser()
parser.read(os.path.normpath(packageDir+'/manifest.ini'))
packageInfos = parser.items('package_infos')
setName = parser.get('set_infos', 'name')
typ = parser.get('set_infos', 'type')
if typ.lower()[-3:] != 'snp' :
typ += 'SNP'
species = parser.get('set_infos', 'species').lower()
genomeSource = parser.get('set_infos', 'source')
snpsFileTmp = parser.get('snps', 'filename').strip()
snpsFile = _getFile(parser.get('snps', 'filename'), packageDir)
return_value = None
try :
SMaster = SNPMaster(setName = setName)
except KeyError :
if typ.lower() == 'casavasnp' :
return_value = _importSNPs_CasavaSNP(setName, species, genomeSource, snpsFile)
elif typ.lower() == 'dbsnpsnp' :
return_value = _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile)
elif typ.lower() == 'dbsnp' :
return_value = _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile)
elif typ.lower() == 'tophatsnp' :
return_value = _importSNPs_TopHatSNP(setName, species, genomeSource, snpsFile)
elif typ.lower() == 'agnosticsnp' :
return_value = _importSNPs_AgnosticSNP(setName, species, genomeSource, snpsFile)
else :
raise FutureWarning('Unknown SNP type in manifest %s' % typ)
else :
raise KeyError("There's already a SNP set by the name %s. Use deleteSNPs() to remove it first" %setName)
if not isDir :
shutil.rmtree(packageDir)
return return_value | python | def importSNPs(packageFile) :
"""The big wrapper, this function should detect the SNP type by the package manifest and then launch the corresponding function.
Here's an example of a SNP manifest file for Casava SNPs::
[package_infos]
description = Casava SNPs for testing purposes
maintainer = Tariq Daouda
maintainer_contact = tariq.daouda [at] umontreal
version = 1
[set_infos]
species = human
name = dummySRY
type = Agnostic
source = my place at the IRIC
[snps]
filename = snps.txt # as with genomes you can either include de file at the root of the package or specify an URL from where it must be downloaded
"""
printf("Importing polymorphism set: %s... (This may take a while)" % packageFile)
isDir = False
if not os.path.isdir(packageFile) :
packageDir = _decompressPackage(packageFile)
else :
isDir = True
packageDir = packageFile
fpMan = os.path.normpath(packageDir+'/manifest.ini')
if not os.path.isfile(fpMan) :
raise ValueError("Not file named manifest.ini! Mais quel SCANDALE!!!!")
parser = SafeConfigParser()
parser.read(os.path.normpath(packageDir+'/manifest.ini'))
packageInfos = parser.items('package_infos')
setName = parser.get('set_infos', 'name')
typ = parser.get('set_infos', 'type')
if typ.lower()[-3:] != 'snp' :
typ += 'SNP'
species = parser.get('set_infos', 'species').lower()
genomeSource = parser.get('set_infos', 'source')
snpsFileTmp = parser.get('snps', 'filename').strip()
snpsFile = _getFile(parser.get('snps', 'filename'), packageDir)
return_value = None
try :
SMaster = SNPMaster(setName = setName)
except KeyError :
if typ.lower() == 'casavasnp' :
return_value = _importSNPs_CasavaSNP(setName, species, genomeSource, snpsFile)
elif typ.lower() == 'dbsnpsnp' :
return_value = _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile)
elif typ.lower() == 'dbsnp' :
return_value = _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile)
elif typ.lower() == 'tophatsnp' :
return_value = _importSNPs_TopHatSNP(setName, species, genomeSource, snpsFile)
elif typ.lower() == 'agnosticsnp' :
return_value = _importSNPs_AgnosticSNP(setName, species, genomeSource, snpsFile)
else :
raise FutureWarning('Unknown SNP type in manifest %s' % typ)
else :
raise KeyError("There's already a SNP set by the name %s. Use deleteSNPs() to remove it first" %setName)
if not isDir :
shutil.rmtree(packageDir)
return return_value | [
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Here's an example of a SNP manifest file for Casava SNPs::
[package_infos]
description = Casava SNPs for testing purposes
maintainer = Tariq Daouda
maintainer_contact = tariq.daouda [at] umontreal
version = 1
[set_infos]
species = human
name = dummySRY
type = Agnostic
source = my place at the IRIC
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filename = snps.txt # as with genomes you can either include de file at the root of the package or specify an URL from where it must be downloaded | [
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | deleteSNPs | def deleteSNPs(setName) :
"""deletes a set of polymorphisms"""
con = conf.db
try :
SMaster = SNPMaster(setName = setName)
con.beginTransaction()
SNPType = SMaster.SNPType
con.delete(SNPType, 'setName = ?', (setName,))
SMaster.delete()
con.endTransaction()
except KeyError :
raise KeyError("Can't delete the setName %s because i can't find it in SNPMaster, maybe there's not set by that name" % setName)
#~ printf("can't delete the setName %s because i can't find it in SNPMaster, maybe there's no set by that name" % setName)
return False
return True | python | def deleteSNPs(setName) :
"""deletes a set of polymorphisms"""
con = conf.db
try :
SMaster = SNPMaster(setName = setName)
con.beginTransaction()
SNPType = SMaster.SNPType
con.delete(SNPType, 'setName = ?', (setName,))
SMaster.delete()
con.endTransaction()
except KeyError :
raise KeyError("Can't delete the setName %s because i can't find it in SNPMaster, maybe there's not set by that name" % setName)
#~ printf("can't delete the setName %s because i can't find it in SNPMaster, maybe there's no set by that name" % setName)
return False
return True | [
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | _importSNPs_AgnosticSNP | def _importSNPs_AgnosticSNP(setName, species, genomeSource, snpsFile) :
"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno wil interpret all positions as 0 based"
printf('importing SNP set %s for species %s...' % (setName, species))
snpData = CSVFile()
snpData.parse(snpsFile, separator = "\t")
AgnosticSNP.dropIndex(('start', 'chromosomeNumber', 'setName'))
conf.db.beginTransaction()
pBar = ProgressBar(len(snpData))
pLabel = ''
currChrNumber = None
for snpEntry in snpData :
tmpChr = snpEntry['chromosomeNumber']
if tmpChr != currChrNumber :
currChrNumber = tmpChr
pLabel = 'Chr %s...' % currChrNumber
snp = AgnosticSNP()
snp.species = species
snp.setName = setName
for f in snp.getFields() :
try :
setattr(snp, f, snpEntry[f])
except KeyError :
if f != 'species' and f != 'setName' :
printf("Warning filetype as no key %s", f)
snp.quality = float(snp.quality)
snp.start = int(snp.start)
snp.end = int(snp.end)
snp.save()
pBar.update(label = pLabel)
pBar.close()
snpMaster = SNPMaster()
snpMaster.set(setName = setName, SNPType = 'AgnosticSNP', species = species)
snpMaster.save()
printf('saving...')
conf.db.endTransaction()
printf('creating indexes...')
AgnosticSNP.ensureGlobalIndex(('start', 'chromosomeNumber', 'setName'))
printf('importation of SNP set %s for species %s done.' %(setName, species))
return True | python | def _importSNPs_AgnosticSNP(setName, species, genomeSource, snpsFile) :
"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno wil interpret all positions as 0 based"
printf('importing SNP set %s for species %s...' % (setName, species))
snpData = CSVFile()
snpData.parse(snpsFile, separator = "\t")
AgnosticSNP.dropIndex(('start', 'chromosomeNumber', 'setName'))
conf.db.beginTransaction()
pBar = ProgressBar(len(snpData))
pLabel = ''
currChrNumber = None
for snpEntry in snpData :
tmpChr = snpEntry['chromosomeNumber']
if tmpChr != currChrNumber :
currChrNumber = tmpChr
pLabel = 'Chr %s...' % currChrNumber
snp = AgnosticSNP()
snp.species = species
snp.setName = setName
for f in snp.getFields() :
try :
setattr(snp, f, snpEntry[f])
except KeyError :
if f != 'species' and f != 'setName' :
printf("Warning filetype as no key %s", f)
snp.quality = float(snp.quality)
snp.start = int(snp.start)
snp.end = int(snp.end)
snp.save()
pBar.update(label = pLabel)
pBar.close()
snpMaster = SNPMaster()
snpMaster.set(setName = setName, SNPType = 'AgnosticSNP', species = species)
snpMaster.save()
printf('saving...')
conf.db.endTransaction()
printf('creating indexes...')
AgnosticSNP.ensureGlobalIndex(('start', 'chromosomeNumber', 'setName'))
printf('importation of SNP set %s for species %s done.' %(setName, species))
return True | [
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | _importSNPs_CasavaSNP | def _importSNPs_CasavaSNP(setName, species, genomeSource, snpsFile) :
"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno positions are 0 based"
printf('importing SNP set %s for species %s...' % (setName, species))
snpData = SNPsTxtFile(snpsFile)
CasavaSNP.dropIndex(('start', 'chromosomeNumber', 'setName'))
conf.db.beginTransaction()
pBar = ProgressBar(len(snpData))
pLabel = ''
currChrNumber = None
for snpEntry in snpData :
tmpChr = snpEntry['chromosomeNumber']
if tmpChr != currChrNumber :
currChrNumber = tmpChr
pLabel = 'Chr %s...' % currChrNumber
snp = CasavaSNP()
snp.species = species
snp.setName = setName
for f in snp.getFields() :
try :
setattr(snp, f, snpEntry[f])
except KeyError :
if f != 'species' and f != 'setName' :
printf("Warning filetype as no key %s", f)
snp.start -= 1
snp.end -= 1
snp.save()
pBar.update(label = pLabel)
pBar.close()
snpMaster = SNPMaster()
snpMaster.set(setName = setName, SNPType = 'CasavaSNP', species = species)
snpMaster.save()
printf('saving...')
conf.db.endTransaction()
printf('creating indexes...')
CasavaSNP.ensureGlobalIndex(('start', 'chromosomeNumber', 'setName'))
printf('importation of SNP set %s for species %s done.' %(setName, species))
return True | python | def _importSNPs_CasavaSNP(setName, species, genomeSource, snpsFile) :
"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno positions are 0 based"
printf('importing SNP set %s for species %s...' % (setName, species))
snpData = SNPsTxtFile(snpsFile)
CasavaSNP.dropIndex(('start', 'chromosomeNumber', 'setName'))
conf.db.beginTransaction()
pBar = ProgressBar(len(snpData))
pLabel = ''
currChrNumber = None
for snpEntry in snpData :
tmpChr = snpEntry['chromosomeNumber']
if tmpChr != currChrNumber :
currChrNumber = tmpChr
pLabel = 'Chr %s...' % currChrNumber
snp = CasavaSNP()
snp.species = species
snp.setName = setName
for f in snp.getFields() :
try :
setattr(snp, f, snpEntry[f])
except KeyError :
if f != 'species' and f != 'setName' :
printf("Warning filetype as no key %s", f)
snp.start -= 1
snp.end -= 1
snp.save()
pBar.update(label = pLabel)
pBar.close()
snpMaster = SNPMaster()
snpMaster.set(setName = setName, SNPType = 'CasavaSNP', species = species)
snpMaster.save()
printf('saving...')
conf.db.endTransaction()
printf('creating indexes...')
CasavaSNP.ensureGlobalIndex(('start', 'chromosomeNumber', 'setName'))
printf('importation of SNP set %s for species %s done.' %(setName, species))
return True | [
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | _importSNPs_dbSNPSNP | def _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile) :
"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno positions are 0 based"
snpData = VCFFile(snpsFile, gziped = True, stream = True)
dbSNPSNP.dropIndex(('start', 'chromosomeNumber', 'setName'))
conf.db.beginTransaction()
pBar = ProgressBar()
pLabel = ''
for snpEntry in snpData :
pBar.update(label = 'Chr %s, %s...' % (snpEntry['#CHROM'], snpEntry['ID']))
snp = dbSNPSNP()
for f in snp.getFields() :
try :
setattr(snp, f, snpEntry[f])
except KeyError :
pass
snp.chromosomeNumber = snpEntry['#CHROM']
snp.species = species
snp.setName = setName
snp.start = snpEntry['POS']-1
snp.alt = snpEntry['ALT']
snp.ref = snpEntry['REF']
snp.end = snp.start+len(snp.alt)
snp.save()
pBar.close()
snpMaster = SNPMaster()
snpMaster.set(setName = setName, SNPType = 'dbSNPSNP', species = species)
snpMaster.save()
printf('saving...')
conf.db.endTransaction()
printf('creating indexes...')
dbSNPSNP.ensureGlobalIndex(('start', 'chromosomeNumber', 'setName'))
printf('importation of SNP set %s for species %s done.' %(setName, species))
return True | python | def _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile) :
"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno positions are 0 based"
snpData = VCFFile(snpsFile, gziped = True, stream = True)
dbSNPSNP.dropIndex(('start', 'chromosomeNumber', 'setName'))
conf.db.beginTransaction()
pBar = ProgressBar()
pLabel = ''
for snpEntry in snpData :
pBar.update(label = 'Chr %s, %s...' % (snpEntry['#CHROM'], snpEntry['ID']))
snp = dbSNPSNP()
for f in snp.getFields() :
try :
setattr(snp, f, snpEntry[f])
except KeyError :
pass
snp.chromosomeNumber = snpEntry['#CHROM']
snp.species = species
snp.setName = setName
snp.start = snpEntry['POS']-1
snp.alt = snpEntry['ALT']
snp.ref = snpEntry['REF']
snp.end = snp.start+len(snp.alt)
snp.save()
pBar.close()
snpMaster = SNPMaster()
snpMaster.set(setName = setName, SNPType = 'dbSNPSNP', species = species)
snpMaster.save()
printf('saving...')
conf.db.endTransaction()
printf('creating indexes...')
dbSNPSNP.ensureGlobalIndex(('start', 'chromosomeNumber', 'setName'))
printf('importation of SNP set %s for species %s done.' %(setName, species))
return True | [
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tariqdaouda/pyGeno | pyGeno/SNP.py | getSNPSetsList | def getSNPSetsList() :
"""Return the names of all imported snp sets"""
import rabaDB.filters as rfilt
f = rfilt.RabaQuery(SNPMaster)
names = []
for g in f.iterRun() :
names.append(g.setName)
return names | python | def getSNPSetsList() :
"""Return the names of all imported snp sets"""
import rabaDB.filters as rfilt
f = rfilt.RabaQuery(SNPMaster)
names = []
for g in f.iterRun() :
names.append(g.setName)
return names | [
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tariqdaouda/pyGeno | pyGeno/tools/io.py | printf | def printf(*s) :
'print + sys.stdout.flush()'
for e in s[:-1] :
print e,
print s[-1]
sys.stdout.flush() | python | def printf(*s) :
'print + sys.stdout.flush()'
for e in s[:-1] :
print e,
print s[-1]
sys.stdout.flush() | [
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tariqdaouda/pyGeno | pyGeno/tools/Stats.py | kullback_leibler | def kullback_leibler(p, q) :
"""Discrete Kullback-Leibler divergence D(P||Q)"""
p = np.asarray(p, dtype=np.float)
q = np.asarray(q, dtype=np.float)
if p.shape != q.shape :
raise ValueError("p and q must be of the same dimensions")
return np.sum(np.where(p > 0, np.log(p / q) * p, 0)) | python | def kullback_leibler(p, q) :
"""Discrete Kullback-Leibler divergence D(P||Q)"""
p = np.asarray(p, dtype=np.float)
q = np.asarray(q, dtype=np.float)
if p.shape != q.shape :
raise ValueError("p and q must be of the same dimensions")
return np.sum(np.where(p > 0, np.log(p / q) * p, 0)) | [
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tariqdaouda/pyGeno | pyGeno/tools/parsers/FastaTools.py | FastaFile.parseFile | def parseFile(self, fil) :
"""Opens a file and parses it"""
f = open(fil)
self.parseStr(f.read())
f.close() | python | def parseFile(self, fil) :
"""Opens a file and parses it"""
f = open(fil)
self.parseStr(f.read())
f.close() | [
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tariqdaouda/pyGeno | pyGeno/tools/parsers/FastaTools.py | FastaFile.add | def add(self, header, data) :
"""appends a new entry to the file"""
if header[0] != '>' :
self.data.append(('>'+header, data))
else :
self.data.append((header, data)) | python | def add(self, header, data) :
"""appends a new entry to the file"""
if header[0] != '>' :
self.data.append(('>'+header, data))
else :
self.data.append((header, data)) | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | findAll | def findAll(haystack, needle) :
"""returns a list of all occurances of needle in haystack"""
h = haystack
res = []
f = haystack.find(needle)
offset = 0
while (f >= 0) :
#print h, needle, f, offset
res.append(f+offset)
offset += f+len(needle)
h = h[f+len(needle):]
f = h.find(needle)
return res | python | def findAll(haystack, needle) :
"""returns a list of all occurances of needle in haystack"""
h = haystack
res = []
f = haystack.find(needle)
offset = 0
while (f >= 0) :
#print h, needle, f, offset
res.append(f+offset)
offset += f+len(needle)
h = h[f+len(needle):]
f = h.find(needle)
return res | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | complementTab | def complementTab(seq=[]):
"""returns a list of complementary sequence without inversing it"""
complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'R': 'Y', 'Y': 'R', 'M': 'K', 'K': 'M',
'W': 'W', 'S': 'S', 'B': 'V', 'D': 'H', 'H': 'D', 'V': 'B', 'N': 'N', 'a': 't',
'c': 'g', 'g': 'c', 't': 'a', 'r': 'y', 'y': 'r', 'm': 'k', 'k': 'm', 'w': 'w',
's': 's', 'b': 'v', 'd': 'h', 'h': 'd', 'v': 'b', 'n': 'n'}
seq_tmp = []
for bps in seq:
if len(bps) == 0:
#Need manage '' for deletion
seq_tmp.append('')
elif len(bps) == 1:
seq_tmp.append(complement[bps])
else:
#Need manage 'ACT' for insertion
#The insertion need to be reverse complement (like seq)
seq_tmp.append(reverseComplement(bps))
#Doesn't work in the second for when bps==''
#seq = [complement[bp] if bp != '' else '' for bps in seq for bp in bps]
return seq_tmp | python | def complementTab(seq=[]):
"""returns a list of complementary sequence without inversing it"""
complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'R': 'Y', 'Y': 'R', 'M': 'K', 'K': 'M',
'W': 'W', 'S': 'S', 'B': 'V', 'D': 'H', 'H': 'D', 'V': 'B', 'N': 'N', 'a': 't',
'c': 'g', 'g': 'c', 't': 'a', 'r': 'y', 'y': 'r', 'm': 'k', 'k': 'm', 'w': 'w',
's': 's', 'b': 'v', 'd': 'h', 'h': 'd', 'v': 'b', 'n': 'n'}
seq_tmp = []
for bps in seq:
if len(bps) == 0:
#Need manage '' for deletion
seq_tmp.append('')
elif len(bps) == 1:
seq_tmp.append(complement[bps])
else:
#Need manage 'ACT' for insertion
#The insertion need to be reverse complement (like seq)
seq_tmp.append(reverseComplement(bps))
#Doesn't work in the second for when bps==''
#seq = [complement[bp] if bp != '' else '' for bps in seq for bp in bps]
return seq_tmp | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | translateDNA_6Frames | def translateDNA_6Frames(sequence) :
"""returns 6 translation of sequence. One for each reading frame"""
trans = (
translateDNA(sequence, 'f1'),
translateDNA(sequence, 'f2'),
translateDNA(sequence, 'f3'),
translateDNA(sequence, 'r1'),
translateDNA(sequence, 'r2'),
translateDNA(sequence, 'r3'),
)
return trans | python | def translateDNA_6Frames(sequence) :
"""returns 6 translation of sequence. One for each reading frame"""
trans = (
translateDNA(sequence, 'f1'),
translateDNA(sequence, 'f2'),
translateDNA(sequence, 'f3'),
translateDNA(sequence, 'r1'),
translateDNA(sequence, 'r2'),
translateDNA(sequence, 'r3'),
)
return trans | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | translateDNA | def translateDNA(sequence, frame = 'f1', translTable_id='default') :
"""Translates DNA code, frame : fwd1, fwd2, fwd3, rev1, rev2, rev3"""
protein = ""
if frame == 'f1' :
dna = sequence
elif frame == 'f2':
dna = sequence[1:]
elif frame == 'f3' :
dna = sequence[2:]
elif frame == 'r1' :
dna = reverseComplement(sequence)
elif frame == 'r2' :
dna = reverseComplement(sequence)
dna = dna[1:]
elif frame == 'r3' :
dna = reverseComplement(sequence)
dna = dna[2:]
else :
raise ValueError('unknown reading frame: %s, should be one of the following: fwd1, fwd2, fwd3, rev1, rev2, rev3' % frame)
for i in range(0, len(dna), 3) :
codon = dna[i:i+3]
# Check if variant messed with selenocysteine codon
if '!' in codon and codon != '!GA':
codon = codon.replace('!', 'T')
if (len(codon) == 3) :
try :
# MC
protein += translTable[translTable_id][codon]
except KeyError :
combinaisons = polymorphicCodonCombinaisons(list(codon))
translations = set()
for ci in range(len(combinaisons)):
translations.add(translTable[translTable_id][combinaisons[ci]])
protein += '/'.join(translations)
return protein | python | def translateDNA(sequence, frame = 'f1', translTable_id='default') :
"""Translates DNA code, frame : fwd1, fwd2, fwd3, rev1, rev2, rev3"""
protein = ""
if frame == 'f1' :
dna = sequence
elif frame == 'f2':
dna = sequence[1:]
elif frame == 'f3' :
dna = sequence[2:]
elif frame == 'r1' :
dna = reverseComplement(sequence)
elif frame == 'r2' :
dna = reverseComplement(sequence)
dna = dna[1:]
elif frame == 'r3' :
dna = reverseComplement(sequence)
dna = dna[2:]
else :
raise ValueError('unknown reading frame: %s, should be one of the following: fwd1, fwd2, fwd3, rev1, rev2, rev3' % frame)
for i in range(0, len(dna), 3) :
codon = dna[i:i+3]
# Check if variant messed with selenocysteine codon
if '!' in codon and codon != '!GA':
codon = codon.replace('!', 'T')
if (len(codon) == 3) :
try :
# MC
protein += translTable[translTable_id][codon]
except KeyError :
combinaisons = polymorphicCodonCombinaisons(list(codon))
translations = set()
for ci in range(len(combinaisons)):
translations.add(translTable[translTable_id][combinaisons[ci]])
protein += '/'.join(translations)
return protein | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | getSequenceCombinaisons | def getSequenceCombinaisons(polymorphipolymorphicDnaSeqSeq, pos = 0) :
"""Takes a dna sequence with polymorphismes and returns all the possible sequences that it can yield"""
if type(polymorphipolymorphicDnaSeqSeq) is not types.ListType :
seq = list(polymorphipolymorphicDnaSeqSeq)
else :
seq = polymorphipolymorphicDnaSeqSeq
if pos >= len(seq) :
return [''.join(seq)]
variants = []
if seq[pos] in polymorphicNucleotides :
chars = decodePolymorphicNucleotide(seq[pos])
else :
chars = seq[pos]#.split('/')
for c in chars :
rseq = copy.copy(seq)
rseq[pos] = c
variants.extend(getSequenceCombinaisons(rseq, pos + 1))
return variants | python | def getSequenceCombinaisons(polymorphipolymorphicDnaSeqSeq, pos = 0) :
"""Takes a dna sequence with polymorphismes and returns all the possible sequences that it can yield"""
if type(polymorphipolymorphicDnaSeqSeq) is not types.ListType :
seq = list(polymorphipolymorphicDnaSeqSeq)
else :
seq = polymorphipolymorphicDnaSeqSeq
if pos >= len(seq) :
return [''.join(seq)]
variants = []
if seq[pos] in polymorphicNucleotides :
chars = decodePolymorphicNucleotide(seq[pos])
else :
chars = seq[pos]#.split('/')
for c in chars :
rseq = copy.copy(seq)
rseq[pos] = c
variants.extend(getSequenceCombinaisons(rseq, pos + 1))
return variants | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | encodePolymorphicNucleotide | def encodePolymorphicNucleotide(polySeq) :
"""returns a single character encoding all nucletides of polySeq
in a single character. PolySeq must have one of the following forms:
['A', 'T', 'G'], 'ATG', 'A/T/G'"""
if type(polySeq) is types.StringType :
if polySeq.find("/") < 0 :
sseq = list(polySeq)
else :
sseq = polySeq.split('/')
else :
sseq = polySeq
seq = []
for n in sseq :
try :
for n2 in polymorphicNucleotides[n] :
seq.append(n2)
except KeyError :
seq.append(n)
seq = set(seq)
if len(seq) == 4:
return 'N'
elif len(seq) == 3 :
if 'T' not in seq :
return 'V'
elif 'G' not in seq :
return 'H'
elif 'C' not in seq :
return 'D'
elif 'A' not in seq :
return 'B'
elif len(seq) == 2 :
if 'A' in seq and 'G' in seq :
return 'R'
elif 'C' in seq and 'T' in seq :
return 'Y'
elif 'A' in seq and 'C' in seq :
return 'M'
elif 'T' in seq and 'G' in seq :
return 'K'
elif 'A' in seq and 'T' in seq :
return 'W'
elif 'C' in seq and 'G' in seq :
return 'S'
elif polySeq[0] in nucleotides :
return polySeq[0]
else :
raise UnknownNucleotide(polySeq) | python | def encodePolymorphicNucleotide(polySeq) :
"""returns a single character encoding all nucletides of polySeq
in a single character. PolySeq must have one of the following forms:
['A', 'T', 'G'], 'ATG', 'A/T/G'"""
if type(polySeq) is types.StringType :
if polySeq.find("/") < 0 :
sseq = list(polySeq)
else :
sseq = polySeq.split('/')
else :
sseq = polySeq
seq = []
for n in sseq :
try :
for n2 in polymorphicNucleotides[n] :
seq.append(n2)
except KeyError :
seq.append(n)
seq = set(seq)
if len(seq) == 4:
return 'N'
elif len(seq) == 3 :
if 'T' not in seq :
return 'V'
elif 'G' not in seq :
return 'H'
elif 'C' not in seq :
return 'D'
elif 'A' not in seq :
return 'B'
elif len(seq) == 2 :
if 'A' in seq and 'G' in seq :
return 'R'
elif 'C' in seq and 'T' in seq :
return 'Y'
elif 'A' in seq and 'C' in seq :
return 'M'
elif 'T' in seq and 'G' in seq :
return 'K'
elif 'A' in seq and 'T' in seq :
return 'W'
elif 'C' in seq and 'G' in seq :
return 'S'
elif polySeq[0] in nucleotides :
return polySeq[0]
else :
raise UnknownNucleotide(polySeq) | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | decodePolymorphicNucleotide | def decodePolymorphicNucleotide(nuc) :
"""the opposite of encodePolymorphicNucleotide, from 'R' to ['A', 'G']"""
if nuc in polymorphicNucleotides :
return polymorphicNucleotides[nuc]
if nuc in nucleotides :
return nuc
raise ValueError('nuc: %s, is not a valid nucleotide' % nuc) | python | def decodePolymorphicNucleotide(nuc) :
"""the opposite of encodePolymorphicNucleotide, from 'R' to ['A', 'G']"""
if nuc in polymorphicNucleotides :
return polymorphicNucleotides[nuc]
if nuc in nucleotides :
return nuc
raise ValueError('nuc: %s, is not a valid nucleotide' % nuc) | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | getNucleotideCodon | def getNucleotideCodon(sequence, x1) :
"""Returns the entire codon of the nucleotide at pos x1 in sequence,
and the position of that nocleotide in the codon in a tuple"""
if x1 < 0 or x1 >= len(sequence) :
return None
p = x1%3
if p == 0 :
return (sequence[x1: x1+3], 0)
elif p ==1 :
return (sequence[x1-1: x1+2], 1)
elif p == 2 :
return (sequence[x1-2: x1+1], 2) | python | def getNucleotideCodon(sequence, x1) :
"""Returns the entire codon of the nucleotide at pos x1 in sequence,
and the position of that nocleotide in the codon in a tuple"""
if x1 < 0 or x1 >= len(sequence) :
return None
p = x1%3
if p == 0 :
return (sequence[x1: x1+3], 0)
elif p ==1 :
return (sequence[x1-1: x1+2], 1)
elif p == 2 :
return (sequence[x1-2: x1+1], 2) | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | showDifferences | def showDifferences(seq1, seq2) :
"""Returns a string highligthing differences between seq1 and seq2:
* Matches by '-'
* Differences : 'A|T'
* Exceeded length : '#'
"""
ret = []
for i in range(max(len(seq1), len(seq2))) :
if i >= len(seq1) :
c1 = '#'
else :
c1 = seq1[i]
if i >= len(seq2) :
c2 = '#'
else :
c2 = seq2[i]
if c1 != c2 :
ret.append('%s|%s' % (c1, c2))
else :
ret.append('-')
return ''.join(ret) | python | def showDifferences(seq1, seq2) :
"""Returns a string highligthing differences between seq1 and seq2:
* Matches by '-'
* Differences : 'A|T'
* Exceeded length : '#'
"""
ret = []
for i in range(max(len(seq1), len(seq2))) :
if i >= len(seq1) :
c1 = '#'
else :
c1 = seq1[i]
if i >= len(seq2) :
c2 = '#'
else :
c2 = seq2[i]
if c1 != c2 :
ret.append('%s|%s' % (c1, c2))
else :
ret.append('-')
return ''.join(ret) | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | highlightSubsequence | def highlightSubsequence(sequence, x1, x2, start=' [', stop = '] ') :
"""returns a sequence where the subsequence in [x1, x2[ is placed
in bewteen 'start' and 'stop'"""
seq = list(sequence)
print x1, x2-1, len(seq)
seq[x1] = start + seq[x1]
seq[x2-1] = seq[x2-1] + stop
return ''.join(seq) | python | def highlightSubsequence(sequence, x1, x2, start=' [', stop = '] ') :
"""returns a sequence where the subsequence in [x1, x2[ is placed
in bewteen 'start' and 'stop'"""
seq = list(sequence)
print x1, x2-1, len(seq)
seq[x1] = start + seq[x1]
seq[x2-1] = seq[x2-1] + stop
return ''.join(seq) | [
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | backUpDB | def backUpDB() :
"""backup the current database version. automatically called by importGenome(). Returns the filename of the backup"""
st = time.ctime().replace(' ', '_')
fn = conf.pyGeno_RABA_DBFILE.replace('.db', '_%s-bck.db' % st)
shutil.copy2(conf.pyGeno_RABA_DBFILE, fn)
return fn | python | def backUpDB() :
"""backup the current database version. automatically called by importGenome(). Returns the filename of the backup"""
st = time.ctime().replace(' ', '_')
fn = conf.pyGeno_RABA_DBFILE.replace('.db', '_%s-bck.db' % st)
shutil.copy2(conf.pyGeno_RABA_DBFILE, fn)
return fn | [
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | deleteGenome | def deleteGenome(species, name) :
"""Removes a genome from the database"""
printf('deleting genome (%s, %s)...' % (species, name))
conf.db.beginTransaction()
objs = []
allGood = True
try :
genome = Genome_Raba(name = name, species = species.lower())
objs.append(genome)
pBar = ProgressBar(label = 'preparing')
for typ in (Chromosome_Raba, Gene_Raba, Transcript_Raba, Exon_Raba, Protein_Raba) :
pBar.update()
f = RabaQuery(typ, namespace = genome._raba_namespace)
f.addFilter({'genome' : genome})
for e in f.iterRun() :
objs.append(e)
pBar.close()
pBar = ProgressBar(nbEpochs = len(objs), label = 'deleting objects')
for e in objs :
pBar.update()
e.delete()
pBar.close()
except KeyError as e :
#~ printf("\tWARNING, couldn't remove genome form db, maybe it's not there: ", e)
raise KeyError("\tWARNING, couldn't remove genome form db, maybe it's not there: ", e)
allGood = False
printf('\tdeleting folder')
try :
shutil.rmtree(conf.getGenomeSequencePath(species, name))
except OSError as e:
#~ printf('\tWARNING, Unable to delete folder: ', e)
OSError('\tWARNING, Unable to delete folder: ', e)
allGood = False
conf.db.endTransaction()
return allGood | python | def deleteGenome(species, name) :
"""Removes a genome from the database"""
printf('deleting genome (%s, %s)...' % (species, name))
conf.db.beginTransaction()
objs = []
allGood = True
try :
genome = Genome_Raba(name = name, species = species.lower())
objs.append(genome)
pBar = ProgressBar(label = 'preparing')
for typ in (Chromosome_Raba, Gene_Raba, Transcript_Raba, Exon_Raba, Protein_Raba) :
pBar.update()
f = RabaQuery(typ, namespace = genome._raba_namespace)
f.addFilter({'genome' : genome})
for e in f.iterRun() :
objs.append(e)
pBar.close()
pBar = ProgressBar(nbEpochs = len(objs), label = 'deleting objects')
for e in objs :
pBar.update()
e.delete()
pBar.close()
except KeyError as e :
#~ printf("\tWARNING, couldn't remove genome form db, maybe it's not there: ", e)
raise KeyError("\tWARNING, couldn't remove genome form db, maybe it's not there: ", e)
allGood = False
printf('\tdeleting folder')
try :
shutil.rmtree(conf.getGenomeSequencePath(species, name))
except OSError as e:
#~ printf('\tWARNING, Unable to delete folder: ', e)
OSError('\tWARNING, Unable to delete folder: ', e)
allGood = False
conf.db.endTransaction()
return allGood | [
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | importGenome | def importGenome(packageFile, batchSize = 50, verbose = 0) :
"""Import a pyGeno genome package. A genome packages is folder or a tar.gz ball that contains at it's root:
* gziped fasta files for all chromosomes, or URLs from where them must be downloaded
* gziped GTF gene_set file from Ensembl, or an URL from where it must be downloaded
* a manifest.ini file such as::
[package_infos]
description = Test package. This package installs only chromosome Y of mus musculus
maintainer = Tariq Daouda
maintainer_contact = tariq.daouda [at] umontreal
version = GRCm38.73
[genome]
species = Mus_musculus
name = GRCm38_test
source = http://useast.ensembl.org/info/data/ftp/index.html
[chromosome_files]
Y = Mus_musculus.GRCm38.73.dna.chromosome.Y.fa.gz / or an url such as ftp://... or http://
[gene_set]
gtf = Mus_musculus.GRCm38.73_Y-only.gtf.gz / or an url such as ftp://... or http://
All files except the manifest can be downloaded from: http://useast.ensembl.org/info/data/ftp/index.html
A rollback is performed if an exception is caught during importation
batchSize sets the number of genes to parse before performing a database save. PCs with little ram like
small values, while those endowed with more memory may perform faster with higher ones.
Verbose must be an int [0, 4] for various levels of verbosity
"""
def reformatItems(items) :
s = str(items)
s = s.replace('[', '').replace(']', '').replace("',", ': ').replace('), ', '\n').replace("'", '').replace('(', '').replace(')', '')
return s
printf('Importing genome package: %s... (This may take a while)' % packageFile)
isDir = False
if not os.path.isdir(packageFile) :
packageDir = _decompressPackage(packageFile)
else :
isDir = True
packageDir = packageFile
parser = SafeConfigParser()
parser.read(os.path.normpath(packageDir+'/manifest.ini'))
packageInfos = parser.items('package_infos')
genomeName = parser.get('genome', 'name')
species = parser.get('genome', 'species')
genomeSource = parser.get('genome', 'source')
seqTargetDir = conf.getGenomeSequencePath(species.lower(), genomeName)
if os.path.isdir(seqTargetDir) :
raise KeyError("The directory %s already exists, Please call deleteGenome() first if you want to reinstall" % seqTargetDir)
gtfFile = _getFile(parser.get('gene_set', 'gtf'), packageDir)
chromosomesFiles = {}
chromosomeSet = set()
for key, fil in parser.items('chromosome_files') :
chromosomesFiles[key] = _getFile(fil, packageDir)
chromosomeSet.add(key)
try :
genome = Genome(name = genomeName, species = species)
except KeyError:
pass
else :
raise KeyError("There seems to be already a genome (%s, %s), please call deleteGenome() first if you want to reinstall it" % (genomeName, species))
genome = Genome_Raba()
genome.set(name = genomeName, species = species, source = genomeSource, packageInfos = packageInfos)
printf("Importing:\n\t%s\nGenome:\n\t%s\n..." % (reformatItems(packageInfos).replace('\n', '\n\t'), reformatItems(parser.items('genome')).replace('\n', '\n\t')))
chros = _importGenomeObjects(gtfFile, chromosomeSet, genome, batchSize, verbose)
os.makedirs(seqTargetDir)
startChro = 0
pBar = ProgressBar(nbEpochs = len(chros))
for chro in chros :
pBar.update(label = "Importing DNA, chro %s" % chro.number)
length = _importSequence(chro, chromosomesFiles[chro.number.lower()], seqTargetDir)
chro.start = startChro
chro.end = startChro+length
startChro = chro.end
chro.save()
pBar.close()
if not isDir :
shutil.rmtree(packageDir)
#~ objgraph.show_most_common_types(limit=20)
return True | python | def importGenome(packageFile, batchSize = 50, verbose = 0) :
"""Import a pyGeno genome package. A genome packages is folder or a tar.gz ball that contains at it's root:
* gziped fasta files for all chromosomes, or URLs from where them must be downloaded
* gziped GTF gene_set file from Ensembl, or an URL from where it must be downloaded
* a manifest.ini file such as::
[package_infos]
description = Test package. This package installs only chromosome Y of mus musculus
maintainer = Tariq Daouda
maintainer_contact = tariq.daouda [at] umontreal
version = GRCm38.73
[genome]
species = Mus_musculus
name = GRCm38_test
source = http://useast.ensembl.org/info/data/ftp/index.html
[chromosome_files]
Y = Mus_musculus.GRCm38.73.dna.chromosome.Y.fa.gz / or an url such as ftp://... or http://
[gene_set]
gtf = Mus_musculus.GRCm38.73_Y-only.gtf.gz / or an url such as ftp://... or http://
All files except the manifest can be downloaded from: http://useast.ensembl.org/info/data/ftp/index.html
A rollback is performed if an exception is caught during importation
batchSize sets the number of genes to parse before performing a database save. PCs with little ram like
small values, while those endowed with more memory may perform faster with higher ones.
Verbose must be an int [0, 4] for various levels of verbosity
"""
def reformatItems(items) :
s = str(items)
s = s.replace('[', '').replace(']', '').replace("',", ': ').replace('), ', '\n').replace("'", '').replace('(', '').replace(')', '')
return s
printf('Importing genome package: %s... (This may take a while)' % packageFile)
isDir = False
if not os.path.isdir(packageFile) :
packageDir = _decompressPackage(packageFile)
else :
isDir = True
packageDir = packageFile
parser = SafeConfigParser()
parser.read(os.path.normpath(packageDir+'/manifest.ini'))
packageInfos = parser.items('package_infos')
genomeName = parser.get('genome', 'name')
species = parser.get('genome', 'species')
genomeSource = parser.get('genome', 'source')
seqTargetDir = conf.getGenomeSequencePath(species.lower(), genomeName)
if os.path.isdir(seqTargetDir) :
raise KeyError("The directory %s already exists, Please call deleteGenome() first if you want to reinstall" % seqTargetDir)
gtfFile = _getFile(parser.get('gene_set', 'gtf'), packageDir)
chromosomesFiles = {}
chromosomeSet = set()
for key, fil in parser.items('chromosome_files') :
chromosomesFiles[key] = _getFile(fil, packageDir)
chromosomeSet.add(key)
try :
genome = Genome(name = genomeName, species = species)
except KeyError:
pass
else :
raise KeyError("There seems to be already a genome (%s, %s), please call deleteGenome() first if you want to reinstall it" % (genomeName, species))
genome = Genome_Raba()
genome.set(name = genomeName, species = species, source = genomeSource, packageInfos = packageInfos)
printf("Importing:\n\t%s\nGenome:\n\t%s\n..." % (reformatItems(packageInfos).replace('\n', '\n\t'), reformatItems(parser.items('genome')).replace('\n', '\n\t')))
chros = _importGenomeObjects(gtfFile, chromosomeSet, genome, batchSize, verbose)
os.makedirs(seqTargetDir)
startChro = 0
pBar = ProgressBar(nbEpochs = len(chros))
for chro in chros :
pBar.update(label = "Importing DNA, chro %s" % chro.number)
length = _importSequence(chro, chromosomesFiles[chro.number.lower()], seqTargetDir)
chro.start = startChro
chro.end = startChro+length
startChro = chro.end
chro.save()
pBar.close()
if not isDir :
shutil.rmtree(packageDir)
#~ objgraph.show_most_common_types(limit=20)
return True | [
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] | Import a pyGeno genome package. A genome packages is folder or a tar.gz ball that contains at it's root:
* gziped fasta files for all chromosomes, or URLs from where them must be downloaded
* gziped GTF gene_set file from Ensembl, or an URL from where it must be downloaded
* a manifest.ini file such as::
[package_infos]
description = Test package. This package installs only chromosome Y of mus musculus
maintainer = Tariq Daouda
maintainer_contact = tariq.daouda [at] umontreal
version = GRCm38.73
[genome]
species = Mus_musculus
name = GRCm38_test
source = http://useast.ensembl.org/info/data/ftp/index.html
[chromosome_files]
Y = Mus_musculus.GRCm38.73.dna.chromosome.Y.fa.gz / or an url such as ftp://... or http://
[gene_set]
gtf = Mus_musculus.GRCm38.73_Y-only.gtf.gz / or an url such as ftp://... or http://
All files except the manifest can be downloaded from: http://useast.ensembl.org/info/data/ftp/index.html
A rollback is performed if an exception is caught during importation
batchSize sets the number of genes to parse before performing a database save. PCs with little ram like
small values, while those endowed with more memory may perform faster with higher ones.
Verbose must be an int [0, 4] for various levels of verbosity | [
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] | train | https://github.com/tariqdaouda/pyGeno/blob/474b1250bf78ce5c7e7c3bbbfdbad9635d5a7d14/pyGeno/importation/Genomes.py#L99-L198 |
tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | _importGenomeObjects | def _importGenomeObjects(gtfFilePath, chroSet, genome, batchSize, verbose = 0) :
"""verbose must be an int [0, 4] for various levels of verbosity"""
class Store(object) :
def __init__(self, conf) :
self.conf = conf
self.chromosomes = {}
self.genes = {}
self.transcripts = {}
self.proteins = {}
self.exons = {}
def batch_save(self) :
self.conf.db.beginTransaction()
for c in self.genes.itervalues() :
c.save()
conf.removeFromDBRegistery(c)
for c in self.transcripts.itervalues() :
c.save()
conf.removeFromDBRegistery(c.exons)
conf.removeFromDBRegistery(c)
for c in self.proteins.itervalues() :
c.save()
conf.removeFromDBRegistery(c)
self.conf.db.endTransaction()
del(self.genes)
del(self.transcripts)
del(self.proteins)
del(self.exons)
self.genes = {}
self.transcripts = {}
self.proteins = {}
self.exons = {}
gc.collect()
def save_chros(self) :
pBar = ProgressBar(nbEpochs = len(self.chromosomes))
for c in self.chromosomes.itervalues() :
pBar.update(label = 'Chr %s' % c.number)
c.save()
pBar.close()
printf('Importing gene set infos from %s...' % gtfFilePath)
printf('Backuping indexes...')
indexes = conf.db.getIndexes()
printf("Droping all your indexes, (don't worry i'll restore them later)...")
Genome_Raba.flushIndexes()
Chromosome_Raba.flushIndexes()
Gene_Raba.flushIndexes()
Transcript_Raba.flushIndexes()
Protein_Raba.flushIndexes()
Exon_Raba.flushIndexes()
printf("Parsing gene set...")
gtf = GTFFile(gtfFilePath, gziped = True)
printf('Done. Importation begins!')
store = Store(conf)
chroNumber = None
pBar = ProgressBar(nbEpochs = len(gtf))
for line in gtf :
chroN = line['seqname']
pBar.update(label = "Chr %s" % chroN)
if (chroN.upper() in chroSet or chroN.lower() in chroSet):
strand = line['strand']
gene_biotype = line['gene_biotype']
regionType = line['feature']
frame = line['frame']
start = int(line['start']) - 1
end = int(line['end'])
if start > end :
start, end = end, start
chroNumber = chroN.upper()
if chroNumber not in store.chromosomes :
store.chromosomes[chroNumber] = Chromosome_Raba()
store.chromosomes[chroNumber].set(genome = genome, number = chroNumber)
try :
geneId = line['gene_id']
geneName = line['gene_name']
except KeyError :
geneId = None
geneName = None
if verbose :
printf('Warning: no gene_id/name found in line %s' % gtf[i])
if geneId is not None :
if geneId not in store.genes :
if len(store.genes) > batchSize :
store.batch_save()
if verbose > 0 :
printf('\tGene %s, %s...' % (geneId, geneName))
store.genes[geneId] = Gene_Raba()
store.genes[geneId].set(genome = genome, id = geneId, chromosome = store.chromosomes[chroNumber], name = geneName, strand = strand, biotype = gene_biotype)
if start < store.genes[geneId].start or store.genes[geneId].start is None :
store.genes[geneId].start = start
if end > store.genes[geneId].end or store.genes[geneId].end is None :
store.genes[geneId].end = end
try :
transId = line['transcript_id']
transName = line['transcript_name']
try :
transcript_biotype = line['transcript_biotype']
except KeyError :
transcript_biotype = None
except KeyError :
transId = None
transName = None
if verbose > 2 :
printf('\t\tWarning: no transcript_id, name found in line %s' % gtf[i])
if transId is not None :
if transId not in store.transcripts :
if verbose > 1 :
printf('\t\tTranscript %s, %s...' % (transId, transName))
store.transcripts[transId] = Transcript_Raba()
store.transcripts[transId].set(genome = genome, id = transId, chromosome = store.chromosomes[chroNumber], gene = store.genes.get(geneId, None), name = transName, biotype=transcript_biotype)
if start < store.transcripts[transId].start or store.transcripts[transId].start is None:
store.transcripts[transId].start = start
if end > store.transcripts[transId].end or store.transcripts[transId].end is None:
store.transcripts[transId].end = end
try :
protId = line['protein_id']
except KeyError :
protId = None
if verbose > 2 :
printf('Warning: no protein_id found in line %s' % gtf[i])
# Store selenocysteine positions in transcript
if regionType == 'Selenocysteine':
store.transcripts[transId].selenocysteine.append(start)
if protId is not None and protId not in store.proteins :
if verbose > 1 :
printf('\t\tProtein %s...' % (protId))
store.proteins[protId] = Protein_Raba()
store.proteins[protId].set(genome = genome, id = protId, chromosome = store.chromosomes[chroNumber], gene = store.genes.get(geneId, None), transcript = store.transcripts.get(transId, None), name = transName)
store.transcripts[transId].protein = store.proteins[protId]
try :
exonNumber = int(line['exon_number']) - 1
exonKey = (transId, exonNumber)
except KeyError :
exonNumber = None
exonKey = None
if verbose > 2 :
printf('Warning: no exon number or id found in line %s' % gtf[i])
if exonKey is not None :
if verbose > 3 :
printf('\t\t\texon %s...' % (exonId))
if exonKey not in store.exons and regionType == 'exon' :
store.exons[exonKey] = Exon_Raba()
store.exons[exonKey].set(genome = genome, chromosome = store.chromosomes[chroNumber], gene = store.genes.get(geneId, None), transcript = store.transcripts.get(transId, None), protein = store.proteins.get(protId, None), strand = strand, number = exonNumber, start = start, end = end)
store.transcripts[transId].exons.append(store.exons[exonKey])
try :
store.exons[exonKey].id = line['exon_id']
except KeyError :
pass
if regionType == 'exon' :
if start < store.exons[exonKey].start or store.exons[exonKey].start is None:
store.exons[exonKey].start = start
if end > store.transcripts[transId].end or store.exons[exonKey].end is None:
store.exons[exonKey].end = end
elif regionType == 'CDS' :
store.exons[exonKey].CDS_start = start
store.exons[exonKey].CDS_end = end
store.exons[exonKey].frame = frame
elif regionType == 'stop_codon' :
if strand == '+' :
if store.exons[exonKey].CDS_end != None :
store.exons[exonKey].CDS_end += 3
if store.exons[exonKey].end < store.exons[exonKey].CDS_end :
store.exons[exonKey].end = store.exons[exonKey].CDS_end
if store.transcripts[transId].end < store.exons[exonKey].CDS_end :
store.transcripts[transId].end = store.exons[exonKey].CDS_end
if store.genes[geneId].end < store.exons[exonKey].CDS_end :
store.genes[geneId].end = store.exons[exonKey].CDS_end
if strand == '-' :
if store.exons[exonKey].CDS_start != None :
store.exons[exonKey].CDS_start -= 3
if store.exons[exonKey].start > store.exons[exonKey].CDS_start :
store.exons[exonKey].start = store.exons[exonKey].CDS_start
if store.transcripts[transId].start > store.exons[exonKey].CDS_start :
store.transcripts[transId].start = store.exons[exonKey].CDS_start
if store.genes[geneId].start > store.exons[exonKey].CDS_start :
store.genes[geneId].start = store.exons[exonKey].CDS_start
pBar.close()
store.batch_save()
conf.db.beginTransaction()
printf('almost done saving chromosomes...')
store.save_chros()
printf('saving genome object...')
genome.save()
conf.db.endTransaction()
conf.db.beginTransaction()
printf('restoring core indexes...')
# Genome.ensureGlobalIndex(('name', 'species'))
# Chromosome.ensureGlobalIndex('genome')
# Gene.ensureGlobalIndex('genome')
# Transcript.ensureGlobalIndex('genome')
# Protein.ensureGlobalIndex('genome')
# Exon.ensureGlobalIndex('genome')
Transcript.ensureGlobalIndex('exons')
printf('commiting changes...')
conf.db.endTransaction()
conf.db.beginTransaction()
printf('restoring user indexes')
pBar = ProgressBar(label = "restoring", nbEpochs = len(indexes))
for idx in indexes :
pBar.update()
conf.db.execute(idx[-1].replace('CREATE INDEX', 'CREATE INDEX IF NOT EXISTS'))
pBar.close()
printf('commiting changes...')
conf.db.endTransaction()
return store.chromosomes.values() | python | def _importGenomeObjects(gtfFilePath, chroSet, genome, batchSize, verbose = 0) :
"""verbose must be an int [0, 4] for various levels of verbosity"""
class Store(object) :
def __init__(self, conf) :
self.conf = conf
self.chromosomes = {}
self.genes = {}
self.transcripts = {}
self.proteins = {}
self.exons = {}
def batch_save(self) :
self.conf.db.beginTransaction()
for c in self.genes.itervalues() :
c.save()
conf.removeFromDBRegistery(c)
for c in self.transcripts.itervalues() :
c.save()
conf.removeFromDBRegistery(c.exons)
conf.removeFromDBRegistery(c)
for c in self.proteins.itervalues() :
c.save()
conf.removeFromDBRegistery(c)
self.conf.db.endTransaction()
del(self.genes)
del(self.transcripts)
del(self.proteins)
del(self.exons)
self.genes = {}
self.transcripts = {}
self.proteins = {}
self.exons = {}
gc.collect()
def save_chros(self) :
pBar = ProgressBar(nbEpochs = len(self.chromosomes))
for c in self.chromosomes.itervalues() :
pBar.update(label = 'Chr %s' % c.number)
c.save()
pBar.close()
printf('Importing gene set infos from %s...' % gtfFilePath)
printf('Backuping indexes...')
indexes = conf.db.getIndexes()
printf("Droping all your indexes, (don't worry i'll restore them later)...")
Genome_Raba.flushIndexes()
Chromosome_Raba.flushIndexes()
Gene_Raba.flushIndexes()
Transcript_Raba.flushIndexes()
Protein_Raba.flushIndexes()
Exon_Raba.flushIndexes()
printf("Parsing gene set...")
gtf = GTFFile(gtfFilePath, gziped = True)
printf('Done. Importation begins!')
store = Store(conf)
chroNumber = None
pBar = ProgressBar(nbEpochs = len(gtf))
for line in gtf :
chroN = line['seqname']
pBar.update(label = "Chr %s" % chroN)
if (chroN.upper() in chroSet or chroN.lower() in chroSet):
strand = line['strand']
gene_biotype = line['gene_biotype']
regionType = line['feature']
frame = line['frame']
start = int(line['start']) - 1
end = int(line['end'])
if start > end :
start, end = end, start
chroNumber = chroN.upper()
if chroNumber not in store.chromosomes :
store.chromosomes[chroNumber] = Chromosome_Raba()
store.chromosomes[chroNumber].set(genome = genome, number = chroNumber)
try :
geneId = line['gene_id']
geneName = line['gene_name']
except KeyError :
geneId = None
geneName = None
if verbose :
printf('Warning: no gene_id/name found in line %s' % gtf[i])
if geneId is not None :
if geneId not in store.genes :
if len(store.genes) > batchSize :
store.batch_save()
if verbose > 0 :
printf('\tGene %s, %s...' % (geneId, geneName))
store.genes[geneId] = Gene_Raba()
store.genes[geneId].set(genome = genome, id = geneId, chromosome = store.chromosomes[chroNumber], name = geneName, strand = strand, biotype = gene_biotype)
if start < store.genes[geneId].start or store.genes[geneId].start is None :
store.genes[geneId].start = start
if end > store.genes[geneId].end or store.genes[geneId].end is None :
store.genes[geneId].end = end
try :
transId = line['transcript_id']
transName = line['transcript_name']
try :
transcript_biotype = line['transcript_biotype']
except KeyError :
transcript_biotype = None
except KeyError :
transId = None
transName = None
if verbose > 2 :
printf('\t\tWarning: no transcript_id, name found in line %s' % gtf[i])
if transId is not None :
if transId not in store.transcripts :
if verbose > 1 :
printf('\t\tTranscript %s, %s...' % (transId, transName))
store.transcripts[transId] = Transcript_Raba()
store.transcripts[transId].set(genome = genome, id = transId, chromosome = store.chromosomes[chroNumber], gene = store.genes.get(geneId, None), name = transName, biotype=transcript_biotype)
if start < store.transcripts[transId].start or store.transcripts[transId].start is None:
store.transcripts[transId].start = start
if end > store.transcripts[transId].end or store.transcripts[transId].end is None:
store.transcripts[transId].end = end
try :
protId = line['protein_id']
except KeyError :
protId = None
if verbose > 2 :
printf('Warning: no protein_id found in line %s' % gtf[i])
# Store selenocysteine positions in transcript
if regionType == 'Selenocysteine':
store.transcripts[transId].selenocysteine.append(start)
if protId is not None and protId not in store.proteins :
if verbose > 1 :
printf('\t\tProtein %s...' % (protId))
store.proteins[protId] = Protein_Raba()
store.proteins[protId].set(genome = genome, id = protId, chromosome = store.chromosomes[chroNumber], gene = store.genes.get(geneId, None), transcript = store.transcripts.get(transId, None), name = transName)
store.transcripts[transId].protein = store.proteins[protId]
try :
exonNumber = int(line['exon_number']) - 1
exonKey = (transId, exonNumber)
except KeyError :
exonNumber = None
exonKey = None
if verbose > 2 :
printf('Warning: no exon number or id found in line %s' % gtf[i])
if exonKey is not None :
if verbose > 3 :
printf('\t\t\texon %s...' % (exonId))
if exonKey not in store.exons and regionType == 'exon' :
store.exons[exonKey] = Exon_Raba()
store.exons[exonKey].set(genome = genome, chromosome = store.chromosomes[chroNumber], gene = store.genes.get(geneId, None), transcript = store.transcripts.get(transId, None), protein = store.proteins.get(protId, None), strand = strand, number = exonNumber, start = start, end = end)
store.transcripts[transId].exons.append(store.exons[exonKey])
try :
store.exons[exonKey].id = line['exon_id']
except KeyError :
pass
if regionType == 'exon' :
if start < store.exons[exonKey].start or store.exons[exonKey].start is None:
store.exons[exonKey].start = start
if end > store.transcripts[transId].end or store.exons[exonKey].end is None:
store.exons[exonKey].end = end
elif regionType == 'CDS' :
store.exons[exonKey].CDS_start = start
store.exons[exonKey].CDS_end = end
store.exons[exonKey].frame = frame
elif regionType == 'stop_codon' :
if strand == '+' :
if store.exons[exonKey].CDS_end != None :
store.exons[exonKey].CDS_end += 3
if store.exons[exonKey].end < store.exons[exonKey].CDS_end :
store.exons[exonKey].end = store.exons[exonKey].CDS_end
if store.transcripts[transId].end < store.exons[exonKey].CDS_end :
store.transcripts[transId].end = store.exons[exonKey].CDS_end
if store.genes[geneId].end < store.exons[exonKey].CDS_end :
store.genes[geneId].end = store.exons[exonKey].CDS_end
if strand == '-' :
if store.exons[exonKey].CDS_start != None :
store.exons[exonKey].CDS_start -= 3
if store.exons[exonKey].start > store.exons[exonKey].CDS_start :
store.exons[exonKey].start = store.exons[exonKey].CDS_start
if store.transcripts[transId].start > store.exons[exonKey].CDS_start :
store.transcripts[transId].start = store.exons[exonKey].CDS_start
if store.genes[geneId].start > store.exons[exonKey].CDS_start :
store.genes[geneId].start = store.exons[exonKey].CDS_start
pBar.close()
store.batch_save()
conf.db.beginTransaction()
printf('almost done saving chromosomes...')
store.save_chros()
printf('saving genome object...')
genome.save()
conf.db.endTransaction()
conf.db.beginTransaction()
printf('restoring core indexes...')
# Genome.ensureGlobalIndex(('name', 'species'))
# Chromosome.ensureGlobalIndex('genome')
# Gene.ensureGlobalIndex('genome')
# Transcript.ensureGlobalIndex('genome')
# Protein.ensureGlobalIndex('genome')
# Exon.ensureGlobalIndex('genome')
Transcript.ensureGlobalIndex('exons')
printf('commiting changes...')
conf.db.endTransaction()
conf.db.beginTransaction()
printf('restoring user indexes')
pBar = ProgressBar(label = "restoring", nbEpochs = len(indexes))
for idx in indexes :
pBar.update()
conf.db.execute(idx[-1].replace('CREATE INDEX', 'CREATE INDEX IF NOT EXISTS'))
pBar.close()
printf('commiting changes...')
conf.db.endTransaction()
return store.chromosomes.values() | [
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | _importSequence | def _importSequence(chromosome, fastaFile, targetDir) :
"Serializes fastas into .dat files"
f = gzip.open(fastaFile)
header = f.readline()
strRes = f.read().upper().replace('\n', '').replace('\r', '')
f.close()
fn = '%s/chromosome%s.dat' % (targetDir, chromosome.number)
f = open(fn, 'w')
f.write(strRes)
f.close()
chromosome.dataFile = fn
chromosome.header = header
return len(strRes) | python | def _importSequence(chromosome, fastaFile, targetDir) :
"Serializes fastas into .dat files"
f = gzip.open(fastaFile)
header = f.readline()
strRes = f.read().upper().replace('\n', '').replace('\r', '')
f.close()
fn = '%s/chromosome%s.dat' % (targetDir, chromosome.number)
f = open(fn, 'w')
f.write(strRes)
f.close()
chromosome.dataFile = fn
chromosome.header = header
return len(strRes) | [
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tariqdaouda/pyGeno | pyGeno/configuration.py | createDefaultConfigFile | def createDefaultConfigFile() :
"""Creates a default configuration file"""
s = "[pyGeno_config]\nsettings_dir=%s\nremote_location=%s" % (pyGeno_SETTINGS_DIR, pyGeno_REMOTE_LOCATION)
f = open('%s/config.ini' % pyGeno_SETTINGS_DIR, 'w')
f.write(s)
f.close() | python | def createDefaultConfigFile() :
"""Creates a default configuration file"""
s = "[pyGeno_config]\nsettings_dir=%s\nremote_location=%s" % (pyGeno_SETTINGS_DIR, pyGeno_REMOTE_LOCATION)
f = open('%s/config.ini' % pyGeno_SETTINGS_DIR, 'w')
f.write(s)
f.close() | [
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tariqdaouda/pyGeno | pyGeno/configuration.py | getSettingsPath | def getSettingsPath() :
"""Returns the path where the settings are stored"""
parser = SafeConfigParser()
try :
parser.read(os.path.normpath(pyGeno_SETTINGS_DIR+'/config.ini'))
return parser.get('pyGeno_config', 'settings_dir')
except :
createDefaultConfigFile()
return getSettingsPath() | python | def getSettingsPath() :
"""Returns the path where the settings are stored"""
parser = SafeConfigParser()
try :
parser.read(os.path.normpath(pyGeno_SETTINGS_DIR+'/config.ini'))
return parser.get('pyGeno_config', 'settings_dir')
except :
createDefaultConfigFile()
return getSettingsPath() | [
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tariqdaouda/pyGeno | pyGeno/configuration.py | pyGeno_init | def pyGeno_init() :
"""This function is automatically called at launch"""
global db, dbConf
global pyGeno_SETTINGS_PATH
global pyGeno_RABA_DBFILE
global pyGeno_DATA_PATH
if not checkPythonVersion() :
raise PythonVersionError("==> FATAL: pyGeno only works with python 2.7 and above, please upgrade your python version")
if not os.path.exists(pyGeno_SETTINGS_DIR) :
os.makedirs(pyGeno_SETTINGS_DIR)
pyGeno_SETTINGS_PATH = getSettingsPath()
pyGeno_RABA_DBFILE = os.path.normpath( os.path.join(pyGeno_SETTINGS_PATH, "pyGenoRaba.db") )
pyGeno_DATA_PATH = os.path.normpath( os.path.join(pyGeno_SETTINGS_PATH, "data") )
if not os.path.exists(pyGeno_SETTINGS_PATH) :
os.makedirs(pyGeno_SETTINGS_PATH)
if not os.path.exists(pyGeno_DATA_PATH) :
os.makedirs(pyGeno_DATA_PATH)
#launching the db
rabaDB.rabaSetup.RabaConfiguration(pyGeno_RABA_NAMESPACE, pyGeno_RABA_DBFILE)
db = rabaDB.rabaSetup.RabaConnection(pyGeno_RABA_NAMESPACE)
dbConf = rabaDB.rabaSetup.RabaConfiguration(pyGeno_RABA_NAMESPACE) | python | def pyGeno_init() :
"""This function is automatically called at launch"""
global db, dbConf
global pyGeno_SETTINGS_PATH
global pyGeno_RABA_DBFILE
global pyGeno_DATA_PATH
if not checkPythonVersion() :
raise PythonVersionError("==> FATAL: pyGeno only works with python 2.7 and above, please upgrade your python version")
if not os.path.exists(pyGeno_SETTINGS_DIR) :
os.makedirs(pyGeno_SETTINGS_DIR)
pyGeno_SETTINGS_PATH = getSettingsPath()
pyGeno_RABA_DBFILE = os.path.normpath( os.path.join(pyGeno_SETTINGS_PATH, "pyGenoRaba.db") )
pyGeno_DATA_PATH = os.path.normpath( os.path.join(pyGeno_SETTINGS_PATH, "data") )
if not os.path.exists(pyGeno_SETTINGS_PATH) :
os.makedirs(pyGeno_SETTINGS_PATH)
if not os.path.exists(pyGeno_DATA_PATH) :
os.makedirs(pyGeno_DATA_PATH)
#launching the db
rabaDB.rabaSetup.RabaConfiguration(pyGeno_RABA_NAMESPACE, pyGeno_RABA_DBFILE)
db = rabaDB.rabaSetup.RabaConnection(pyGeno_RABA_NAMESPACE)
dbConf = rabaDB.rabaSetup.RabaConfiguration(pyGeno_RABA_NAMESPACE) | [
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tariqdaouda/pyGeno | pyGeno/Exon.py | Exon.pluck | def pluck(self) :
"""Returns a plucked object. Plucks the exon off the tree, set the value of self.transcript into str(self.transcript). This effectively disconnects the object and
makes it much more lighter in case you'd like to pickle it"""
e = copy.copy(self)
e.transcript = str(self.transcript)
return e | python | def pluck(self) :
"""Returns a plucked object. Plucks the exon off the tree, set the value of self.transcript into str(self.transcript). This effectively disconnects the object and
makes it much more lighter in case you'd like to pickle it"""
e = copy.copy(self)
e.transcript = str(self.transcript)
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tariqdaouda/pyGeno | pyGeno/Exon.py | Exon.previousExon | def previousExon(self) :
"""Returns the previous exon of the transcript, or None if there is none"""
if self.number == 0 :
return None
try :
return self.transcript.exons[self.number-1]
except IndexError :
return None | python | def previousExon(self) :
"""Returns the previous exon of the transcript, or None if there is none"""
if self.number == 0 :
return None
try :
return self.transcript.exons[self.number-1]
except IndexError :
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tariqdaouda/pyGeno | pyGeno/tools/parsers/FastqTools.py | FastqFile.parseStr | def parseStr(self, st) :
"""Parses a string"""
self.data = st.replace('\r', '\n')
self.data = self.data.replace('\n\n', '\n')
self.data = self.data.split('\n') | python | def parseStr(self, st) :
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self.data = st.replace('\r', '\n')
self.data = self.data.replace('\n\n', '\n')
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tariqdaouda/pyGeno | pyGeno/tools/parsers/FastqTools.py | FastqFile.get | def get(self, li) :
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i = li*4
self.__splitEntry(i)
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i = li*4
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tariqdaouda/pyGeno | pyGeno/tools/parsers/FastqTools.py | FastqFile.newEntry | def newEntry(self, ident = "", seq = "", plus = "", qual = "") :
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self.data.append(e)
return e | python | def newEntry(self, ident = "", seq = "", plus = "", qual = "") :
"""Appends an empty entry at the end of the CSV and returns it"""
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tariqdaouda/pyGeno | pyGeno/bootstrap.py | listRemoteDatawraps | def listRemoteDatawraps(location = conf.pyGeno_REMOTE_LOCATION) :
"""Lists all the datawraps availabe from a remote a remote location."""
loc = location + "/datawraps.json"
response = urllib2.urlopen(loc)
js = json.loads(response.read())
return js | python | def listRemoteDatawraps(location = conf.pyGeno_REMOTE_LOCATION) :
"""Lists all the datawraps availabe from a remote a remote location."""
loc = location + "/datawraps.json"
response = urllib2.urlopen(loc)
js = json.loads(response.read())
return js | [
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tariqdaouda/pyGeno | pyGeno/bootstrap.py | printRemoteDatawraps | def printRemoteDatawraps(location = conf.pyGeno_REMOTE_LOCATION) :
"""
print all available datawraps from a remote location the location must have a datawraps.json in the following format::
{
"Ordered": {
"Reference genomes": {
"Human" : ["GRCh37.75", "GRCh38.78"],
"Mouse" : ["GRCm38.78"],
},
"SNPs":{
}
},
"Flat":{
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"GRCm38.78": "Mouse.GRCm38.78.tar.gz"
},
"SNPs":{
}
}
}
"""
l = listRemoteDatawraps(location)
printf("Available datawraps for bootstraping\n")
print json.dumps(l["Ordered"], sort_keys=True, indent=4, separators=(',', ': ')) | python | def printRemoteDatawraps(location = conf.pyGeno_REMOTE_LOCATION) :
"""
print all available datawraps from a remote location the location must have a datawraps.json in the following format::
{
"Ordered": {
"Reference genomes": {
"Human" : ["GRCh37.75", "GRCh38.78"],
"Mouse" : ["GRCm38.78"],
},
"SNPs":{
}
},
"Flat":{
"Reference genomes": {
"GRCh37.75": "Human.GRCh37.75.tar.gz",
"GRCh38.78": "Human.GRCh37.75.tar.gz",
"GRCm38.78": "Mouse.GRCm38.78.tar.gz"
},
"SNPs":{
}
}
}
"""
l = listRemoteDatawraps(location)
printf("Available datawraps for bootstraping\n")
print json.dumps(l["Ordered"], sort_keys=True, indent=4, separators=(',', ': ')) | [
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tariqdaouda/pyGeno | pyGeno/bootstrap.py | importRemoteGenome | def importRemoteGenome(name, batchSize = 100) :
"""Import a genome available from http://pygeno.iric.ca (might work)."""
try :
dw = listRemoteDatawraps()["Flat"]["Reference genomes"][name]
except AttributeError :
raise AttributeError("There's no remote genome datawrap by the name of: '%s'" % name)
finalFile = _DW(name, dw["url"])
PG.importGenome(finalFile, batchSize) | python | def importRemoteGenome(name, batchSize = 100) :
"""Import a genome available from http://pygeno.iric.ca (might work)."""
try :
dw = listRemoteDatawraps()["Flat"]["Reference genomes"][name]
except AttributeError :
raise AttributeError("There's no remote genome datawrap by the name of: '%s'" % name)
finalFile = _DW(name, dw["url"])
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tariqdaouda/pyGeno | pyGeno/bootstrap.py | importRemoteSNPs | def importRemoteSNPs(name) :
"""Import a SNP set available from http://pygeno.iric.ca (might work)."""
try :
dw = listRemoteDatawraps()["Flat"]["SNPs"]
except AttributeError :
raise AttributeError("There's no remote genome datawrap by the name of: '%s'" % name)
finalFile = _DW(name, dw["url"])
PS.importSNPs(finalFile) | python | def importRemoteSNPs(name) :
"""Import a SNP set available from http://pygeno.iric.ca (might work)."""
try :
dw = listRemoteDatawraps()["Flat"]["SNPs"]
except AttributeError :
raise AttributeError("There's no remote genome datawrap by the name of: '%s'" % name)
finalFile = _DW(name, dw["url"])
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tariqdaouda/pyGeno | pyGeno/bootstrap.py | listDatawraps | def listDatawraps() :
"""Lists all the datawraps pyGeno comes with"""
l = {"Genomes" : [], "SNPs" : []}
for f in os.listdir(os.path.join(this_dir, "bootstrap_data/genomes")) :
if f.find(".tar.gz") > -1 :
l["Genomes"].append(f)
for f in os.listdir(os.path.join(this_dir, "bootstrap_data/SNPs")) :
if f.find(".tar.gz") > -1 :
l["SNPs"].append(f)
return l | python | def listDatawraps() :
"""Lists all the datawraps pyGeno comes with"""
l = {"Genomes" : [], "SNPs" : []}
for f in os.listdir(os.path.join(this_dir, "bootstrap_data/genomes")) :
if f.find(".tar.gz") > -1 :
l["Genomes"].append(f)
for f in os.listdir(os.path.join(this_dir, "bootstrap_data/SNPs")) :
if f.find(".tar.gz") > -1 :
l["SNPs"].append(f)
return l | [
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tariqdaouda/pyGeno | pyGeno/bootstrap.py | printDatawraps | def printDatawraps() :
"""print all available datawraps for bootstraping"""
l = listDatawraps()
printf("Available datawraps for boostraping\n")
for k, v in l.iteritems() :
printf(k)
printf("~"*len(k) + "|")
for vv in v :
printf(" "*len(k) + "|" + "~~~:> " + vv)
printf('\n') | python | def printDatawraps() :
"""print all available datawraps for bootstraping"""
l = listDatawraps()
printf("Available datawraps for boostraping\n")
for k, v in l.iteritems() :
printf(k)
printf("~"*len(k) + "|")
for vv in v :
printf(" "*len(k) + "|" + "~~~:> " + vv)
printf('\n') | [
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tariqdaouda/pyGeno | pyGeno/bootstrap.py | importGenome | def importGenome(name, batchSize = 100) :
"""Import a genome shipped with pyGeno. Most of the datawraps only contain URLs towards data provided by third parties."""
path = os.path.join(this_dir, "bootstrap_data", "genomes/" + name)
PG.importGenome(path, batchSize) | python | def importGenome(name, batchSize = 100) :
"""Import a genome shipped with pyGeno. Most of the datawraps only contain URLs towards data provided by third parties."""
path = os.path.join(this_dir, "bootstrap_data", "genomes/" + name)
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path = os.path.join(this_dir, "bootstrap_data", "SNPs/" + name)
PS.importSNPs(path) | python | def importSNPs(name) :
"""Import a SNP set shipped with pyGeno. Most of the datawraps only contain URLs towards data provided by third parties."""
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tariqdaouda/pyGeno | pyGeno/tools/ProgressBar.py | ProgressBar.log | def log(self) :
"""logs stats about the progression, without printing anything on screen"""
self.logs['epochDuration'].append(self.lastEpochDuration)
self.logs['avg'].append(self.avg)
self.logs['runtime'].append(self.runtime)
self.logs['remtime'].append(self.remtime) | python | def log(self) :
"""logs stats about the progression, without printing anything on screen"""
self.logs['epochDuration'].append(self.lastEpochDuration)
self.logs['avg'].append(self.avg)
self.logs['runtime'].append(self.runtime)
self.logs['remtime'].append(self.remtime) | [
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tariqdaouda/pyGeno | pyGeno/tools/ProgressBar.py | ProgressBar.saveLogs | def saveLogs(self, filename) :
"""dumps logs into a nice pickle"""
f = open(filename, 'wb')
cPickle.dump(self.logs, f)
f.close() | python | def saveLogs(self, filename) :
"""dumps logs into a nice pickle"""
f = open(filename, 'wb')
cPickle.dump(self.logs, f)
f.close() | [
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tariqdaouda/pyGeno | pyGeno/tools/ProgressBar.py | ProgressBar.update | def update(self, label = '', forceRefresh = False, log = False) :
"""the function to be called at each iteration. Setting log = True is the same as calling log() just after update()"""
self.currEpoch += 1
tim = time.time()
if (tim - self.lastPrintTime > self.minRefeshTime) or forceRefresh :
self._update()
wheelState = self.wheel[self.currEpoch%len(self.wheel)]
if label == '' :
slabel = self.label
else :
slabel = label
if self.nbEpochs > 1 :
ratio = self.currEpoch/self.nbEpochs
snakeLen = int(self.width*ratio)
voidLen = int(self.width - (self.width*ratio))
if snakeLen + voidLen < self.width :
snakeLen = self.width - voidLen
self.bar = "%s %s[%s:>%s] %.2f%% (%d/%d) runtime: %s, remaining: %s, avg: %s" %(wheelState, slabel, "~-" * snakeLen, " " * voidLen, ratio*100, self.currEpoch, self.nbEpochs, self.runtime_hr, self.remtime_hr, self.formatTime(self.avg))
if self.currEpoch == self.nbEpochs :
self.close()
else :
w = self.width - len(self.miniSnake)
v = self.currEpoch%(w+1)
snake = "%s%s%s" %(" " * (v), self.miniSnake, " " * (w-v))
self.bar = "%s %s[%s] %s%% (%d/%s) runtime: %s, remaining: %s, avg: %s" %(wheelState, slabel, snake, '?', self.currEpoch, '?', self.runtime_hr, '?', self.formatTime(self.avg))
sys.stdout.write("\b" * (len(self.bar)+1))
sys.stdout.write(" " * (len(self.bar)+1))
sys.stdout.write("\b" * (len(self.bar)+1))
sys.stdout.write(self.bar)
sys.stdout.flush()
self.lastPrintTime = time.time()
if log :
self.log() | python | def update(self, label = '', forceRefresh = False, log = False) :
"""the function to be called at each iteration. Setting log = True is the same as calling log() just after update()"""
self.currEpoch += 1
tim = time.time()
if (tim - self.lastPrintTime > self.minRefeshTime) or forceRefresh :
self._update()
wheelState = self.wheel[self.currEpoch%len(self.wheel)]
if label == '' :
slabel = self.label
else :
slabel = label
if self.nbEpochs > 1 :
ratio = self.currEpoch/self.nbEpochs
snakeLen = int(self.width*ratio)
voidLen = int(self.width - (self.width*ratio))
if snakeLen + voidLen < self.width :
snakeLen = self.width - voidLen
self.bar = "%s %s[%s:>%s] %.2f%% (%d/%d) runtime: %s, remaining: %s, avg: %s" %(wheelState, slabel, "~-" * snakeLen, " " * voidLen, ratio*100, self.currEpoch, self.nbEpochs, self.runtime_hr, self.remtime_hr, self.formatTime(self.avg))
if self.currEpoch == self.nbEpochs :
self.close()
else :
w = self.width - len(self.miniSnake)
v = self.currEpoch%(w+1)
snake = "%s%s%s" %(" " * (v), self.miniSnake, " " * (w-v))
self.bar = "%s %s[%s] %s%% (%d/%s) runtime: %s, remaining: %s, avg: %s" %(wheelState, slabel, snake, '?', self.currEpoch, '?', self.runtime_hr, '?', self.formatTime(self.avg))
sys.stdout.write("\b" * (len(self.bar)+1))
sys.stdout.write(" " * (len(self.bar)+1))
sys.stdout.write("\b" * (len(self.bar)+1))
sys.stdout.write(self.bar)
sys.stdout.flush()
self.lastPrintTime = time.time()
if log :
self.log() | [
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tariqdaouda/pyGeno | pyGeno/SNPFiltering.py | DefaultSNPFilter.filter | def filter(self, chromosome, **kwargs) :
"""The default filter mixes applied all SNPs and ignores Insertions and Deletions."""
def appendAllele(alleles, sources, snp) :
pos = snp.start
if snp.alt[0] == '-' :
pass
# print warn % ('DELETION', snpSet, snp.start, snp.chromosomeNumber)
elif snp.ref[0] == '-' :
pass
# print warn % ('INSERTION', snpSet, snp.start, snp.chromosomeNumber)
else :
sources[snpSet] = snp
alleles.append(snp.alt) #if not an indel append the polymorphism
refAllele = chromosome.refSequence[pos]
alleles.append(refAllele)
sources['ref'] = refAllele
return alleles, sources
warn = 'Warning: the default snp filter ignores indels. IGNORED %s of SNP set: %s at pos: %s of chromosome: %s'
sources = {}
alleles = []
for snpSet, data in kwargs.iteritems() :
if type(data) is list :
for snp in data :
alleles, sources = appendAllele(alleles, sources, snp)
else :
allels, sources = appendAllele(alleles, sources, data)
#appends the refence allele to the lot
#optional we keep a record of the polymorphisms that were used during the process
return SequenceSNP(alleles, sources = sources) | python | def filter(self, chromosome, **kwargs) :
"""The default filter mixes applied all SNPs and ignores Insertions and Deletions."""
def appendAllele(alleles, sources, snp) :
pos = snp.start
if snp.alt[0] == '-' :
pass
# print warn % ('DELETION', snpSet, snp.start, snp.chromosomeNumber)
elif snp.ref[0] == '-' :
pass
# print warn % ('INSERTION', snpSet, snp.start, snp.chromosomeNumber)
else :
sources[snpSet] = snp
alleles.append(snp.alt) #if not an indel append the polymorphism
refAllele = chromosome.refSequence[pos]
alleles.append(refAllele)
sources['ref'] = refAllele
return alleles, sources
warn = 'Warning: the default snp filter ignores indels. IGNORED %s of SNP set: %s at pos: %s of chromosome: %s'
sources = {}
alleles = []
for snpSet, data in kwargs.iteritems() :
if type(data) is list :
for snp in data :
alleles, sources = appendAllele(alleles, sources, snp)
else :
allels, sources = appendAllele(alleles, sources, data)
#appends the refence allele to the lot
#optional we keep a record of the polymorphisms that were used during the process
return SequenceSNP(alleles, sources = sources) | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | aux_insertTree | def aux_insertTree(childTree, parentTree):
"""This a private (You shouldn't have to call it) recursive function that inserts a child tree into a parent tree."""
if childTree.x1 != None and childTree.x2 != None :
parentTree.insert(childTree.x1, childTree.x2, childTree.name, childTree.referedObject)
for c in childTree.children:
aux_insertTree(c, parentTree) | python | def aux_insertTree(childTree, parentTree):
"""This a private (You shouldn't have to call it) recursive function that inserts a child tree into a parent tree."""
if childTree.x1 != None and childTree.x2 != None :
parentTree.insert(childTree.x1, childTree.x2, childTree.name, childTree.referedObject)
for c in childTree.children:
aux_insertTree(c, parentTree) | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | aux_moveTree | def aux_moveTree(offset, tree):
"""This a private recursive (You shouldn't have to call it) function that translates tree(and it's children) to a given x1"""
if tree.x1 != None and tree.x2 != None :
tree.x1, tree.x2 = tree.x1+offset, tree.x2+offset
for c in tree.children:
aux_moveTree(offset, c) | python | def aux_moveTree(offset, tree):
"""This a private recursive (You shouldn't have to call it) function that translates tree(and it's children) to a given x1"""
if tree.x1 != None and tree.x2 != None :
tree.x1, tree.x2 = tree.x1+offset, tree.x2+offset
for c in tree.children:
aux_moveTree(offset, c) | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.insert | def insert(self, x1, x2, name = '', referedObject = []) :
"""Insert the segment in it's right place and returns it.
If there's already a segment S as S.x1 == x1 and S.x2 == x2. S.name will be changed to 'S.name U name' and the
referedObject will be appended to the already existing list"""
if x1 > x2 :
xx1, xx2 = x2, x1
else :
xx1, xx2 = x1, x2
rt = None
insertId = None
childrenToRemove = []
for i in range(len(self.children)) :
if self.children[i].x1 == xx1 and xx2 == self.children[i].x2 :
self.children[i].name = self.children[i].name + ' U ' + name
self.children[i].referedObject.append(referedObject)
return self.children[i]
if self.children[i].x1 <= xx1 and xx2 <= self.children[i].x2 :
return self.children[i].insert(x1, x2, name, referedObject)
elif xx1 <= self.children[i].x1 and self.children[i].x2 <= xx2 :
if rt == None :
if type(referedObject) is types.ListType :
rt = SegmentTree(xx1, xx2, name, referedObject, self, self.level+1)
else :
rt = SegmentTree(xx1, xx2, name, [referedObject], self, self.level+1)
insertId = i
rt.__addChild(self.children[i])
self.children[i].father = rt
childrenToRemove.append(self.children[i])
elif xx1 <= self.children[i].x1 and xx2 <= self.children[i].x2 :
insertId = i
break
if rt != None :
self.__addChild(rt, insertId)
for c in childrenToRemove :
self.children.remove(c)
else :
if type(referedObject) is types.ListType :
rt = SegmentTree(xx1, xx2, name, referedObject, self, self.level+1)
else :
rt = SegmentTree(xx1, xx2, name, [referedObject], self, self.level+1)
if insertId != None :
self.__addChild(rt, insertId)
else :
self.__addChild(rt)
return rt | python | def insert(self, x1, x2, name = '', referedObject = []) :
"""Insert the segment in it's right place and returns it.
If there's already a segment S as S.x1 == x1 and S.x2 == x2. S.name will be changed to 'S.name U name' and the
referedObject will be appended to the already existing list"""
if x1 > x2 :
xx1, xx2 = x2, x1
else :
xx1, xx2 = x1, x2
rt = None
insertId = None
childrenToRemove = []
for i in range(len(self.children)) :
if self.children[i].x1 == xx1 and xx2 == self.children[i].x2 :
self.children[i].name = self.children[i].name + ' U ' + name
self.children[i].referedObject.append(referedObject)
return self.children[i]
if self.children[i].x1 <= xx1 and xx2 <= self.children[i].x2 :
return self.children[i].insert(x1, x2, name, referedObject)
elif xx1 <= self.children[i].x1 and self.children[i].x2 <= xx2 :
if rt == None :
if type(referedObject) is types.ListType :
rt = SegmentTree(xx1, xx2, name, referedObject, self, self.level+1)
else :
rt = SegmentTree(xx1, xx2, name, [referedObject], self, self.level+1)
insertId = i
rt.__addChild(self.children[i])
self.children[i].father = rt
childrenToRemove.append(self.children[i])
elif xx1 <= self.children[i].x1 and xx2 <= self.children[i].x2 :
insertId = i
break
if rt != None :
self.__addChild(rt, insertId)
for c in childrenToRemove :
self.children.remove(c)
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if type(referedObject) is types.ListType :
rt = SegmentTree(xx1, xx2, name, referedObject, self, self.level+1)
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self.__addChild(rt, insertId)
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self.__addChild(rt)
return rt | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.intersect | def intersect(self, x1, x2 = None) :
"""Returns a list of all segments intersected by [x1, x2]"""
def condition(x1, x2, tree) :
#print self.id, tree.x1, tree.x2, x1, x2
if (tree.x1 != None and tree.x2 != None) and (tree.x1 <= x1 and x1 < tree.x2 or tree.x1 <= x2 and x2 < tree.x2) :
return True
return False
if x2 == None :
xx1, xx2 = x1, x1
elif x1 > x2 :
xx1, xx2 = x2, x1
else :
xx1, xx2 = x1, x2
c1 = self.__dichotomicSearch(xx1)
c2 = self.__dichotomicSearch(xx2)
if c1 == -1 or c2 == -1 :
return []
if xx1 < self.children[c1].x1 :
c1 -= 1
inter = self.__radiateDown(x1, x2, c1, condition)
if self.children[c1].id == self.children[c2].id :
inter.extend(self.__radiateUp(x1, x2, c2+1, condition))
else :
inter.extend(self.__radiateUp(x1, x2, c2, condition))
ret = []
for c in inter :
ret.extend(c.intersect(x1, x2))
inter.extend(ret)
return inter | python | def intersect(self, x1, x2 = None) :
"""Returns a list of all segments intersected by [x1, x2]"""
def condition(x1, x2, tree) :
#print self.id, tree.x1, tree.x2, x1, x2
if (tree.x1 != None and tree.x2 != None) and (tree.x1 <= x1 and x1 < tree.x2 or tree.x1 <= x2 and x2 < tree.x2) :
return True
return False
if x2 == None :
xx1, xx2 = x1, x1
elif x1 > x2 :
xx1, xx2 = x2, x1
else :
xx1, xx2 = x1, x2
c1 = self.__dichotomicSearch(xx1)
c2 = self.__dichotomicSearch(xx2)
if c1 == -1 or c2 == -1 :
return []
if xx1 < self.children[c1].x1 :
c1 -= 1
inter = self.__radiateDown(x1, x2, c1, condition)
if self.children[c1].id == self.children[c2].id :
inter.extend(self.__radiateUp(x1, x2, c2+1, condition))
else :
inter.extend(self.__radiateUp(x1, x2, c2, condition))
ret = []
for c in inter :
ret.extend(c.intersect(x1, x2))
inter.extend(ret)
return inter | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.__radiateDown | def __radiateDown(self, x1, x2, childId, condition) :
"Radiates down: walks self.children downward until condition is no longer verifed or there's no childrens left "
ret = []
i = childId
while 0 <= i :
if condition(x1, x2, self.children[i]) :
ret.append(self.children[i])
else :
break
i -= 1
return ret | python | def __radiateDown(self, x1, x2, childId, condition) :
"Radiates down: walks self.children downward until condition is no longer verifed or there's no childrens left "
ret = []
i = childId
while 0 <= i :
if condition(x1, x2, self.children[i]) :
ret.append(self.children[i])
else :
break
i -= 1
return ret | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.__radiateUp | def __radiateUp(self, x1, x2, childId, condition) :
"Radiates uo: walks self.children upward until condition is no longer verifed or there's no childrens left "
ret = []
i = childId
while i < len(self.children):
if condition(x1, x2, self.children[i]) :
ret.append(self.children[i])
else :
break
i += 1
return ret | python | def __radiateUp(self, x1, x2, childId, condition) :
"Radiates uo: walks self.children upward until condition is no longer verifed or there's no childrens left "
ret = []
i = childId
while i < len(self.children):
if condition(x1, x2, self.children[i]) :
ret.append(self.children[i])
else :
break
i += 1
return ret | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.removeGaps | def removeGaps(self) :
"""Remove all gaps between regions"""
for i in range(1, len(self.children)) :
if self.children[i].x1 > self.children[i-1].x2:
aux_moveTree(self.children[i-1].x2-self.children[i].x1, self.children[i]) | python | def removeGaps(self) :
"""Remove all gaps between regions"""
for i in range(1, len(self.children)) :
if self.children[i].x1 > self.children[i-1].x2:
aux_moveTree(self.children[i-1].x2-self.children[i].x1, self.children[i]) | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.getIndexedLength | def getIndexedLength(self) :
"""Returns the total length of indexed regions"""
if self.x1 != None and self.x2 != None:
return self.x2 - self.x1
else :
if len(self.children) == 0 :
return 0
else :
l = self.children[0].x2 - self.children[0].x1
for i in range(1, len(self.children)) :
l += self.children[i].x2 - self.children[i].x1 - max(0, self.children[i-1].x2 - self.children[i].x1)
return l | python | def getIndexedLength(self) :
"""Returns the total length of indexed regions"""
if self.x1 != None and self.x2 != None:
return self.x2 - self.x1
else :
if len(self.children) == 0 :
return 0
else :
l = self.children[0].x2 - self.children[0].x1
for i in range(1, len(self.children)) :
l += self.children[i].x2 - self.children[i].x1 - max(0, self.children[i-1].x2 - self.children[i].x1)
return l | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.getFirstLevel | def getFirstLevel(self) :
"""returns a list of couples (x1, x2) of all the first level indexed regions"""
res = []
if len(self.children) > 0 :
for c in self.children:
res.append((c.x1, c.x2))
else :
if self.x1 != None :
res = [(self.x1, self.x2)]
else :
res = None
return res | python | def getFirstLevel(self) :
"""returns a list of couples (x1, x2) of all the first level indexed regions"""
res = []
if len(self.children) > 0 :
for c in self.children:
res.append((c.x1, c.x2))
else :
if self.x1 != None :
res = [(self.x1, self.x2)]
else :
res = None
return res | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.flatten | def flatten(self) :
"""Flattens the tree. The tree become a tree of depth 1 where overlapping regions have been merged together"""
if len(self.children) > 1 :
children = self.children
self.emptyChildren()
children[0].emptyChildren()
x1 = children[0].x1
x2 = children[0].x2
refObjs = [children[0].referedObject]
name = children[0].name
for i in range(1, len(children)) :
children[i].emptyChildren()
if children[i-1] >= children[i] :
x2 = children[i].x2
refObjs.append(children[i].referedObject)
name += " U " + children[i].name
else :
if len(refObjs) == 1 :
refObjs = refObjs[0]
self.insert(x1, x2, name, refObjs)
x1 = children[i].x1
x2 = children[i].x2
refObjs = [children[i].referedObject]
name = children[i].name
if len(refObjs) == 1 :
refObjs = refObjs[0]
self.insert(x1, x2, name, refObjs) | python | def flatten(self) :
"""Flattens the tree. The tree become a tree of depth 1 where overlapping regions have been merged together"""
if len(self.children) > 1 :
children = self.children
self.emptyChildren()
children[0].emptyChildren()
x1 = children[0].x1
x2 = children[0].x2
refObjs = [children[0].referedObject]
name = children[0].name
for i in range(1, len(children)) :
children[i].emptyChildren()
if children[i-1] >= children[i] :
x2 = children[i].x2
refObjs.append(children[i].referedObject)
name += " U " + children[i].name
else :
if len(refObjs) == 1 :
refObjs = refObjs[0]
self.insert(x1, x2, name, refObjs)
x1 = children[i].x1
x2 = children[i].x2
refObjs = [children[i].referedObject]
name = children[i].name
if len(refObjs) == 1 :
refObjs = refObjs[0]
self.insert(x1, x2, name, refObjs) | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.move | def move(self, newX1) :
"""Moves tree to a new starting position, updates x1s of children"""
if self.x1 != None and self.x2 != None :
offset = newX1-self.x1
aux_moveTree(offset, self)
elif len(self.children) > 0 :
offset = newX1-self.children[0].x1
aux_moveTree(offset, self) | python | def move(self, newX1) :
"""Moves tree to a new starting position, updates x1s of children"""
if self.x1 != None and self.x2 != None :
offset = newX1-self.x1
aux_moveTree(offset, self)
elif len(self.children) > 0 :
offset = newX1-self.children[0].x1
aux_moveTree(offset, self) | [
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.encode | def encode(self, sequence):
"""Returns a tuple (binary reprensentation, default sequence, polymorphisms list)"""
polymorphisms = []
defaultSequence = ''
binSequence = array.array(self.forma.typecode)
b = 0
i = 0
trueI = 0 #not inc in case if poly
poly = set()
while i < len(sequence)-1:
b = b | self.forma[self.charToBin[sequence[i]]]
if sequence[i+1] == '/' :
poly.add(sequence[i])
i += 2
else :
binSequence.append(b)
if len(poly) > 0 :
poly.add(sequence[i])
polymorphisms.append((trueI, poly))
poly = set()
bb = 0
while b % 2 != 0 :
b = b/2
defaultSequence += sequence[i]
b = 0
i += 1
trueI += 1
if i < len(sequence) :
b = b | self.forma[self.charToBin[sequence[i]]]
binSequence.append(b)
if len(poly) > 0 :
if sequence[i] not in poly :
poly.add(sequence[i])
polymorphisms.append((trueI, poly))
defaultSequence += sequence[i]
return (binSequence, defaultSequence, polymorphisms) | python | def encode(self, sequence):
"""Returns a tuple (binary reprensentation, default sequence, polymorphisms list)"""
polymorphisms = []
defaultSequence = ''
binSequence = array.array(self.forma.typecode)
b = 0
i = 0
trueI = 0 #not inc in case if poly
poly = set()
while i < len(sequence)-1:
b = b | self.forma[self.charToBin[sequence[i]]]
if sequence[i+1] == '/' :
poly.add(sequence[i])
i += 2
else :
binSequence.append(b)
if len(poly) > 0 :
poly.add(sequence[i])
polymorphisms.append((trueI, poly))
poly = set()
bb = 0
while b % 2 != 0 :
b = b/2
defaultSequence += sequence[i]
b = 0
i += 1
trueI += 1
if i < len(sequence) :
b = b | self.forma[self.charToBin[sequence[i]]]
binSequence.append(b)
if len(poly) > 0 :
if sequence[i] not in poly :
poly.add(sequence[i])
polymorphisms.append((trueI, poly))
defaultSequence += sequence[i]
return (binSequence, defaultSequence, polymorphisms) | [
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.findPolymorphisms | def findPolymorphisms(self, strSeq, strict = False):
"""
Compares strSeq with self.sequence.
If not 'strict', this function ignores the cases of matching heterozygocity (ex: for a given position i, strSeq[i] = A and self.sequence[i] = 'A/G'). If 'strict' it returns all positions where strSeq differs self,sequence
"""
arr = self.encode(strSeq)[0]
res = []
if not strict :
for i in range(len(arr)+len(self)) :
if i >= len(arr) or i > len(self) :
break
if arr[i] & self[i] == 0:
res.append(i)
else :
for i in range(len(arr)+len(self)) :
if i >= len(arr) or i > len(self) :
break
if arr[i] != self[i] :
res.append(i)
return res | python | def findPolymorphisms(self, strSeq, strict = False):
"""
Compares strSeq with self.sequence.
If not 'strict', this function ignores the cases of matching heterozygocity (ex: for a given position i, strSeq[i] = A and self.sequence[i] = 'A/G'). If 'strict' it returns all positions where strSeq differs self,sequence
"""
arr = self.encode(strSeq)[0]
res = []
if not strict :
for i in range(len(arr)+len(self)) :
if i >= len(arr) or i > len(self) :
break
if arr[i] & self[i] == 0:
res.append(i)
else :
for i in range(len(arr)+len(self)) :
if i >= len(arr) or i > len(self) :
break
if arr[i] != self[i] :
res.append(i)
return res | [
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Subsets and Splits