scripts/processing/threshold_selector.py
def threshold_family_with_rfmake(family_dir, gathering_threshold, full_align=True):
    """
    Calls rfmake.pl to set the gathering threshold of a family

    family_dir: The path to an Rfam family directory
    gathering_threshold: A float value specifying the gathering threshold for the
    family

    return: Full alignment path if it exists or None if not. True upon completion
    and full_align=False
    """

    # change to family directory
    os.chdir(family_dir)

    cmd = "rfmake.pl -t %f"

    if full_align is True:
        cmd = "rfmake.pl -t %f -a"

    subprocess.call(cmd % gathering_threshold, shell=True)

    if full_align is True:
        full_align_path = os.path.join(family_dir, "align")
        if os.path.exists(full_align_path):
            return full_align_path
        else:
            return None

    return True

    Calls rfmake.pl to set the gathering threshold of a family

    family_dir: The path to an Rfam family directory
    gathering_threshold: A float value specifying the gathering threshold for the
    family

    return: Full alignment path if it exists or None if not. True upon completion
    and full_align=False
    
Calls rfmake.pl to set the gathering threshold of a family
family_dir: The path to an Rfam family directory
gathering_threshold: A float value specifying the gathering threshold for the
family

Full alignment path if it exists or None if not. True upon completion
and full_align=False
Calls rfmake . pl to set the gathering threshold of a family family_dir : The path to an Rfam family directory gathering_threshold : A float value specifying the gathering threshold for the family Full alignment path if it exists or None if not . True upon completion and full_align = False
def threshold_family_with_rfmake(family_dir, gathering_threshold, full_align=True):
    os.chdir(family_dir)
    cmd = "rfmake.pl -t %f"
    if full_align is True:
        cmd = "rfmake.pl -t %f -a"
    subprocess.call(cmd % gathering_threshold, shell=True)
    if full_align is True:
        full_align_path = os.path.join(family_dir, "align")
        if os.path.exists(full_align_path):
            return full_align_path
        else:
            return None
    return True
def threshold_family_with_rfmake ( family_dir , gathering_threshold , full_align = True ) : os . chdir ( family_dir ) cmd = "rfmake.pl -t %f" if full_align is True : cmd = "rfmake.pl -t %f -a" subprocess . call ( cmd % gathering_threshold , shell = True ) if full_align is True : full_align_path = os . path . join ( family_dir , "align" ) if os . path . exists ( full_align_path ) : return full_align_path else : return None return True
Calls rfmake.pl to set the gathering threshold of a family
family_dir: The path to an Rfam family directory
gathering_threshold: A float value specifying the gathering threshold for the
family
Calls rfmake . pl to set the gathering threshold of a family family_dir : The path to an Rfam family directory gathering_threshold : A float value specifying the gathering threshold for the family
"""
    Calls rfmake.pl to set the gathering threshold of a family

    family_dir: The path to an Rfam family directory
    gathering_threshold: A float value specifying the gathering threshold for the
    family

    return: Full alignment path if it exists or None if not. True upon completion
    and full_align=False
    """ # change to family directory
family_dir
gathering_threshold
full_align