scripts/release/rethreshold_family.py
def submit_new_rfsearch_job(family_dir, rfmake=False):
    """
    Submits a new lsf job that runs rfsearch to update SCORES for a new release.
    If no threshold is set with rfsearch.pl, it uses existing thresholds by default.

    family_dir: The physical location of the family directory
    rfmake: If True, run rfmake after rfsearch completes. Default False

    return: None
    """

    # use the pre-process command to change directory to family_dir
    rfam_acc = os.path.basename(family_dir)
    lsf_err_file = os.path.join(family_dir, "auto_rfsearch.err")
    lsf_out_file = os.path.join(family_dir, "auto_rfsearch.out")
    cmd = ("bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %s -g %s -q production-rh7 "
           "-J %s \"cd %s && rfsearch.pl -cnompi -q production-rh7 -relax\"")

    # If rfmake is set to True, runs rfmake following rfsearch, otherwise run rfsearch
    # only by default

    if rfmake is True:
        cmd = ("bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %s -g %s -q production-rh7 "
               "-J %s \"cd %s && rfsearch.pl -cnompi -q production-rh7 -relax && rfmake.pl\"")

    subprocess.call(cmd % (MEMORY, MEMORY, lsf_out_file, lsf_err_file,
                           CPU, LSF_GROUP, rfam_acc, family_dir), shell=True)

    Submits a new lsf job that runs rfsearch to update SCORES for a new release.
    If no threshold is set with rfsearch.pl, it uses existing thresholds by default.

    family_dir: The physical location of the family directory
    rfmake: If True, run rfmake after rfsearch completes. Default False

    return: None
    
Submits a new lsf job that runs rfsearch to update SCORES for a new release.
If no threshold is set with rfsearch.pl, it uses existing thresholds by default.

The physical location of the family directory
rfmake: If True, run rfmake after rfsearch completes. Default False

None
Submits a new lsf job that runs rfsearch to update SCORES for a new release . If no threshold is set with rfsearch . pl it uses existing thresholds by default . The physical location of the family directory rfmake : If True run rfmake after rfsearch completes . Default False None
def submit_new_rfsearch_job(family_dir, rfmake=False):
    rfam_acc = os.path.basename(family_dir)
    lsf_err_file = os.path.join(family_dir, "auto_rfsearch.err")
    lsf_out_file = os.path.join(family_dir, "auto_rfsearch.out")
    cmd = ("bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %s -g %s -q production-rh7 "
           "-J %s \"cd %s && rfsearch.pl -cnompi -q production-rh7 -relax\"")
    if rfmake is True:
        cmd = ("bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %s -g %s -q production-rh7 "
               "-J %s \"cd %s && rfsearch.pl -cnompi -q production-rh7 -relax && rfmake.pl\"")
    subprocess.call(cmd % (MEMORY, MEMORY, lsf_out_file, lsf_err_file,
                           CPU, LSF_GROUP, rfam_acc, family_dir), shell=True)
def submit_new_rfsearch_job ( family_dir , rfmake = False ) : rfam_acc = os . path . basename ( family_dir ) lsf_err_file = os . path . join ( family_dir , "auto_rfsearch.err" ) lsf_out_file = os . path . join ( family_dir , "auto_rfsearch.out" ) cmd = ( "bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %s -g %s -q production-rh7 " "-J %s \"cd %s && rfsearch.pl -cnompi -q production-rh7 -relax\"" ) if rfmake is True : cmd = ( "bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %s -g %s -q production-rh7 " "-J %s \"cd %s && rfsearch.pl -cnompi -q production-rh7 -relax && rfmake.pl\"" ) subprocess . call ( cmd % ( MEMORY , MEMORY , lsf_out_file , lsf_err_file , CPU , LSF_GROUP , rfam_acc , family_dir ) , shell = True )
Submits a new lsf job that runs rfsearch to update SCORES for a new release.
Submits a new lsf job that runs rfsearch to update SCORES for a new release .
"""
    Submits a new lsf job that runs rfsearch to update SCORES for a new release.
    If no threshold is set with rfsearch.pl, it uses existing thresholds by default.

    family_dir: The physical location of the family directory
    rfmake: If True, run rfmake after rfsearch completes. Default False

    return: None
    """ # use the pre-process command to change directory to family_dir # If rfmake is set to True, runs rfmake following rfsearch, otherwise run rfsearch # only by default
family_dir
rfmake