
# ----------------------------------------------------------------------------------

import os
import sys
import subprocess
import argparse

# ------------------------------------- GLOBALS ------------------------------------

LSF_GROUP = "/family_srch"
MEMORY = 8000

# ----------------------------------------------------------------------------------

def checkout_family(rfam_acc):
    """
    Checks out a family from Rfam based on a valid Rfam accession.

    rfam_acc: A valid Rfam accession

    return:
    """

    cmd = "rfco.pl %s" % rfam_acc

    subprocess.call(cmd, shell=True)

    # add some checks here

# ----------------------------------------------------------------------------------

if __name__== '__main__':

    pass

# ----------------------------------------------------------------------------------

import os
import sys
import subprocess
import argparse

# ------------------------------------- GLOBALS ------------------------------------

LSF_GROUP = "/family_srch"
MEMORY = 8000

# ----------------------------------------------------------------------------------

def checkout_family(rfam_acc):
    """
    Checks out a family from Rfam based on a valid Rfam accession.

    rfam_acc: A valid Rfam accession

    return: None
    """

    cmd = "rfco.pl %s" % rfam_acc

    subprocess.call(cmd, shell=True)

    # add some checks here

# ----------------------------------------------------------------------------------

def submit_new_rfsearch_job(family_dir):
    """
    Submits a new lsf job that runs rfsearch to update SCORES for a new release

    family_dir: The physical location of the family directory

    return: None
    """
    # use the pre-process command to change directory to family_dir
    cmd = """
          bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %8 -g %s -R \"span[hosts=1]\"
          cd %s && rfsearch.pl -cnompi
          """

# ----------------------------------------------------------------------------------

if __name__ == '__main__':

    pass
Add function to run rfsearch on the cluster
Add function to run rfsearch on the cluster

  
  # ----------------------------------------------------------------------------------
  
  import os
  import sys
  import subprocess
  import argparse
  
  # ------------------------------------- GLOBALS ------------------------------------
  
  LSF_GROUP = "/family_srch"
  MEMORY = 8000
  
  # ----------------------------------------------------------------------------------
  
  def checkout_family(rfam_acc):
      """
      Checks out a family from Rfam based on a valid Rfam accession.
  
      rfam_acc: A valid Rfam accession
  
-     return:
+     return: None
      """
  
      cmd = "rfco.pl %s" % rfam_acc
  
      subprocess.call(cmd, shell=True)
  
      # add some checks here
  
  # ----------------------------------------------------------------------------------
  
+ def submit_new_rfsearch_job(family_dir):
+     """
+     Submits a new lsf job that runs rfsearch to update SCORES for a new release
+ 
+     family_dir: The physical location of the family directory
+ 
+     return: None
+     """
+     # use the pre-process command to change directory to family_dir
+     cmd = """
+           bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %8 -g %s -R \"span[hosts=1]\"
+           cd %s && rfsearch.pl -cnompi
+           """
+ 
+ # ----------------------------------------------------------------------------------
+ 
- if __name__== '__main__':
+ if __name__ == '__main__':
  
      pass
Add function to run rfsearch on the cluster
## Code Before:

# ----------------------------------------------------------------------------------

import os
import sys
import subprocess
import argparse

# ------------------------------------- GLOBALS ------------------------------------

LSF_GROUP = "/family_srch"
MEMORY = 8000

# ----------------------------------------------------------------------------------

def checkout_family(rfam_acc):
    """
    Checks out a family from Rfam based on a valid Rfam accession.

    rfam_acc: A valid Rfam accession

    return:
    """

    cmd = "rfco.pl %s" % rfam_acc

    subprocess.call(cmd, shell=True)

    # add some checks here

# ----------------------------------------------------------------------------------

if __name__== '__main__':

    pass
## Instruction:
Add function to run rfsearch on the cluster
## Code After:

# ----------------------------------------------------------------------------------

import os
import sys
import subprocess
import argparse

# ------------------------------------- GLOBALS ------------------------------------

LSF_GROUP = "/family_srch"
MEMORY = 8000

# ----------------------------------------------------------------------------------

def checkout_family(rfam_acc):
    """
    Checks out a family from Rfam based on a valid Rfam accession.

    rfam_acc: A valid Rfam accession

    return: None
    """

    cmd = "rfco.pl %s" % rfam_acc

    subprocess.call(cmd, shell=True)

    # add some checks here

# ----------------------------------------------------------------------------------

def submit_new_rfsearch_job(family_dir):
    """
    Submits a new lsf job that runs rfsearch to update SCORES for a new release

    family_dir: The physical location of the family directory

    return: None
    """
    # use the pre-process command to change directory to family_dir
    cmd = """
          bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %8 -g %s -R \"span[hosts=1]\"
          cd %s && rfsearch.pl -cnompi
          """

# ----------------------------------------------------------------------------------

if __name__ == '__main__':

    pass