production code finalised

Author: kalvari

__init__.py

@@ -0,0 +1,148 @@
+#!/usr/bin/python
+'''
+Created on 30 Mar 2016
+
+@author: ikalvari
+
+Description: Calls fasta_generator to generate fasta files for all Rfam
+             families in rfam_live
+
+Comments:    It is a prerequisite that the sequence file is indexed using
+             esl-sfetch --index option
+'''
+
+# ---------------------------------IMPORTS-------------------------------------
+
+import os
+import sys
+import subprocess
+from utils import RfamDB
+
+# -----------------------------------------------------------------------------
+
+LSF_GROUP = "/rfam_fa"
+
+# -----------------------------------------------------------------------------
+
+
+def fasta_gen_handler(seq_file, out_dir):
+    '''
+        This purpose of this script is to handle the fasta generation process,
+        generate individual shell scripts for each available family and submit
+        them to the cluster.
+
+        seq_file: Path to the input sequence file (e.g. rfamseq11.fa)
+        out_dir: The output directory where the fasta files will be generated.
+
+    '''
+
+    # fetch family accessions
+    cnx = RfamDB.connect()
+
+    cursor = cnx.cursor(buffered=True)
+
+    query = ("SELECT rfam_acc FROM family")
+
+    cursor.execute(query)
+
+    families = cursor.fetchall()
+
+    cursor.close()
+    RfamDB.disconnect(cnx)
+
+    # create scripts dir within output directory
+    if (not os.path.exists(os.path.join(out_dir, "scripts"))):
+        os.mkdir(os.path.join(out_dir, "scripts"))
+
+    for fam in families:
+
+        # 1. Generate script file
+        sh_path = shell_script_generator(
+            seq_file, str(fam[0]), out_dir, os.path.join(out_dir, "scripts"))
+
+        # 2. submit job under group
+        cmd = "bsub < %s" % (sh_path)
+        subprocess.call(cmd, shell=True)
+
+# -----------------------------------------------------------------------------
+
+
+def shell_script_generator(seq_file, rfam_acc, fa_outdir, out_dir=None):
+    '''
+        Generates family specific shell scripts to split fasta generation into
+        individual jobs.
+
+        seq_file: The path to sequence file (e.g. )
+    '''
+
+    # If no specific directory is provided for the shell scripts, generate them
+    # in the fa output directory
+
+    if out_dir is None:
+        file_path = os.path.join(fa_outdir, rfam_acc + '.sh')
+    else:
+        file_path = os.path.join(out_dir, rfam_acc + '.sh')
+
+    fp = open(file_path, 'w')
+
+    fp.write("#!/bin/csh\n")
+    fp.write("#BSUB -M 8000\n")
+    fp.write("#BSUB -R \"rusage[mem=8000,tmp=1000]\"\n")
+    fp.write("#BSUB -o \"/tmp/%J.out\"\n")
+    fp.write("#BSUB -e \"/tmp/%J.err\"\n")
+
+    fp.write(
+        "#BSUB -f \"/nfs/research2/nobackup/rfamp/fa_gen_err/%s.out < \
+        /tmp/%sJ.out\"\n" % (rfam_acc, chr(37)))
+
+    fp.write(
+        "#BSUB -f \"/nfs/research2/nobackup/rfamp/fa_gen_err/%s.err < \
+        /tmp/%sJ.err\"\n" % (rfam_acc, chr(37)))
+
+    fp.write("#BSUB -Ep \"rm /tmp/$LSB_JOBID.*\"\n")
+    fp.write("#BSUB -g %s \n\n" % (LSF_GROUP))
+    fp.write("/nfs/research2/nobackup/rfamp/code/fasta_generator.py %s %s %s \n" %
+             (seq_file, rfam_acc, fa_outdir))
+
+    fp.close()
+
+    return file_path
+
+# -----------------------------------------------------------------------------
+
+
+def usage():
+    '''
+        Displays information on how to run fasta_gen_handler
+    '''
+
+    print "\nUsage:\n------"
+
+    print "\npython fasta_gen_handler.py seq_file out_dir"
+
+    print "\nseq_file: Path to sequence for sequence export (e.g. rfamseq11.fa)"
+    print "out_dir: The path to the output directory"
+    print "\n-h option to display usage\n"
+
+# -----------------------------------------------------------------------------
+
+if __name__ == '__main__':
+
+    # minor input checks
+    if (sys.argv[1] == "-h"):
+        usage()
+        sys.exit()
+
+    elif(len(sys.argv) == 3):
+        seq_file = sys.argv[1]
+        out_dir = sys.argv[2]
+
+        if (os.path.isfile(seq_file) and os.path.isdir(out_dir)):
+            fasta_gen_handler(seq_file, out_dir)
+
+        else:
+            print "\nIncorrect Input."
+            usage()
+
+    else:
+        usage()