really rough bam processing pipeline

bam_pipe.py

#!/usr/bin/python

import sys, getopt
import glob
import os
import ntpath

from time import strftime
print '******bam_pipe******'
print strftime("%Y-%m-%d %H:%M:%S")
print '********************'
print '\n'

def sub_index_bam(bam_file):  
    import subprocess

    process = subprocess.Popen(('samtools index %s') % \
                               (bam_file),
                               stdout=subprocess.PIPE,
                               stderr=subprocess.PIPE,
                               shell=True)
    # todo handle non zero
    process.wait()
    for line in process.stdout:
        print line
    
    for line in process.stderr:
        print line

        
#n = 10
#source = '/mnt/ceph/mbp/servers/bioinformatics-platform/home/steve/projects/aspree_bam_pipe/source'
#dest = '/mnt/ceph/mbp/servers/bioinformatics-platform/home/steve/projects/aspree_bam_pipe/dest'


def bam_pipe(source, dest, n):
    source_path = source
    if not source.startswith(os.path.sep):
        #relative
        source_path = os.path.join(os.getcwd(), source)

    print 'source path is: %s' % source
    print 'dest path is: %s' % dest
    if not n == None:
        print 'files to process in source (up to): %s' % n
    print '\n'

    skipped = 0
    processed = 0
    count = 0

    for name in glob.glob('%s/*.bam' % source_path):
        if n == None:
            pass
        elif count == int(n):
            print 'ENDING run because file limit count reached: %s' % count
            break

        basename = ntpath.basename(name)   

        print '*** bam file: %s ***' % basename

        dest_path = os.path.join(dest, basename)
        if not dest.startswith(os.path.sep):
            #relative
            dest_path = os.path.join(os.getcwd(), dest_path)

        source_file = os.path.join(source_path, basename)

        #print source_file
        #print dest_path

        if os.path.exists(dest_path):
            skipped = skipped + 1
            print 'SKIPPING processing of file because it exists in destination'
        else:
            processed = processed + 1
            print 'LINKING source file in destination location for processing'
            os.symlink(source_file, dest_path)
            print 'PROCESSING bam file (creating INDEX)'
            sub_index_bam(dest_path)

        count = count + 1
        print '\n'

    print '\nDone. Files Processed: %s. Files Skipped: %s.' % (processed, skipped)
    return

def main(argv):
    inputfile = ''
    outputfile = ''
    number = None
    fail = False
    
    try:
        opts, args = getopt.getopt(argv,"hi:o:n:",["ifile=","ofile=","number="])
    except getopt.GetoptError:
        print 'test.py -i <inputfile> -o <outputfile> | tee -a logfile.txt)'
        print 'optional argument eg. -n 10 (to limit to 10 files)' 
        sys.exit(2)
    for opt, arg in opts:
        if opt == '-h':
            print 'test.py -i <inputfile> -o <outputfile> (optional: -n <number of files> | tee -a logfile.txt)'
            print 'optional argument eg. -n 10 (to limit to 10 files)'            
            sys.exit()
        elif opt in ("-i", "--ifile"):
            inputfile = arg
        elif opt in ("-o", "--ofile"):
            outputfile = arg
        elif opt in ("-n", "--number"):
            number = arg                

    if not inputfile:
          print 'need input directory parameter (-i)'
          fail = True

    if not outputfile:
          print 'need output directory parameter (-o)'
          fail = True        

    if not fail:
        bam_pipe(inputfile, outputfile, number)
        
if __name__ == "__main__":
    main(sys.argv[1:])