dodir_seqnoisem.py

dodir_seqnoisem.py

import os
import sys
import glob

TRUNCATE_LENGTH = int(sys.argv[2])

def system(cmd):
    print >>sys.stderr, cmd
    os.system(cmd)

# dodir_pyro.py directory

directory = sys.argv[1]

owd = os.getcwd()
os.chdir(directory)

for ln in sys.stdin:
    cols = ln.split("\t")

    name = cols[0]
    barcode = cols[1]

    print name, barcode

    cmd = "Parse.pl %s %s < %s_s60_c01_cd.fa > %s_s60_c01_T%d.fa" % (barcode, TRUNCATE_LENGTH, name, name, TRUNCATE_LENGTH)
    system(cmd)

    cmd = "mpirun SeqDistM -in %s_s60_c01_T%d.fa > %s_s60_c01_T%d.seqdist" % (name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH)
    system(cmd)

    cmd = "FClusterM -in %s_s60_c01_T%d.seqdist -out %s_s60_c01_T%d > %s_s60_c01_T%d.fcout" % (name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH)
    system(cmd)

    cmd = "mpirun SeqNoiseM -in %s_s60_c01_T%d.fa -din %s_s60_c01_T%d.seqdist -out %s_s60_c01_T%d_s25_c08 -lin %s_s60_c01_T%d.list -min %s_s60_c01.mapping -s 25.0 -c 0.08 > %s_s60_c01_T%d_s25_c08.snout" % (name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH, name, name, TRUNCATE_LENGTH)
    system(cmd)

    cmd = "mpirun SeqNoiseM -in %s_s60_c01_T%d.fa -din %s_s60_c01_T%d.seqdist -out %s_s60_c01_T%d_s15_c08 -lin %s_s60_c01_T%d.list -min %s_s60_c01.mapping -s 15.0 -c 0.08 > %s_s60_c01_T%d_s15_c08.snout" % (name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH, name, TRUNCATE_LENGTH, name, name, TRUNCATE_LENGTH)
    system(cmd)