lf_danglers

#!/usr/bin/env python

import os
import sys
import itertools
import subprocess as sp
import argparse

parser = argparse.ArgumentParser(description='find danglers')

parser.add_argument('-t', '--threads', default=10, type=int)
parser.add_argument('bowtie2_database')
parser.add_argument('forward_reads')
parser.add_argument('reverse_reads')
parser.add_argument('output')
parser.add_argument('-p', '--bowtie_preset', default='fast')


args = parser.parse_args()

def run_bowtie2(db, fq):
    cl = "bowtie2 --%s --reorder --no-head --quiet -p %d -x %s -U %s" % (
        args.bowtie_preset, args.threads, db, fq)
    process = sp.Popen(cl, shell=True, stdout=sp.PIPE)
    for line in process.stdout:
        if line[0] == '@': continue
        yield line.split()

i = 0; j = 1
with open(args.output, 'w') as F:
    for forward, reverse in itertools.izip(
        run_bowtie2(args.bowtie2_database, args.forward_reads),
        run_bowtie2(args.bowtie2_database, args.reverse_reads)):

        i += 1
        fflag = int(forward[1])
        rflag = int(reverse[1])
        if fflag & 0x4 == rflag & 0x4:
            #either both map, or both do not map
            #not dangling
            continue

        if fflag & 0x4:
            #forward is dangling        
            tag = 'R' + {0:'+', 0x10:'-'}[rflag & 0x10]
            F.write('@%s__%s__%s\n' % (reverse[2], tag, forward[0]))
            F.write('%s\n+\n%s\n' % (forward[9], forward[10]))

        else:
            #reverse is dangling
            tag = 'F' + {0:'+', 0x10:'-'}[fflag & 0x10]
            F.write('@%s__%s__%s\n' % (forward[2], tag, reverse[0]))
            F.write('%s\n+\n%s\n' % (reverse[9], reverse[10]))