root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/pwm/pwm_score_motifs.py @ 3

#!/usr/bin/env python2.4
"""
Returns all positions of a maf with any pwm score > threshold
The positions are projected onto human coordinates
"""

import psyco_full
from bx.align import maf as align_maf
import position_weight_matrix as pwmx
from bx.pwm.pwm_score_maf import MafMotifScorer
import sys
from bx import intervals

def isnan(x):
    return not x==x

def main():

    if len(sys.argv) < 4:
        print >>sys.stderr, "%s motif inmaf spec1,spec2,... " % sys.argv[0]
        sys.exit(0)

    targmotif = sys.argv[1]
    inmaf = open(sys.argv[2])
    threshold = 0

    species = []

    for sp in sys.argv[3].split(','):
        species.append( sp )

    for maf in align_maf.Reader(inmaf):
        mafchrom = maf.components[0].src.split('.')[1]
        mafstart = maf.components[0].start
        mafend = maf.components[0].end
        reftext = maf.components[0].text

        # maf block scores for each matrix
        for scoremax,width,headers in MafMotifScorer(species, maf,targmotif):
            #print >>sys.stderr,headers
            blocklength = width
            mafsrc,mafstart,mafend = headers[0]
            mafchrom = mafsrc.split('.')[1]

            # lists of scores for each position in scoremax
            mx = scoremax
            for offset in range(blocklength):

                # scan all species with threshold
                for i in range(len(species)):
                    if mx[i][offset] > threshold:
                        refstart = mafstart + offset - reftext.count('-',0,offset)
                        refend = refstart + len( targmotif )
                        data = " ".join([ "%.2f" % mx[x][offset] for x in range(len(species))])
                        # quote the motif
                        print mafchrom,refstart,refend,"'"+targmotif+"'",data
                        break

if __name__ == '__main__': main()