In [25]:

    

# convert fimo to BED
with open('/Users/bergeric/data/motif_alignments_flyFactor_dm6.2L_BED.txt', 'w+') as outfile:
    with open('/Users/bergeric/data/motif_alignments_flyFactor_dm6.2L.txt') as f:
        for line in f:
            if not line.startswith("#"):
                s = line.split('\t')
                chrom = s[1]; start = s[2]; end = s[3]; name = s[0]; score = s[5]; strand = s[4]
                reorder = chrom + '\t' + start + '\t' + end + '\t' + name + '\t' + score + '\t' + strand + '\n'
                outfile.write(reorder)


    

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