[3] | 1 | #!/usr/bin/python2.6 |
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| 2 | |
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| 3 | """ |
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| 4 | Read a maf file and print the regions covered to a set of bed files (one for |
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| 5 | each sequence source referenced in the maf). Only blocks with a positive |
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| 6 | percent identity are written out. |
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| 7 | |
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| 8 | TODO: Can this be generalized to be made more useful? |
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| 9 | |
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| 10 | usage: %prog bed_outfile_prefix < maf |
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| 11 | """ |
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| 12 | |
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| 13 | from __future__ import division |
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| 14 | |
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| 15 | import psyco_full |
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| 16 | import bx.align.maf |
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| 17 | import sys |
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| 18 | |
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| 19 | def block_pid( comp1, comp2 ): |
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| 20 | match = 0 |
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| 21 | total = 0 |
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| 22 | t1 = comp1.text.lower() |
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| 23 | t2 = comp2.text.lower() |
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| 24 | for i in range( 0, len(t1) ): |
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| 25 | a, b = t1[i], t2[i] |
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| 26 | if a == '-' or b == '-': |
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| 27 | continue |
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| 28 | elif a == b: |
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| 29 | match += 1 |
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| 30 | total += 1 |
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| 31 | if total == 0: return None |
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| 32 | return ( match / total ) |
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| 33 | |
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| 34 | def main(): |
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| 35 | out_prefix = sys.argv[1] |
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| 36 | print out_prefix |
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| 37 | out_files = dict() |
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| 38 | for block in bx.align.maf.Reader( sys.stdin ): |
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| 39 | ref_comp = block.components[0] |
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| 40 | ref_chrom = ref_comp.src.split('.')[1] |
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| 41 | for comp in block.components[1:]: |
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| 42 | comp_species, comp_chrom = comp.src.split('.')[:2] |
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| 43 | if comp_species not in out_files: |
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| 44 | f = open( "%s%s.bed" % ( out_prefix, comp_species ), "w" ) |
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| 45 | out_files[comp_species] = f |
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| 46 | pid = block_pid( ref_comp, comp ) |
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| 47 | if pid: |
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| 48 | out_files[comp_species].write( "%s\t%d\t%d\t%s:%d-%d,%s\t%f\n" % |
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| 49 | ( ref_chrom, ref_comp.forward_strand_start, ref_comp.forward_strand_end, \ |
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| 50 | comp_chrom, comp.start, comp.end, comp.strand, pid ) ) |
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| 51 | |
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| 52 | for f in out_files.values(): |
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| 53 | f.close() |
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| 54 | |
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| 55 | |
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| 56 | if __name__ == "__main__": main() |
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