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86 lines
2.7 KiB
Python
86 lines
2.7 KiB
Python
#!/usr/bin/env python
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#Guruprasad ANanda
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"""
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Fetches substitutions from pairwise alignments.
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"""
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from galaxy import eggs
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from galaxy.tools.util import maf_utilities
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import bx.align.maf
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import sys
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def stop_err(msg):
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sys.stderr.write(msg)
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sys.exit()
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if len(sys.argv) < 3:
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stop_err("Incorrect number of arguments.")
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inp_file = sys.argv[1]
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out_file = sys.argv[2]
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fout = open(out_file, 'w')
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def fetchSubs(block):
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src1 = block.components[0].src
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sequence1 = block.components[0].text
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start1 = block.components[0].start
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end1 = block.components[0].end
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len1_withgap = len(sequence1)
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for seq in range (1, len(block.components)):
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src2 = block.components[seq].src
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sequence2 = block.components[seq].text
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start2 = block.components[seq].start
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end2 = block.components[seq].end
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sub_begin = None
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sub_end = None
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begin = False
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for nt in range(len1_withgap):
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if sequence1[nt] not in '-#$^*?' and sequence2[nt] not in '-#$^*?': # Not a gap or masked character
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if sequence1[nt].upper() != sequence2[nt].upper():
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if not(begin):
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sub_begin = nt
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begin = True
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sub_end = nt
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else:
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if begin:
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print >> fout, "%s\t%s\t%s" % ( src1, start1+sub_begin-sequence1[0:sub_begin].count('-'), start1+sub_end-sequence1[0:sub_end].count('-') )
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print >> fout, "%s\t%s\t%s" % ( src2, start2+sub_begin-sequence2[0:sub_begin].count('-'), start2+sub_end-sequence2[0:sub_end].count('-') )
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begin = False
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else:
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if begin:
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print >> fout, "%s\t%s\t%s" % ( src1, start1+sub_begin-sequence1[0:sub_begin].count('-'), end1+sub_end-sequence1[0:sub_end].count('-') )
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print >> fout, "%s\t%s\t%s" % ( src2, start2+sub_begin-sequence2[0:sub_begin].count('-'), end2+sub_end-sequence2[0:sub_end].count('-') )
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begin = False
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def main():
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skipped = 0
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not_pairwise = 0
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try:
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maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
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except:
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stop_err("Your MAF file appears to be malformed.")
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print >> fout, "#Chr\tStart\tEnd"
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for block in maf_reader:
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if len(block.components) != 2:
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not_pairwise += 1
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continue
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try:
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fetchSubs(block)
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except:
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skipped += 1
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if not_pairwise:
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print "Skipped %d non-pairwise blocks" % (not_pairwise)
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if skipped:
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print "Skipped %d blocks" % (skipped)
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if __name__ == "__main__":
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main()
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