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124 lines
4.6 KiB
Python
124 lines
4.6 KiB
Python
#!/usr/bin/env python
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"""
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Estimate INDELs for pair-wise alignments.
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usage: %prog maf_input out_file1 out_file2
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"""
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from __future__ import division
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require( "bx-python" )
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try:
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pkg_resources.require("numpy")
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except:
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pass
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import sys
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from bx.cookbook import doc_optparse
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from galaxy.tools.exception_handling import *
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import bx.align.maf
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assert sys.version_info[:2] >= ( 2, 4 )
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def main():
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# Parsing Command Line here
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options, args = doc_optparse.parse( __doc__ )
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try:
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inp_file, out_file1 = args
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except:
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print >> sys.stderr, "Tool initialization error."
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sys.exit()
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try:
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open(inp_file, 'r')
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except:
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print >> sys.stderr, "Unable to open input file"
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sys.exit()
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try:
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fout1 = open(out_file1, 'w')
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#fout2 = open(out_file2, 'w')
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except:
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print >> sys.stderr, "Unable to open output file"
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sys.exit()
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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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print >> sys.stderr, "Your MAF file appears to be malformed."
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sys.exit()
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print >> fout1, "#Block\tSource\tSeq1_Start\tSeq1_End\tSeq2_Start\tSeq2_End\tIndel_length"
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for block_ind, block in enumerate(maf_reader):
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if len(block.components) < 2:
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continue
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seq1 = block.components[0].text
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src1 = block.components[0].src
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start1 = block.components[0].start
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if len(block.components) == 2:
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seq2 = block.components[1].text
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src2 = block.components[1].src
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start2 = block.components[1].start
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#for pos in range(len(seq1)):
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nt_pos1 = start1-1 #position of the nucleotide (without counting gaps)
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nt_pos2 = start2-1
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pos = 0 #character column position
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gaplen1 = 0
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gaplen2 = 0
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prev_pos_gap1 = 0
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prev_pos_gap2 = 0
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while pos < len(seq1):
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if prev_pos_gap1 == 0:
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gaplen1 = 0
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if prev_pos_gap2 == 0:
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gaplen2 = 0
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if seq1[pos] == '-':
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if seq2[pos] != '-':
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nt_pos2 += 1
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gaplen1 += 1
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prev_pos_gap1 = 1
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#write 2
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if prev_pos_gap2 == 1:
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prev_pos_gap2 = 0
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print >> fout1, "%d\t%s\t%s\t%s\t%s\t%s\t%s" % ( block_ind+1, src2, nt_pos1, nt_pos1+1, nt_pos2-1, nt_pos2-1+gaplen2, gaplen2 )
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if pos == len(seq1)-1:
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print >> fout1, "%d\t%s\t%s\t%s\t%s\t%s\t%s" % ( block_ind+1, src1, nt_pos1, nt_pos1+1, nt_pos2+1-gaplen1, nt_pos2+1, gaplen1 )
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else:
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prev_pos_gap1 = 0
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prev_pos_gap2 = 0
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"""
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if prev_pos_gap1 == 1:
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prev_pos_gap1 = 0
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print >> fout1, "%d\t%s\t%s\t%s\t%s" % ( block_ind+1, src1, nt_pos1-1, nt_pos1, gaplen1 )
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elif prev_pos_gap2 == 1:
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prev_pos_gap2 = 0
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print >> fout1, "%d\t%s\t%s\t%s\t%s" % ( block_ind+1, src2, nt_pos2-1, nt_pos2, gaplen2 )
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"""
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else:
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nt_pos1 += 1
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if seq2[pos] != '-':
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nt_pos2 += 1
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#write both
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if prev_pos_gap1 == 1:
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prev_pos_gap1 = 0
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print >> fout1, "%d\t%s\t%s\t%s\t%s\t%s\t%s" % ( block_ind+1, src1, nt_pos1-1, nt_pos1, nt_pos2-gaplen1, nt_pos2, gaplen1 )
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elif prev_pos_gap2 == 1:
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prev_pos_gap2 = 0
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print >> fout1, "%d\t%s\t%s\t%s\t%s\t%s\t%s" % ( block_ind+1, src2, nt_pos1-gaplen2, nt_pos1, nt_pos2-1, nt_pos2, gaplen2 )
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else:
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gaplen2 += 1
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prev_pos_gap2 = 1
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#write 1
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if prev_pos_gap1 == 1:
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prev_pos_gap1 = 0
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print >> fout1, "%d\t%s\t%s\t%s\t%s\t%s\t%s" % ( block_ind+1, src1, nt_pos1-1, nt_pos1, nt_pos2, nt_pos2+gaplen1, gaplen1 )
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if pos == len(seq1)-1:
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print >> fout1, "%d\t%s\t%s\t%s\t%s\t%s\t%s" % ( block_ind+1, src2, nt_pos1+1-gaplen2, nt_pos1+1, nt_pos2, nt_pos2+1, gaplen2 )
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pos += 1
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if __name__ == "__main__":
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main()
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