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1 #!/usr/bin/env python
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2
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3 """
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4 Estimate INDELs for pair-wise alignments.
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5
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6 usage: %prog maf_input out_file1 out_file2
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7 """
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8
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9 from __future__ import division
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10 import sys
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11 from bx.cookbook import doc_optparse
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12 import bx.align.maf
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13
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14 assert sys.version_info[:2] >= ( 2, 4 )
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15
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16 def main():
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17 # Parsing Command Line here
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18 options, args = doc_optparse.parse( __doc__ )
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19
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20 try:
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21 inp_file, out_file1 = args
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22 except:
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23 print >> sys.stderr, "Tool initialization error."
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24 sys.exit()
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25
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26 try:
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27 open(inp_file, 'r')
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28 except:
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29 print >> sys.stderr, "Unable to open input file"
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30 sys.exit()
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31 try:
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32 fout1 = open(out_file1, 'w')
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33 #fout2 = open(out_file2, 'w')
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34 except:
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35 print >> sys.stderr, "Unable to open output file"
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36 sys.exit()
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37
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38 try:
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39 maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
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40 except:
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41 print >> sys.stderr, "Your MAF file appears to be malformed."
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42 sys.exit()
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43
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44 print >> fout1, "#Block\tSource\tSeq1_Start\tSeq1_End\tSeq2_Start\tSeq2_End\tIndel_length"
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45 for block_ind, block in enumerate(maf_reader):
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46 if len(block.components) < 2:
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47 continue
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48 seq1 = block.components[0].text
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49 src1 = block.components[0].src
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50 start1 = block.components[0].start
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51 if len(block.components) == 2:
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52 seq2 = block.components[1].text
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53 src2 = block.components[1].src
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54 start2 = block.components[1].start
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55 #for pos in range(len(seq1)):
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56 nt_pos1 = start1-1 #position of the nucleotide (without counting gaps)
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57 nt_pos2 = start2-1
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58 pos = 0 #character column position
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59 gaplen1 = 0
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60 gaplen2 = 0
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61 prev_pos_gap1 = 0
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62 prev_pos_gap2 = 0
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63 while pos < len(seq1):
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64 if prev_pos_gap1 == 0:
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65 gaplen1 = 0
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66 if prev_pos_gap2 == 0:
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67 gaplen2 = 0
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68
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69 if seq1[pos] == '-':
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70 if seq2[pos] != '-':
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71 nt_pos2 += 1
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72 gaplen1 += 1
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73 prev_pos_gap1 = 1
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74 #write 2
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75 if prev_pos_gap2 == 1:
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76 prev_pos_gap2 = 0
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77 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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78 if pos == len(seq1)-1:
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79 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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80 else:
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81 prev_pos_gap1 = 0
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82 prev_pos_gap2 = 0
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83 """
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84 if prev_pos_gap1 == 1:
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85 prev_pos_gap1 = 0
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86 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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87 elif prev_pos_gap2 == 1:
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88 prev_pos_gap2 = 0
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89 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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90 """
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91 else:
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92 nt_pos1 += 1
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93 if seq2[pos] != '-':
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94 nt_pos2 += 1
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95 #write both
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96 if prev_pos_gap1 == 1:
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97 prev_pos_gap1 = 0
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98 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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99 elif prev_pos_gap2 == 1:
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100 prev_pos_gap2 = 0
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101 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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102 else:
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103 gaplen2 += 1
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104 prev_pos_gap2 = 1
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105 #write 1
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106 if prev_pos_gap1 == 1:
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107 prev_pos_gap1 = 0
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108 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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109 if pos == len(seq1)-1:
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110 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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111 pos += 1
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112
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113
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114 if __name__ == "__main__":
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115 main()
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