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1 #!/usr/bin/env python
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2 """
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3 Script to mutate SNP codons.
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4 Dan Blankenberg
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5 """
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6
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7 import sys, string
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8
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9 def strandify( fields, column ):
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10 strand = '+'
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11 if column >= 0 and column < len( fields ):
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12 strand = fields[ column ]
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13 if strand not in [ '+', '-' ]:
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14 strand = '+'
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15 return strand
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16
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17 def main():
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18 # parse command line
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19 input_file = sys.argv[1]
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20 out = open( sys.argv[2], 'wb+' )
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21 codon_chrom_col = int( sys.argv[3] ) - 1
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22 codon_start_col = int( sys.argv[4] ) - 1
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23 codon_end_col = int( sys.argv[5] ) - 1
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24 codon_strand_col = int( sys.argv[6] ) - 1
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25 codon_seq_col = int( sys.argv[7] ) - 1
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26
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27 snp_chrom_col = int( sys.argv[8] ) - 1
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28 snp_start_col = int( sys.argv[9] ) - 1
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29 snp_end_col = int( sys.argv[10] ) - 1
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30 snp_strand_col = int( sys.argv[11] ) - 1
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31 snp_observed_col = int( sys.argv[12] ) - 1
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32
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33 max_field_index = max( codon_chrom_col, codon_start_col, codon_end_col, codon_strand_col, codon_seq_col, snp_chrom_col, snp_start_col, snp_end_col, snp_strand_col, snp_observed_col )
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34
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35 DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" )
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36 skipped_lines = 0
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37 errors = {}
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38 for name, message in [ ('max_field_index','not enough fields'), ( 'codon_len', 'codon length must be 3' ), ( 'codon_seq', 'codon sequence must have length 3' ), ( 'snp_len', 'SNP length must be 3' ), ( 'snp_observed', 'SNP observed values must have length 3' ), ( 'empty_comment', 'empty or comment'), ( 'no_overlap', 'codon and SNP do not overlap' ) ]:
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39 errors[ name ] = { 'count':0, 'message':message }
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40 line_count = 0
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41 for line_count, line in enumerate( open( input_file ) ):
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42 line = line.rstrip( '\n\r' )
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43 if line and not line.startswith( '#' ):
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44 fields = line.split( '\t' )
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45 if max_field_index >= len( fields ):
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46 skipped_lines += 1
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47 errors[ 'max_field_index' ]['count'] += 1
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48 continue
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49
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50 #read codon info
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51 codon_chrom = fields[codon_chrom_col]
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52 codon_start = int( fields[codon_start_col] )
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53 codon_end = int( fields[codon_end_col] )
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54 if codon_end - codon_start != 3:
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55 #codons must be length 3
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56 skipped_lines += 1
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57 errors[ 'codon_len' ]['count'] += 1
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58 continue
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59 codon_strand = strandify( fields, codon_strand_col )
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60 codon_seq = fields[codon_seq_col].upper()
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61 if len( codon_seq ) != 3:
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62 #codon sequence must have length 3
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63 skipped_lines += 1
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64 errors[ 'codon_seq' ]['count'] += 1
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65 continue
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66
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67 #read snp info
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68 snp_chrom = fields[snp_chrom_col]
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69 snp_start = int( fields[snp_start_col] )
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70 snp_end = int( fields[snp_end_col] )
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71 if snp_end - snp_start != 1:
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72 #snps must be length 1
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73 skipped_lines += 1
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74 errors[ 'snp_len' ]['count'] += 1
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75 continue
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76 snp_strand = strandify( fields, snp_strand_col )
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77 snp_observed = fields[snp_observed_col].split( '/' )
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78 snp_observed = [ observed for observed in snp_observed if len( observed ) == 1 ]
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79 if not snp_observed:
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80 #sequence replacements must be length 1
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81 skipped_lines += 1
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82 errors[ 'snp_observed' ]['count'] += 1
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83 continue
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84
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85 #Determine index of replacement for observed values into codon
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86 offset = snp_start - codon_start
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87 #Extract DNA on neg strand codons will have positions reversed relative to interval positions; i.e. position 0 == position 2
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88 if codon_strand == '-':
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89 offset = 2 - offset
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90 if offset < 0 or offset > 2: #assert offset >= 0 and offset <= 2, ValueError( 'Impossible offset determined: %s' % offset )
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91 #codon and snp do not overlap
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92 skipped_lines += 1
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93 errors[ 'no_overlap' ]['count'] += 1
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94 continue
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95
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96 for observed in snp_observed:
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97 if codon_strand != snp_strand:
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98 #if our SNP is on a different strand than our codon, take complement of provided observed SNP base
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99 observed = observed.translate( DNA_COMP )
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100 snp_codon = [ char for char in codon_seq ]
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101 snp_codon[offset] = observed.upper()
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102 snp_codon = ''.join( snp_codon )
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103
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104 if codon_seq != snp_codon: #only output when we actually have a different codon
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105 out.write( "%s\t%s\n" % ( line, snp_codon ) )
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106 else:
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107 skipped_lines += 1
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108 errors[ 'empty_comment' ]['count'] += 1
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109 if skipped_lines:
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110 print "Skipped %i (%4.2f%%) of %i lines; reasons: %s" % ( skipped_lines, ( float( skipped_lines )/float( line_count ) ) * 100, line_count, ', '.join( [ "%s (%i)" % ( error['message'], error['count'] ) for error in errors.itervalues() if error['count'] ] ) )
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111
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112 if __name__ == "__main__": main()
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