[2] | 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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