Mercurial > repos > devteam > mutate_snp_codon
comparison mutate_snp_codon.py @ 0:50333b5ac867 draft default tip
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author | devteam |
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date | Tue, 20 Aug 2013 11:03:11 -0400 |
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-1:000000000000 | 0:50333b5ac867 |
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1 #!/usr/bin/env python | |
2 """ | |
3 Script to mutate SNP codons. | |
4 Dan Blankenberg | |
5 """ | |
6 | |
7 import sys, string | |
8 | |
9 def strandify( fields, column ): | |
10 strand = '+' | |
11 if column >= 0 and column < len( fields ): | |
12 strand = fields[ column ] | |
13 if strand not in [ '+', '-' ]: | |
14 strand = '+' | |
15 return strand | |
16 | |
17 def main(): | |
18 # parse command line | |
19 input_file = sys.argv[1] | |
20 out = open( sys.argv[2], 'wb+' ) | |
21 codon_chrom_col = int( sys.argv[3] ) - 1 | |
22 codon_start_col = int( sys.argv[4] ) - 1 | |
23 codon_end_col = int( sys.argv[5] ) - 1 | |
24 codon_strand_col = int( sys.argv[6] ) - 1 | |
25 codon_seq_col = int( sys.argv[7] ) - 1 | |
26 | |
27 snp_chrom_col = int( sys.argv[8] ) - 1 | |
28 snp_start_col = int( sys.argv[9] ) - 1 | |
29 snp_end_col = int( sys.argv[10] ) - 1 | |
30 snp_strand_col = int( sys.argv[11] ) - 1 | |
31 snp_observed_col = int( sys.argv[12] ) - 1 | |
32 | |
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 ) | |
34 | |
35 DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" ) | |
36 skipped_lines = 0 | |
37 errors = {} | |
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' ) ]: | |
39 errors[ name ] = { 'count':0, 'message':message } | |
40 line_count = 0 | |
41 for line_count, line in enumerate( open( input_file ) ): | |
42 line = line.rstrip( '\n\r' ) | |
43 if line and not line.startswith( '#' ): | |
44 fields = line.split( '\t' ) | |
45 if max_field_index >= len( fields ): | |
46 skipped_lines += 1 | |
47 errors[ 'max_field_index' ]['count'] += 1 | |
48 continue | |
49 | |
50 #read codon info | |
51 codon_chrom = fields[codon_chrom_col] | |
52 codon_start = int( fields[codon_start_col] ) | |
53 codon_end = int( fields[codon_end_col] ) | |
54 if codon_end - codon_start != 3: | |
55 #codons must be length 3 | |
56 skipped_lines += 1 | |
57 errors[ 'codon_len' ]['count'] += 1 | |
58 continue | |
59 codon_strand = strandify( fields, codon_strand_col ) | |
60 codon_seq = fields[codon_seq_col].upper() | |
61 if len( codon_seq ) != 3: | |
62 #codon sequence must have length 3 | |
63 skipped_lines += 1 | |
64 errors[ 'codon_seq' ]['count'] += 1 | |
65 continue | |
66 | |
67 #read snp info | |
68 snp_chrom = fields[snp_chrom_col] | |
69 snp_start = int( fields[snp_start_col] ) | |
70 snp_end = int( fields[snp_end_col] ) | |
71 if snp_end - snp_start != 1: | |
72 #snps must be length 1 | |
73 skipped_lines += 1 | |
74 errors[ 'snp_len' ]['count'] += 1 | |
75 continue | |
76 snp_strand = strandify( fields, snp_strand_col ) | |
77 snp_observed = fields[snp_observed_col].split( '/' ) | |
78 snp_observed = [ observed for observed in snp_observed if len( observed ) == 1 ] | |
79 if not snp_observed: | |
80 #sequence replacements must be length 1 | |
81 skipped_lines += 1 | |
82 errors[ 'snp_observed' ]['count'] += 1 | |
83 continue | |
84 | |
85 #Determine index of replacement for observed values into codon | |
86 offset = snp_start - codon_start | |
87 #Extract DNA on neg strand codons will have positions reversed relative to interval positions; i.e. position 0 == position 2 | |
88 if codon_strand == '-': | |
89 offset = 2 - offset | |
90 if offset < 0 or offset > 2: #assert offset >= 0 and offset <= 2, ValueError( 'Impossible offset determined: %s' % offset ) | |
91 #codon and snp do not overlap | |
92 skipped_lines += 1 | |
93 errors[ 'no_overlap' ]['count'] += 1 | |
94 continue | |
95 | |
96 for observed in snp_observed: | |
97 if codon_strand != snp_strand: | |
98 #if our SNP is on a different strand than our codon, take complement of provided observed SNP base | |
99 observed = observed.translate( DNA_COMP ) | |
100 snp_codon = [ char for char in codon_seq ] | |
101 snp_codon[offset] = observed.upper() | |
102 snp_codon = ''.join( snp_codon ) | |
103 | |
104 if codon_seq != snp_codon: #only output when we actually have a different codon | |
105 out.write( "%s\t%s\n" % ( line, snp_codon ) ) | |
106 else: | |
107 skipped_lines += 1 | |
108 errors[ 'empty_comment' ]['count'] += 1 | |
109 if skipped_lines: | |
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'] ] ) ) | |
111 | |
112 if __name__ == "__main__": main() |