Mercurial > repos > john-mccallum > pcr_markers
comparison vcf_gff.py @ 5:b321e0517be3 draft
Uploaded
author | ben-warren |
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date | Thu, 22 May 2014 20:30:19 -0400 |
parents | 402c3f0fe807 |
children |
comparison
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4:be070a68521e | 5:b321e0517be3 |
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44 rec = rec[1:] | 44 rec = rec[1:] |
45 else: | 45 else: |
46 record_type = "SNP" | 46 record_type = "SNP" |
47 for entry in rec: | 47 for entry in rec: |
48 detail = entry.split("=") | 48 detail = entry.split("=") |
49 if len(detail) < 2: | |
50 continue | |
49 INFO[detail[0]] = detail[1] | 51 INFO[detail[0]] = detail[1] |
50 if INFO.has_key("DP"): | 52 if INFO.has_key("DP"): |
51 reads = INFO.get("DP") | 53 reads = INFO.get("DP") |
52 else: | 54 else: |
53 reads = "NA" | 55 reads = "NA" |
106 gen = "HOM_mut" | 108 gen = "HOM_mut" |
107 if genotypes == "0/1": | 109 if genotypes == "0/1": |
108 gen = "HET" | 110 gen = "HET" |
109 if genotypes == "0/0": | 111 if genotypes == "0/0": |
110 gen = "HOM_ref" | 112 gen = "HOM_ref" |
111 else: | 113 try: # set gen to 'NA' if still unset |
114 gen | |
115 except NameError: | |
112 gen = "NA" | 116 gen = "NA" |
113 geno = ("%s:%s " % (reads, gen)) | 117 geno = ("%s:%s " % (reads, gen)) |
114 genos += geno | 118 genos += geno |
115 sample_dict = {} | 119 sample_dict = {} |
116 return genos | 120 return genos |
139 end = start + len(reference) | 143 end = start + len(reference) |
140 else: | 144 else: |
141 end = start | 145 end = start |
142 gen = get_gen(info[8:], reference) | 146 gen = get_gen(info[8:], reference) |
143 out_gff_file.write( | 147 out_gff_file.write( |
144 ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%d;Variant" + | 148 ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%s:%d;Variant" + |
145 "_seq=%s;Reference_seq=%s;Total_reads=%s;Zygosity=%s\n") % | 149 "_seq=%s;Reference_seq=%s;Total_reads=%s;Zygosity=%s\n") % |
146 ( seqid, source,record_type, start, end, score, strand, phase,seqid, | 150 ( seqid, source,record_type, start, end, score, strand, phase,seqid, |
147 record_type, start, variant, reference, reads, gen)) | 151 source, record_type, start, variant, reference, reads, gen)) |
148 | 152 |
149 out_gff_file.close() | 153 out_gff_file.close() |
150 | 154 |
151 | 155 |