diff vcf_gff.py @ 5:b321e0517be3 draft

Uploaded

--- a/vcf_gff.py	Thu Oct 18 19:47:07 2012 -0400
+++ b/vcf_gff.py	Thu May 22 20:30:19 2014 -0400
@@ -46,6 +46,8 @@
         record_type = "SNP"
     for entry in rec:
         detail = entry.split("=")
+        if len(detail) < 2:
+            continue
         INFO[detail[0]] = detail[1]
     if INFO.has_key("DP"):
         reads = INFO.get("DP")
@@ -108,7 +110,9 @@
                 gen = "HET"
             if genotypes == "0/0":
                 gen = "HOM_ref"
-        else:
+        try: # set gen to 'NA' if still unset
+            gen
+        except NameError:
             gen = "NA"
         geno = ("%s:%s " % (reads, gen))
         genos += geno
@@ -141,11 +145,11 @@
             end = start 
         gen = get_gen(info[8:], reference)
         out_gff_file.write(
-            ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%d;Variant" +
+            ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%s:%d;Variant" +
              "_seq=%s;Reference_seq=%s;Total_reads=%s;Zygosity=%s\n") %
             ( seqid, source,record_type, start, end, score, strand, phase,seqid, 
-              record_type, start, variant, reference, reads, gen))
-    
+              source, record_type, start, variant, reference, reads, gen))
+
 out_gff_file.close()