[glu-genetics] push by bioinformed@gmail.com - Do not attempt to infer variant type by looking at the affect on AA... on 2012-07-31 01:23 GMT

[glu-ge...@googlecode.com]

Revision: b1b26dbc5930
Author: Kevin B. Jacobs <jac...@bioinformed.com>
Date: Mon Jul 30 10:58:19 2012
Log: Do not attempt to infer variant type by looking at the affect on
AA
sequence. Variant type is based on the relative sizes of the reference and
variant alleles.
http://code.google.com/p/glu-genetics/source/detail?r=b1b26dbc5930

Modified:
/glu/lib/seqlib/vannotator.py

=======================================
--- /glu/lib/seqlib/vannotator.py Fri Jul 20 09:47:00 2012
+++ /glu/lib/seqlib/vannotator.py Mon Jul 30 10:58:19 2012
@@ -351,6 +351,13 @@

mut_type = []

+ if len(ref_nuc)==len(var_nuc):
+ mut_type.append('SUBSTITUTION')
+ elif len(ref_nuc)>len(var_nuc):
+ mut_type.append('DELETION')
+ else:
+ mut_type.append('INSERTION')
+
if exon_start<5:
mut_type.append('POSSIBLE-SPLICE5')
if cds.end-exon_end<5:
@@ -446,13 +453,6 @@
elif ref_cds_aa[-1]=='*' and var_cds_aa[-1]!='*':
mut_type.append('LOSS_OF_STOP')

- if len(r)==len(v):
- mut_type.append('SUBSTITUTION')
- elif len(r)>len(v):
- mut_type.append('DELETION')
- else:
- mut_type.append('INSERTION')
-
if 0:
print ' REF_NUC:',ref_cds_nuc
print ' VAR_NUC:',var_cds_nuc