PhyloSkims/annotate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Check the translation for stop codon and add a pseudogene qualifier if

Browse Source 
present.

Former-commit-id: 11b612fcdfa1fdd2a2614148b5b1772954e62e70
Former-commit-id: 02c87c99e5ece530640e521a577867e74ed1541e
This commit is contained in:
Eric Coissac
2018-11-20 15:59:57 +01:00
parent 671c12605a
commit a040adb132
1 changed files with 4 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
detectors/cds/lib/toEmbl.awk
View File

@ -181,6 +181,10 @@ function Unk(s) {
QQualifier("product", Product) QQualifier("product", Product)
QQualifier("inference", "similar to DNA sequence:" Simil) QQualifier("inference", "similar to DNA sequence:" Simil)
QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo) QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo)
if (match(Translat,/\*/)>0) {
QQualifier("pseudogene","unknown")
QQualifier("note","nonfunctional due to stop codon")
}
if (FrameShift==0) if (FrameShift==0)
QQualifier("translation", Translat) QQualifier("translation", Translat)