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

Add the management of pseudogenes

Browse Source 
Former-commit-id: 26d91366e483cf17c440b251ab1e8ac5390699fe
Former-commit-id: 0d3d69ba351bd174fe08387a474fd1137559e38a
This commit is contained in:
Eric Coissac
2016-10-06 08:56:45 -03:00
parent d4da1d01fd
commit 860cd217d4
1 changed files with 37 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files

57
detectors/cds/lib/toEmbl.awk
View File

@ -95,6 +95,7 @@ function Unk(s) {
/^c begin_entry/ { /^c begin_entry/ {
Nexon = 0 Nexon = 0
FrameShift=0
delete Exon delete Exon
next next
} }
@ -107,6 +108,9 @@ function Unk(s) {
Exon[Nexon]["indels"] = $9 "+" $12 Exon[Nexon]["indels"] = $9 "+" $12
modif = $15; gsub("\"", "", modif) modif = $15; gsub("\"", "", modif)
Exon[Nexon]["modif"] = modif Exon[Nexon]["modif"] = modif
if ( $0 ~ /frameshifts +[0-9]+/)
FrameShift=1
next next
} }
@ -123,34 +127,39 @@ function Unk(s) {
/^c end_entry/ { /^c end_entry/ {
GeneName = Unk(GeneName) GeneName = Unk(GeneName)
PassType = Unk(PassType) PassType = Unk(PassType)
gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene) gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene)
locus = "" locus = ""
Feature("gene", GeneLocation()) Feature("gene", GeneLocation())
QQualifier("gene", gname) QQualifier("gene", gname)
QQualifier("locus_tag", locus) QQualifier("locus_tag", locus)
if (FrameShift)
QQualifier("pseudogene","unknown")
Feature("CDS", CdsLocation()) Feature("CDS", CdsLocation())
SQualifier("codon_start", 1) SQualifier("codon_start", 1)
SQualifier("transl_table", 11) SQualifier("transl_table", 11)
QQualifier("gene", gname) QQualifier("gene", gname)
QQualifier("locus_tag", locus) QQualifier("locus_tag", locus)
QQualifier("product", Product) if (FrameShift)
QQualifier("inference", "similar to DNA sequence:" Simil) QQualifier("pseudogene","unknown")
QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo) QQualifier("product", Product)
QQualifier("translation", Translat) QQualifier("inference", "similar to DNA sequence:" Simil)
QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo)
if (FrameShift==0)
QQualifier("translation", Translat)
if (Nexon > 1) { if (Nexon > 1) {
for (i = 1 ; i <= Nexon ; i++) { for (i = 1 ; i <= Nexon ; i++) {
Feature("exon", ExonLocation(i)) Feature("exon", ExonLocation(i))
QQualifier("gene", gname) QQualifier("gene", gname)
QQualifier("locus_tag", locus) QQualifier("locus_tag", locus)
SQualifier("number", Exon[1]["strand"] == "+" ? i : Nexon-i+1) SQualifier("number", Exon[1]["strand"] == "+" ? i : Nexon-i+1)
} }
} }
} }