Comments (4)
from master_gff3_parser.
For tobacco, there are no alternative IDs to convert to (not even genbank IDs).
It does work if we convert from refSeq to refSeq:
$ time seqconv convert --ref Ntab-TN90 --out rs ref_Ntab-TN90_top_level.gff3.gz >test_tobacco_gb.gff3
Converting from None to rs
Starting Conversion
FORMAT detected: rs
real 0m16.931s
user 0m14.429s
sys 0m1.302s
from master_gff3_parser.
Fro Salmon, it appears to work ok:
$ time seqconv convert --ref ICSASG_v2 --out gb ref_ICSASG_v2_top_level.gff3.gz> test_salmon.gff3
Converting from None to gb
Starting Conversion
No corresponding id for nc_001960.1 from rs
FORMAT detected: rs
real 0m50.122s
user 0m37.864s
sys 0m3.102s
from master_gff3_parser.
text output
$ head -n 20 test_salmon.gff3
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/233/375/GCF_000233375.1_ICSASG_v2/GCF_000233375.1_ICSASG_v2_assembly_report.txt
##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build ICSASG_v2
#!genome-build-accession NCBI_Assembly:GCF_000233375.1
#!annotation-date 22 September 2015
#!annotation-source NCBI Salmo salar Annotation Release 100
##sequence-region CM003279.1 1 159038749
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=8030
CM003279.1 RefSeq region 1 159038749 . + . ID=id0;Dbxref=taxon:8030;Name=ssa01;breed=double haploid;chromosome=ssa01;dev-stage=adult;gbkey=Src;genome=chromosome;isolate=Sally;mol_type=genomic DNA;sex=female;tissue-type=muscle
CM003279.1 Gnomon gene 5501 62139 . - . ID=gene0;Dbxref=GeneID:106560212;Name=LOC106560212;gbkey=Gene;gene=LOC106560212;gene_biotype=protein_coding
CM003279.1 Gnomon mRNA 5501 62139 . - . ID=rna0;Parent=gene0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;Name=XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
CM003279.1 Gnomon exon 61647 62139 . - . ID=id1;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
CM003279.1 Gnomon exon 43486 43714 . - . ID=id2;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
CM003279.1 Gnomon exon 23978 24241 . - . ID=id3;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
CM003279.1 Gnomon exon 16966 17019 . - . ID=id4;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
CM003279.1 Gnomon exon 5501 5691 . - . ID=id5;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XM_014160784.1;gbkey=mRNA;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;transcript_id=XM_014160784.1
CM003279.1 Gnomon CDS 43486 43633 . - 0 ID=cds0;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XP_014016259.1;Name=XP_014016259.1;gbkey=CDS;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;protein_id=XP_014016259.1
CM003279.1 Gnomon CDS 23978 24241 . - 2 ID=cds0;Parent=rna0;Dbxref=GeneID:106560212,Genbank:XP_014016259.1;Name=XP_014016259.1;gbkey=CDS;gene=LOC106560212;product=fibroblast growth factor receptor 3-like;protein_id=XP_014016259.1
from master_gff3_parser.
Related Issues (15)
- Semi Successful test for USCS cat 4 to refseq ids HOT 3
- alt mouse failing HOT 2
- Testing the main mouse assembly rs to gb HOT 5
- Add IDs (not just convert) HOT 1
- Ensembl GTF features with no version may fail to convert
- the assembly_report URL is printed to STDOUT
- test_cli.py HOT 2
- seqconv adds assembly_report.txt line to the gtf file HOT 1
- Additional thoughts on format guessing
- Guessing the ID source in Target fields HOT 1
- setting UC for output format gives gb formatted ids
- problem testing a UCSC file HOT 2
- seqconv_debugging
- Test successful NCBI Cat 8.0 to UCSC HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. πππ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from master_gff3_parser.