Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

the assembly_report URL is printed to STDOUT #15

Open
childers opened this issue Mar 22, 2017 · 0 comments
Open

the assembly_report URL is printed to STDOUT #15

childers opened this issue Mar 22, 2017 · 0 comments
Labels

Comments

@childers
Copy link
Collaborator

childers commented Mar 22, 2017

When running a conversion, the first line of the output is a link to the assembly_report file.

$ time seqconv convert --ref ICSASG_v2 --out gb  ref_ICSASG_v2_top_level.gff3.gz> test_salmon.gff3
$ 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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant