Code Monkey home page Code Monkey logo

Comments (2)

Lioscro avatar Lioscro commented on June 14, 2024

Hi, @crazyhottommy
I just took a look at the gtf file you used, and it doesn't seem like it is in a format supported by kb.
kb is only able to parse GTF files formatted as so:

1 transcribed_unprocessed_pseudogene  gene        11869 14409 . + . gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; 
1 processed_transcript                transcript  11869 14409 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana";

Specifically, kb looks for gene_id gene_name transcript_id GTF attributes, and these attributes must be semicolon-separated list of tag-value pairs separated by a single space.

Whereas the GTF file you used has lines like so (notice the last part of the lines are different).

NC_013896.1	RefSeq	region	1	210400635	.	+	.	ID=NC_013896.1:1..210400635;Dbxref=taxon:9483;Name=1;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA
NC_013896.1	Gnomon	gene	166187	208374	.	-	.	ID=gene-LOC108590668;Dbxref=GeneID:108590668;Name=LOC108590668;gbkey=Gene;gene=LOC108590668;gene_biotype=lncRNA

If there is any way you can get a GTF file that is in a different format, or manually modify the GTF entries to be in that format, it should work.

from kb_python.

crazyhottommy avatar crazyhottommy commented on June 14, 2024

Thanks! The one I downloaded is gff file, I converted to gtf

gffread  GCF_000004665.1_Callithrix_jacchus-3.2_genomic.gff -T -o GCF_000004665.1_Callithrix_jacchus-3.2_genomic.gtf

This still does not work

NC_013896.1     Gnomon  exon    166187  166804  .       -       .       transcript_id "rna0"; gene_id "gene0"; gene_name "LOC108590668";
NC_013896.1     Gnomon  exon    198620  198707  .       -       .       transcript_id "rna0"; gene_id "gene0"; gene_name "LOC108590668";
NC_013896.1     Gnomon  exon    208220  208374  .       -       .       transcript_id "rna0"; gene_id "gene0"; gene_name "LOC108590668";

I guess the gene_0 gene_1 for each gene for this conversion is the problem. I will hack around. thanks

from kb_python.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

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.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.