KgToGff

Convert UCSC genpred/knowngene file to gff3 or gtf

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar kg2gff  [options] Files

Usage: kg2gff [options] Files
  Options:
    --coding
      select coding transcript only.
      Default: false
    --gtf
      use the GTF writer instead of GFF3
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --modulo3
      discard transcripts where CDS length isn't a modulo 3 (eg. remove 
      xeno-transcript mapped on another build)
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    --score
      default score (-1: undefined)
      Default: -1
    --source
      label for column 'source' in the output
      Default: ucsc
    --version
      print version and exit

Keywords

• gff
• gff3
• ucsc
• genpred

See also in Biostars

• https://www.biostars.org/p/9610527

Creation Date

20210106

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/kg2gff/KgToGff.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite kg2gff ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Warning

ouput is escaped for UTF8, some characters like ':' might be converted to a hexadecimal encoding.

Example

headjeter.kg -n1 | java -jar dist/jvarkit.jar kg2gff 
##gff-version 3.1.25
chr1    ucsc    gene    55039456    55064852    .   +   .   ID=gene%3APCSK9;Name=PCSK9;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;gene_type=protein_coding
chr1    ucsc    mRNA    55039456    55064852    .   +   .   ID=ENST00000710286.1;Parent=gene%3APCSK9;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    exon    55039456    55040044    .   +   .   ID=ENST00000710286.1%3AE0;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE0
chr1    ucsc    exon    55043843    55044034    .   +   .   ID=ENST00000710286.1%3AE1;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE1
chr1    ucsc    exon    55046523    55046646    .   +   .   ID=ENST00000710286.1%3AE2;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE2
chr1    ucsc    exon    55052278    55052411    .   +   .   ID=ENST00000710286.1%3AE3;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE3
chr1    ucsc    exon    55052650    55052791    .   +   .   ID=ENST00000710286.1%3AE4;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE4
chr1    ucsc    exon    55055993    55056189    .   +   .   ID=ENST00000710286.1%3AE5;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE5
chr1    ucsc    exon    55057331    55057514    .   +   .   ID=ENST00000710286.1%3AE6;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE6
chr1    ucsc    exon    55058036    55058209    .   +   .   ID=ENST00000710286.1%3AE7;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE7
chr1    ucsc    exon    55058499    55058647    .   +   .   ID=ENST00000710286.1%3AE8;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE8
chr1    ucsc    exon    55059486    55059663    .   +   .   ID=ENST00000710286.1%3AE9;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE9
chr1    ucsc    exon    55061375    55061556    .   +   .   ID=ENST00000710286.1%3AE10;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE10
chr1    ucsc    exon    55063369    55064852    .   +   .   ID=ENST00000710286.1%3AE11;Parent=ENST00000710286.1;Name=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1;exon_id=ENST00000710286.1%3AE11
chr1    ucsc    CDS 55039481    55040044    .   +   0   ID=ENST00000710286.1%3AC1;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55043843    55044034    .   +   0   ID=ENST00000710286.1%3AC2;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55046523    55046646    .   +   0   ID=ENST00000710286.1%3AC3;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55052278    55052411    .   +   2   ID=ENST00000710286.1%3AC4;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55052650    55052791    .   +   0   ID=ENST00000710286.1%3AC5;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55055993    55056189    .   +   2   ID=ENST00000710286.1%3AC6;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55057331    55057514    .   +   0   ID=ENST00000710286.1%3AC7;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55058036    55058209    .   +   2   ID=ENST00000710286.1%3AC8;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55058499    55058647    .   +   2   ID=ENST00000710286.1%3AC9;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55059486    55059663    .   +   0   ID=ENST00000710286.1%3AC10;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55061375    55061556    .   +   2   ID=ENST00000710286.1%3AC11;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    CDS 55063369    55063584    .   +   0   ID=ENST00000710286.1%3AC12;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    5_prime_UTR 55039456    55039480    .   +   .   ID=ENST00000710286.1%3AU55039456;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1
chr1    ucsc    3_prime_UTR 55063585    55064852    .   +   .   ID=ENST00000710286.1%3AU55063585;Parent=ENST00000710286.1;biotype=protein_coding;gene_id=gene%3APCSK9;gene_name=PCSK9;transcript_id=ENST00000710286.1