KgToGff

Last commit

Convert UCSC genpred file to gff3

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
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --source
      gff source field
      Default: ucsc
    --version
      print version and exit

Keywords

gff
gff3
ucsc
genpred

Creation Date

20210106

Source code

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

$ head -n1  ~/jeter.kg | java -jar dist/kg2gff.jar   | sed 's/%3A/:/g'  

##gff-version 3.1.25
chr22   ucsc    gene    18317101    18507325    .   -   .   ID=gene:uc002znh.2.g1;Name=uc002znh.2.1;biotype=protein_coding;gene_id=uc002znh.2.g1
chr22   ucsc    mRNA    18317101    18507325    .   -   .   ID=transcript:uc002znh.2.g1;Parent=gene:uc002znh.2.g1;Name=uc002znh.2.1;biotype=protein_coding;transcript_id=uc002znh.2.t1
chr22   ucsc    exon    18317101    18317315    .   -   .   ID=uc002znh.2:E0;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E0
chr22   ucsc    CDS 18317216    18317315    .   -   1   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS0;protein_id=uc002znh.2
chr22   ucsc    exon    18324588    18324783    .   -   .   ID=uc002znh.2:E1;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E1
chr22   ucsc    CDS 18324588    18324783    .   -   2   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS1;protein_id=uc002znh.2
chr22   ucsc    exon    18347665    18347752    .   -   .   ID=uc002znh.2:E2;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E2
chr22   ucsc    CDS 18347665    18347752    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS2;protein_id=uc002znh.2
chr22   ucsc    exon    18348690    18348778    .   -   .   ID=uc002znh.2:E3;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E3
chr22   ucsc    CDS 18348690    18348778    .   -   2   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS3;protein_id=uc002znh.2
chr22   ucsc    exon    18354603    18354789    .   -   .   ID=uc002znh.2:E4;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E4
chr22   ucsc    CDS 18354603    18354789    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS4;protein_id=uc002znh.2
chr22   ucsc    exon    18368644    18368817    .   -   .   ID=uc002znh.2:E5;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E5
chr22   ucsc    CDS 18368644    18368817    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS5;protein_id=uc002znh.2
chr22   ucsc    exon    18369936    18369998    .   -   .   ID=uc002znh.2:E6;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E6
chr22   ucsc    CDS 18369936    18369998    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS6;protein_id=uc002znh.2
chr22   ucsc    exon    18370089    18370201    .   -   .   ID=uc002znh.2:E7;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E7
chr22   ucsc    CDS 18370089    18370201    .   -   2   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS7;protein_id=uc002znh.2
chr22   ucsc    exon    18371800    18371996    .   -   .   ID=uc002znh.2:E8;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E8
chr22   ucsc    CDS 18371800    18371996    .   -   1   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS8;protein_id=uc002znh.2
chr22   ucsc    exon    18374251    18374398    .   -   .   ID=uc002znh.2:E9;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E9
chr22   ucsc    CDS 18374251    18374398    .   -   2   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS9;protein_id=uc002znh.2
chr22   ucsc    exon    18376574    18376670    .   -   .   ID=uc002znh.2:E10;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E10
chr22   ucsc    CDS 18376574    18376670    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS10;protein_id=uc002znh.2
chr22   ucsc    exon    18378050    18378176    .   -   .   ID=uc002znh.2:E11;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E11
chr22   ucsc    CDS 18378050    18378176    .   -   1   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS11;protein_id=uc002znh.2
chr22   ucsc    exon    18379012    18379127    .   -   .   ID=uc002znh.2:E12;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E12
chr22   ucsc    CDS 18379012    18379127    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS12;protein_id=uc002znh.2
chr22   ucsc    exon    18379490    18379747    .   -   .   ID=uc002znh.2:E13;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E13
chr22   ucsc    CDS 18379490    18379747    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS13;protein_id=uc002znh.2
chr22   ucsc    exon    18382214    18382314    .   -   .   ID=uc002znh.2:E14;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E14
chr22   ucsc    CDS 18382214    18382314    .   -   2   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS14;protein_id=uc002znh.2
chr22   ucsc    exon    18383608    18383763    .   -   .   ID=uc002znh.2:E15;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E15
chr22   ucsc    CDS 18383608    18383763    .   -   2   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS15;protein_id=uc002znh.2
chr22   ucsc    exon    18384644    18384745    .   -   .   ID=uc002znh.2:E16;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E16
chr22   ucsc    CDS 18384644    18384745    .   -   2   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS16;protein_id=uc002znh.2
chr22   ucsc    exon    18385397    18385513    .   -   .   ID=uc002znh.2:E17;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E17
chr22   ucsc    CDS 18385397    18385513    .   -   2   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS17;protein_id=uc002znh.2
chr22   ucsc    exon    18387398    18387605    .   -   .   ID=uc002znh.2:E18;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E18
chr22   ucsc    CDS 18387398    18387605    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS18;protein_id=uc002znh.2
chr22   ucsc    exon    18389315    18389652    .   -   .   ID=uc002znh.2:E19;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E19
chr22   ucsc    CDS 18389315    18389578    .   -   0   Parent=transcript:uc002znh.2.g1;ID=CDS:uc002znh.2:CDS19;protein_id=uc002znh.2
chr22   ucsc    exon    18507047    18507325    .   -   .   ID=uc002znh.2:E20;Parent=transcript:uc002znh.2.g1;Name=uc002znh.2;biotype=protein_coding;exon_id=uc002znh.2:E20