Biostar81455

Defining precisely the exonic genomic context based on a position .

Usage

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

Usage: java -jar dist/jvarkit.jar biostar81455  [options] Files

Usage: biostar81455 [options] Files
  Options:
  * -gtf, --gtf
      A GTF (General Transfer Format) file. See 
      https://www.ensembl.org/info/website/upload/gff.html . Please note that 
      CDS are only detected if a start and stop codons are defined.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -1
      The coordinate are one-based. The default is zero based.
      Default: false

Keywords

• bed
• gene
• gtf

See also in Biostars

• https://www.biostars.org/p/81455

Creation Date

20130918

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar81455.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar81455Test.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 biostar81455 ? 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

Input

tab delimited file. 2 columns: CHROM and POS

Example

The example below is old, we now use a GTF instead of a ucsc gene file.

echo -e "chr22\t41258261\nchr22\t52000000\nchr22\t0" |\
    java   dist/biostar81455.jar

chr22   41258261    uc003azg.2  41253084    41258785    POSITIVE    Exon 2  41257621    41258785    0
chr22   41258261    uc011aox.2  41253084    41305239    POSITIVE    Exon 1  41253084    41253249    -5012
chr22   41258261    uc003azi.3  41253084    41328823    POSITIVE    Exon 1  41253084    41253249    -5012
chr22   41258261    uc003azj.3  41255553    41258130    NEGATIVE    Exon 1  41255553    41258130    -131
chr22   41258261    uc010gyh.1  41258260    41282519    POSITIVE    Exon 1  41258260    41258683    0
chr22   41258261    uc011aoy.1  41258260    41363888    POSITIVE    Exon 1  41258260    41258683    0
chr22   52000000    uc011asd.2  51195513    51227614    POSITIVE    Exon 4  51227177    51227614    -772386
chr22   52000000    uc003bni.3  51195513    51238065    POSITIVE    Exon 4  51237082    51238065    -761935
chr22   52000000    uc011ase.1  51205919    51220775    NEGATIVE    Exon 1  51220615    51220775    -779225
chr22   52000000    uc003bnl.1  51205919    51222087    NEGATIVE    Exon 1  51221928    51222087    -777913
chr22   52000000    uc003bns.3  51222156    51238065    POSITIVE    Exon 3  51237082    51238065    -761935
chr22   52000000    uc003bnq.1  51222224    51227600    POSITIVE    Exon 4  51227322    51227600    -772400
chr22   52000000    uc003bnr.1  51222224    51227781    POSITIVE    Exon 4  51227319    51227781    -772219
chr22   52000000    uc010hbj.3  51222224    51238065    POSITIVE    Exon 3  51237082    51238065    -761935
chr22   0   uc002zks.4  16150259    16193004    NEGATIVE    Exon 8  16150259    16151821    16150259
chr22   0   uc002zkt.3  16162065    16172265    POSITIVE    Exon 1  16162065    16162388    16162065
chr22   0   uc002zku.3  16179617    16181004    NEGATIVE    Exon 1  16179617    16181004    16179617
chr22   0   uc002zkv.3  16187164    16193004    NEGATIVE    Exon 5  16187164    16187302    16187164