jvarkit

KnownGeneToFasta

Last commit

convert ucsc genpred to fasta

Usage

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

Usage: java -jar dist/jvarkit.jar kg2fa  [options] Files

Usage: kg2fa [options] Files
  Options:
    --coding
      ignore non-coding transcripts.
      Default: false
    --empty
      Discard empty sequences.
      Default: false
    --hide, --exclude
      Exclude the following type of sequence: mRNA, cDNA, peptide, utr5, utr3 
      , uORF, uPeptide (case insensitive, comma/space separated)
      Default: <empty string>
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
  * -r, -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -sql, --sql
      SQL Schema URI. Each instance of transcript can be associated to a .sql 
      schema to help the software to decode the semantics of the columns. Eg.: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/wgEncodeGencodeBasicV20.sql
      Default: <empty string>
    --version
      print version and exit
    -L
      fasta line length.
      Default: 50

Keywords

Creation Date

20190213

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/kg2fa/KnownGeneToFasta.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite kg2fa ? 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

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