jvarkit

GenomicJaspar

Find jaspar patterns in FASTA sequences. Reports a BED file.

Usage

Usage: genomicjaspar [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --version
      print version and exit
  * -J
       jaspar PFM uri. required. example: http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_vertebrates.txt
    -f
      (0<ratio<1) fraction of best score
      Default: 0.95
    -o
      Output file. Optional . Default: stdout

Keywords

• jaspar
• genomic
• pattern

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew genomicjaspar

The java jar file will be installed in the dist directory.

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/jaspar/GenomicJasparTest.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 genomicjaspar ? 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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