jvarkit

FastqJavascript

Filters a FASTQ file using javascript( java nashorn engine).

Usage

Usage: fastqjs [options] Files
  Options:
    -R1, --R1
      for paired/interleaved input, save R1 reads in this file
    -R2, --R2
      for paired/interleaved input, save R2 reads in this file
    -X, --failing
      Save dicarded reads in that file. Optional. Default: no file
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -i, --interleaved
      interleaved input
      Default: false
    -N, --limit
      limit to 'N' records -1:all
      Default: -1
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -e
      javascript expression
    -f
      javascript file

Keywords

• fastq

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 fastqjs

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/fastq/FastqJavascript.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 fastqjs ? 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

Motivation

The script puts ‘rec’ a FastqRecord, or ‘pair’ for an interleaved input, into the script context

Example

Find pairs of fastq where both reads contains a PmeI restriction site ( GTTT/AAAC )

$ paste <(gunzip -c F.fastq.gz | paste - - - -)  <(gunzip -c R.fastq.gz | paste - - - -) |\
  tr "\t" "\n" |\
  java -jar dist/fastqjs.jar -i -e 'pair.get(0).getReadString().contains("GTTTAAAC") && pair.get(1).getReadString().contains("GTTTAAAC") '

@HWI-1KL149:13:C0RNFACXX:8:1309:5373:60519 1:N:0:CTTGTA
TTCCAAAAATGTTTAAACTTTACAAATTTTCTTTCTGCAAAGGATATTTAAAACTTTGTCAAGACAAATATAAAAGTCTGTTCTTTTCATTAGTCTCTATA
+
CCCFFFFFHHHHHJJJJJJJJJBHIIJJJJJJJJJJIJIJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJIJJIFEHIJHIJHHHHHHHFFFFFFFEEDE
@HWI-1KL149:13:C0RNFACXX:8:1309:5373:60519 2:N:0:CTTGTA
ACGCTTGATATTTGGTTTAAACATTTCTTGATTCAGAGAAGGTAGATGGTTATAGAGACTAATGAAAAGAACAGACTTTTATATTTGTCTTGACAAAGTTT
+
CCCFFFFFHHHHHJIIIJJIJJJJJIJJJJEHIJJJGIIIJJ?FHGIGIDDFHJJJJJJJIIJJIJJJJJJJJJIJHHHHHHHFFFFFFFEEEEEEDDDDC
@HWI-1KL149:13:C0RNFACXX:8:1309:6861:76085 1:N:0:CTTGTA
ACAGTATATCTATGTGAAAGTTAAAAAGAAATCGCTGTTTAGATGGAAGATGAGACCAGGTTATCATAGTTTTAGAAGAGGAGTTTAAACTTCATGCAGTG
+
CCCFDFFFHHHHHJIJJJJJIIJJJJJJJJJJJJJJJIJJJJIJJJJJJJJIIJJJJJJJFHIJJJJJJHIIJIJJHHHHHFFFFEEEEEEEDDEDDDDDD
@HWI-1KL149:13:C0RNFACXX:8:1309:6861:76085 2:N:0:CTTGTA
GGGTAGTCCACAAACAATGTGTTCATGTTGTCTCCCTCTTACTCACAAGCCTTCTGTAGCTCCCAACATTCACTGCATGAAGTTTAAACTCCTCTTCTAAA
+
@CCDDDFFHHHHHJJIJJJIJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJGIIJIJIIJJJJJJJJJIJJJIJJHHHHHHFFFFFFCEEEEEEDDDDDDED

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