jvarkit

SetFileTools

Utilities for the setfile format

Usage

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

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

Usage: setfiletools [options] Files
  Options:
    --bed
      Restrict input to this bed file.
    --disable-uniq
      disable unique-name checker.
      Default: false
    --extend
      Extends each interval. Extending interval. The following syntaxes are 
      supported: 1000; 1kb; 1,000; 30%(shrink); 150% (extend); 0.5 (shrink); 
      1.5 (extend)
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -J, --jobs
      number of clusters. (or specify --size)
      Default: -1
    --min-variants-per-setfile
      when using vcf, only keep the setfile is there are at least 'x' 
      overlapping variants.
      Default: 1
    -o, --out
      Output file. Optional . Default: stdout. For action=cluster, output is: 
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -U, --remove-unused-interval
      Remove
      Default: false
    -S, --size
      number of bases max per bin. (or specify --jobs). A distance specified 
      as a positive integer.Commas are removed. The following suffixes are 
      interpreted : b,bp,k,kb,m,mb,g,gb
      Default: -1
    --stringency
      Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    -t, --trim-chr
      Remove chr prefix in chromosome names on output.
      Default: false
    --vcf, --vcfs
      Restrict input to thoses vcf file(s). A file with the '.list' suffix is 
      interpreted as a list of paths to the vcfs.
      Default: []
    --version
      print version and exit

Keywords

• setfile
• bed

Creation Date

20210125

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/setfile/SetFileTools.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 setfiletools ? 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

action = frombed

$ echo -e "RF01\t150\t200\tA\nRF01\t190\t300\tA\nRF01\t350\t400\tA\nRF01\t150\t200\tB" |\
	java -jar dist/setfiletools.jar -R src/test/resources/rotavirus_rf.fa frombed

A	RF01:151-300,RF01:351-400
B	RF01:151-200

action = combine

$ echo -e "w RF01:150-200\nx RF01:1-100,RF02:1-100\ny RF01:90-200,RF03:1-100\nz RF03:50-150,RF04:100-200" | java -jar dist/setfiletools.jar -R src/test/resources/rotavirus_rf.fa combine
w_x	RF01:1-100,RF01:150-200,RF02:1-100
w_y	RF01:90-200,RF03:1-100
w_z	RF01:150-200,RF03:50-150,RF04:100-200
x_y	RF01:1-200,RF02:1-100,RF03:1-100
x_z	RF01:1-100,RF02:1-100,RF03:50-150,RF04:100-200
y_z	RF01:90-200,RF03:1-150,RF04:100-200

action = bedbed

creates a setfile from two bed files. First bed is “peaks.bed” second bed is “genes.bed”. The output is a set file . Each record in the output setFile is a ‘gene’ where all items are the overlapping peaks.

gunzip -c in.gtf.gz|\
awk -F '\t' '($3=="gene") {B=int($4)-1;X=100;printf("%s\t%d\t%s\n",$1,(B<X?0:B-X),int($5)+X);}' |\
sort -t $'\t' -k1,1 -k2,2n  |\
java -jar dist/setfiletools.jar -R ref.dict  in.bed.gz -

action = intersectbed

print whole setrecords overlapping bed file, there is to trimming

java -jar dist/setfiletools.jar -R ref.dict  in.bed.gz in.setfile

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