jvarkit

SkipXmlElements

Filter XML elements with a javascript (java rhino) expression. Context contain ‘element’ the current element. It implementsthe interface Tag described in SkipXmlElements.class

Usage

Usage: skipxmlelements [options] Files
  Options:
    -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
    -e
       (js expression). Optional.
    -f
       (js file). Optional.

Keywords

• xml
• javascript

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 skipxmlelements

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/misc/SkipXmlElements.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 skipxmlelements ? 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

Example

$  java -jar dist-1.128/skipxmlelements.jar -e 'element.depth < 5;'  out.blastn.xml 

output:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>blastn</BlastOutput_program>
  <BlastOutput_version>BLASTN 2.2.30+</BlastOutput_version>
  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997)
, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
  <BlastOutput_db>GPIPE/9606/current/all_top_level GPIPE/9606/current/rna</BlastOutput_db>
  <BlastOutput_query-ID>1113</BlastOutput_query-ID>
  <BlastOutput_query-def>gi|11051787</BlastOutput_query-def>
  <BlastOutput_query-len>728</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_expect>10</Parameters_expect>
      <Parameters_sc-match>2</Parameters_sc-match>
      <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
      <Parameters_gap-open>5</Parameters_gap-open>
      <Parameters_gap-extend>2</Parameters_gap-extend>
      <Parameters_filter>L;R -d repeatmasker/repeat_9606;m;</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
  <BlastOutput_iterations>
    <Iteration>
      <Iteration_iter-num>1</Iteration_iter-num>
      <Iteration_query-ID>1113</Iteration_query-ID>
      <Iteration_query-def>gi|11051787</Iteration_query-def>
      <Iteration_query-len>728</Iteration_query-len>
      <Iteration_hits>
</Iteration_hits>
      <Iteration_stat>
  </Iteration_stat>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>2</Iteration_iter-num>
      <Iteration_query-ID>1114</Iteration_query-ID>
      <Iteration_query-def>gi|10812511</Iteration_query-def>
      <Iteration_query-len>331</Iteration_query-len>
      <Iteration_hits>
</Iteration_hits>
      <Iteration_stat>
  </Iteration_stat>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>3</Iteration_iter-num>
      <Iteration_query-ID>1115</Iteration_query-ID>
      <Iteration_query-def>gi|10811235</Iteration_query-def>
      <Iteration_query-len>629</Iteration_query-len>
      <Iteration_hits>
</Iteration_hits>
      <Iteration_stat>
  </Iteration_stat>
    </Iteration>
  </BlastOutput_iterations>
</BlastOutput>

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