jvarkit

Biostar165777

Last commit

Split a XML file

Usage

Usage: biostar165777 [options] Files
  Options:
    -N, --count
      Number of files to be created
      Default: 100
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -o, --output
      Output file. Must contains __SPLIT__
    -T, --tag
      XML tag to be split.e.g 'Hit' in blast
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar165777

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/biostar/Biostar165777.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite biostar165777 ? 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-1.139/biostar165777.jar -o out__SPLIT__.xml -T Hit -N 5 ~/blastn.xml

$ ls -la ~/blastn.xml out*.xml
-rw-rw-r-- 1 lindenb lindenb 422606 nov.  14 12:47 /home/lindenb/blastn.xml
-rw-rw-r-- 1 lindenb lindenb  86319 nov.  14 16:17 out001.xml
-rw-rw-r-- 1 lindenb lindenb  83570 nov.  14 16:17 out002.xml
-rw-rw-r-- 1 lindenb lindenb  85096 nov.  14 16:17 out003.xml
-rw-rw-r-- 1 lindenb lindenb  88297 nov.  14 16:17 out004.xml
-rw-rw-r-- 1 lindenb lindenb  87123 nov.  14 16:17 out005.xml


$ grep -cF "<Hit>" ~/blastn.xml out*.xml
/home/lindenb/blastn.xml:100
out001.xml:20
out002.xml:20
out003.xml:20
out004.xml:20
out005.xml:20