jvarkit

MergeBlastXml

merge XML blast results (same Iteration/Iteration_query-def in multiple xml files

Usage

Usage: mergeblastxml [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --maxRecordsInRam
      Max Records in RAM
      Default: 50000
    -o, --out
      Output SVG file or stdout
    --tmpDir
      Tmp Directory
      Default: /tmp
    --version
      print version and exit

Keywords

• blast
• xml

See also in Biostars

• https://www.biostars.org/p/246958

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 mergeblastxml

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/blast/MergeBlastXml.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 mergeblastxml ? 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/mergeblastxml.jar input1.blastn.xml  input2.blastn.xml  input2.blastn.xml > out.xml

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