jvarkit

BlastFilterJS

Filters a BlastOutput with a javascript expression. The script injects each as the variable 'blasthit'. The user script should return 'true' to keep the hit.

Usage

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

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

Usage: blastfilterjs [options] Files
  Options:
    -e, --expression
       (js expression). Optional.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -f, --script
       (js file). Optional.
    --version
      print version and exit

Keywords

• blast
• js
• javascript
• filter

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastFilterJS.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 blastfilterjs ? 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

Examples

Filter Hit having <1500

$ java -jar dist/blastfilterjs.jar blastn.xml  -e 'parseInt(hit.getHitLen())<1500' 2> /dev/null |\
  xmllint --format - | grep "Hit_len"
  
   <Hit_len>1492</Hit_len>
   <Hit_len>1488</Hit_len>
   <Hit_len>1477</Hit_len>
   <Hit_len>1452</Hit_len>
   <Hit_len>1430</Hit_len>
   <Hit_len>1064</Hit_len>
   <Hit_len>1283</Hit_len>
   <Hit_len>1052</Hit_len>
   <Hit_len>1272</Hit_len>
   <Hit_len>693</Hit_len>
     

keep hsp having 100 > Hsp_align-len <= 200

$ cat filter.js

// keep hsp having 100>= Hsp_align-len <= 200 
function rmhsps()
	{
	var hsps = hit.getHitHsps().getHsp();
	var i=0;
	while(i< hsps.size())
		{
		var hsp = hsps.get(i);
		var hsplen = parseInt(hsp.getHspAlignLen());
		
		if( hsplen < 100 || hsplen > 300 )
			{
			hsps.remove(i);
			}
		else
			{
			i++;
			}
		}
	return true;
	}
rmhsps();

$ java -jar dist/blastfilterjs.jar -f filter.js blastn.xml 2> /dev/null |\
	xmllint --format - | grep -F 'Hsp_align-len'

	 <Hsp_align-len>289</Hsp_align-len>
	 <Hsp_align-len>291</Hsp_align-len>
	 <Hsp_align-len>197</Hsp_align-len>
	 <Hsp_align-len>227</Hsp_align-len>

See also

This site is open source. Improve this page.