jvarkit

BlastFilterJS

Last commit

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

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

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 blastfilterjs

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/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>