jvarkit

Biostar86480

Genomic restriction finder

Usage

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

Usage: java -jar dist/jvarkit.jar biostar86480  [options] Files

Usage: biostar86480 [options] Files
  Options:
    -E, --enzyme
      restrict to that enzyme name.
      Default: []
    --faidx
      FASTA input is the output of samtools faidx. Parse sequence name and 
      sequence start from Fasta header.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --min-size, --min-weight
      restrict to that enzyme 'size/weight'. ignore if 'x' <=0
      Default: 0.0
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -l
      list available enzymes

Keywords

• rebase
• genome
• enzyme
• restricion
• genome
• fasta

See also in Biostars

• https://www.biostars.org/p/86480
• https://www.biostars.org/p/9520528

Creation Date

20131114

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar86480.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar86480Test.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 biostar86480 ? 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

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr3.fa.gz" |\
gunzip -c  |\
java -jar dist/biostar86480.jar -E AarI -E EcoRI  

chr3	60645	60651	GAATTC	1000	+	EcoRI	G^AATTC
chr3	60953	60959	GAATTC	1000	+	EcoRI	G^AATTC
chr3	68165	68172	GCAGGTG	1000	-	AarI	CACCTGC(4/8)
chr3	70263	70269	GAATTC	1000	+	EcoRI	G^AATTC
chr3	70945	70952	GCAGGTG	1000	-	AarI	CACCTGC(4/8)
chr3	71140	71146	GAATTC	1000	+	EcoRI	G^AATTC
chr3	72264	72270	GAATTC	1000	+	EcoRI	G^AATTC
chr3	74150	74156	GAATTC	1000	+	EcoRI	G^AATTC
chr3	75063	75069	GAATTC	1000	+	EcoRI	G^AATTC
chr3	78438	78444	GAATTC	1000	+	EcoRI	G^AATTC
chr3	81052	81059	CACCTGC	1000	+	AarI	CACCTGC(4/8)
chr3	84498	84504	GAATTC	1000	+	EcoRI	G^AATTC
chr3	84546	84552	GAATTC	1000	+	EcoRI	G^AATTC
chr3	84780	84787	CACCTGC	1000	+	AarI	CACCTGC(4/8)
chr3	87771	87777	GAATTC	1000	+	EcoRI	G^AATTC
chr3	95344	95351	GCAGGTG	1000	-	AarI	CACCTGC(4/8)
chr3	96358	96364	GAATTC	1000	+	EcoRI	G^AATTC
chr3	96734	96740	GAATTC	1000	+	EcoRI	G^AATTC
chr3	105956	105962	GAATTC	1000	+	EcoRI	G^AATTC
chr3	107451	107457	GAATTC	1000	+	EcoRI	G^AATTC
(...)

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