jvarkit

MapUniProtFeatures

map uniprot features on reference genome.

Usage

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

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

Usage: mapuniprot [options] Files
  Options:
    --format
      output format 'annotate' is suitable for bcftools annotate
      Default: bed12
      Possible Values: [annotate, bed12]
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -k, --transcripts, --genpred
      Transcrips as genpred format 
      https://genome.ucsc.edu/FAQ/FAQformat.html#format9  . The genePred 
      format is a compact alternative to GFF/GTF because one transcript is 
      described using only one line.	Beware chromosome names are formatted the 
      same as your REFERENCE. A typical KnownGene file is http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/wgEncodeGencodeBasicV47.txt.gz 
      .If you only have a gff file, you can try to generate a knownGene file 
      with [http://lindenb.github.io/jvarkit/Gff2KnownGene.html](http://lindenb.github.io/jvarkit/Gff2KnownGene.html)
    --version
      print version and exit
  * -R
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -o
      Output file. Optional . Default: stdout

Keywords

• uniprot
• bed
• fasta
• reference
• xml

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/uniprot/MapUniProtFeatures.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 mapuniprot ? 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

Warning

this program is not fully tested. Please check the results

##Example

wget -O knownGene.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/wgEncodeGencodeBasicV47.txt.gz
wget -O knownGene.sql http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/wgEncodeGencodeBasicV47.sql


$ java  -jar dist/jvarkit mapuniprot \
	-R /path/to/hg38.fasta \
	-u /path/uri/uniprot.org/uniprot_sprot.xml.gz  \
	-k knownGene.txt.gz | gunzip -c | awk -F '        ' '{if($2 ~ ".*_.*") next; OFS="       "; gsub(/chr/,"",$2);print;}'   ) |\
	LC_ALL=C sort -t '	' -k1,1 -k2,2n -k3,3n  | uniq | head


1	69090	69144	topological_domain	1000	+	69090	69144	255,0,0	1	54	0
1	69144	69216	transmembrane_region	1000	+	69144	69216	255,0,0	1	72	0
1	69216	69240	topological_domain	1000	+	69216	69240	255,0,0	1	24	0
1	69240	69306	transmembrane_region	1000	+	69240	69306	255,0,0	1	66	0
1	69306	69369	topological_domain	1000	+	69306	69369	255,0,0	1	63	0
1	69357	69636	disulfide_bond	1000	+	69357	69636	255,0,0	1	279	0
1	69369	69429	transmembrane_region	1000	+	69369	69429	255,0,0	1	60	0
1	69429	69486	topological_domain	1000	+	69429	69486	255,0,0	1	57	0
1	69486	69543	transmembrane_region	1000	+	69486	69543	255,0,0	1	57	0
1	69543	69654	topological_domain	1000	+	69543	69654	255,0,0	1	111	0

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