jvarkit

BlastMapAnnotations

Maps uniprot/genbank annotations on a blast result.

Usage

Usage: blastmapannots [options] Files
  Options:
    --exclude
      Exclude uniprot/feature/type of genbank/feature/key.
      Default: []
  * -u, -g, --genbank, --uniprot
      XML sequence file Genbank.xml or uniprot.xml.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --include
      Restrict to uniprot/feature/type of genbank/feature/key.
      Default: []
    --version
      print version and exit
  * -APC
      append the sequence accession before the feature name.
      Default: false

Keywords

• blast
• annotation
• genbank
• uniprot

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 blastmapannots

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/blastmapannots/BlastMapAnnotations.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 blastmapannots ? 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

Download uniprot P04514 ( Rotavirus Non-structural protein 3 ) as XML

$ curl -o P04514.xml "http://www.uniprot.org/uniprot/P04514.xml"

Download the same P04514 as fasta

$ curl -o P04514.fasta "http://www.uniprot.org/uniprot/P04514.fasta"

TblastN P04514.fasta vs a RNA of NSP3 in genbank http://www.ncbi.nlm.nih.gov/nuccore/AY065842.1 and save the ouput as XML:

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>tblastn</BlastOutput_program>
(...)
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gi|18139606|gb|AY065842.1|</Hit_id>
  <Hit_def>Rhesus rotavirus nonstructural protein 3 (NSP3) gene, complete cds</Hit_def>
  <Hit_accession>AY065842</Hit_accession>
  <Hit_len>1078</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_bit-score>546.584</Hsp_bit-score>
      <Hsp_score>1407</Hsp_score>
      <Hsp_evalue>0</Hsp_evalue>
      <Hsp_query-from>1</Hsp_query-from>
      <Hsp_query-to>313</Hsp_query-to>
      <Hsp_hit-from>26</Hsp_hit-from>
      <Hsp_hit-to>964</Hsp_hit-to> <Hsp_qseq>MLKMESTQQMASSIINTSFEAAVVAATSTLELMGIQYDYNEIYTRVKSKFDYVMDDSGVKNNLLGKAATIDQALNGKFGSVMRNKNWMTDSRTVAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSVIKCTRLMKDKIERGAVEVDDSFVEEKMEVDTVDWKSRYDQLERRFESLKQRVNEKYTTWVQKAKKVNENMYSLQNVISQQQNQIADLQNYCSKLEADLQNKVGSLVSSVEWYLKSMELPDEVKTDIEQQLNSIDTISPINAIDDLEILIRNLIHDYDRTFLMFKGLLRQCNYEYAYE</Hsp_qseq>
      <Hsp_hseq>MLKMESTQQMASSIINSSFEAAVVAATSTLELMGIQYDYNEVYTRVKSKFDLVMDDSGVKNNLIGKAITIDQALNGKFSSAIRNRNWMTDSRTVAKLDEDVNKLRIMLSSKGIDQKMRVLNACFSVKRIPGKSSSIVKCTRLMKDKLERGEVEVDDSFVEEKMEVDTIDWKSRYEQLEKRFESLKHRVNEKYNHWVLKARKVNENMNSLQNVISQQQAHINELQMYNNKLERDLQSKIGSVVSSIEWYLRSMELSDDVKSDIEQQLNSIDQLNPVNAIDDFESILRNLISDYDRLFIMFKGLLQQCNYTYTYE</Hsp_hseq>
      <Hsp_midline>MLKMESTQQMASSIIN SFEAAVVAATSTLELMGIQYDYNE YTRVKSKFD VMDDSGVKNNL GKA TIDQALNGKF S  RN NWMTDSRTVAKLDEDVNKLR MLSSKGIDQKMRVLNACFSVKRIPGKSSS  KCTRLMKDK ERG VEVDDSFVEEKMEVDT DWKSRY QLE RFESLK RVNEKY  WV KA KVNENM SLQNVISQQQ  I  LQ Y  KLE DLQ K GS VSS EWYL SMEL D VK DIEQQLNSID   P NAIDD E   RNLI DYDR F MFKGLL QCNY Y YE</Hsp_midline>
    </Hsp>
  </Hit_hsps>
</Hit>
(...)
</Iteration>
</BlastOutput_iterations>
</BlastOutput>

Now produce a BED file with this blast result to map the features of P04514 to AY065842.

$ java -jar dist/blastmapannots.jar I=P04514.xml B=blast.xml

AY065842	25	961	Non-structural_protein_3	943	+	25961	255,255,255	1	936	25
AY065842	34	469	RNA-binding	970	+	34	469	255,255,255	1	435	34
AY065842	472	640	Dimerization	947	+	472	640	255,255,255	1	168	472
AY065842	532	724	Interaction_with_ZC3H7B	917	+	532	724	255,255,255	1	192	532
AY065842	646	961	Interaction_with_EIF4G1	905	+	646	961	255,255,255	1	315	646
AY065842	520	733	coiled-coil_region	916	+	520	733	255,255,255	1	213	520

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