jvarkit

Biostar3654

show blast alignment with annotations

Usage

Usage: biostar3654 [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -L, --length
      Fasta Line kength
      Default: 50
    --ncbi-api-key
      NCBI API Key see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ 
      .If undefined, it will try to get in that order:  1) environment 
      variable ${NCBI_API_KEY} ;  2) the jvm property "ncbi.api.key" ;	3) A 
      java property file ${HOME}/.ncbi.properties and key api_key
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• blast
• xml
• annotation

See also in Biostars

• https://www.biostars.org/p/3654

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 biostar3654

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/biostar/Biostar3654.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar3654Test.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 biostar3654 ? 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

$ cat ~/jeter.blastn.xml 
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
(...)
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gi|14971104|gb|AF338247.1|</Hit_id>
  <Hit_def>Human rotavirus A strain M clone M1 NSP3 genes, complete cds</Hit_def>
  <Hit_accession>AF338247</Hit_accession>
  <Hit_len>2032</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_num>1</Hsp_num>

$ java -jar dist/biostar3654.jar ~/jeter.blastn.xml 2> /dev/null  | cut -c-${COLUMNS} 

QUERY: No definition line
       ID:Query_186611 Len:980
>Human rotavirus A strain M clone M1 NSP3 genes, complete cds
 AF338247
 id:gi|14971104|gb|AF338247.1| len:2032

   e-value:0 gap:0 bitScore:1764.98

QUERY 000000001 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGC 000000050
                ||||||||||||||||||||||||||||||||||||||||||||||||||
HIT   000000001 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGC 000000050
                ################################################## source organi
                ##################################                 5'UTR
                                                  ################ CDS codon_sta

QUERY 000000051 AGATGGTAAGCTCTATTATTAATACTTCTTTTGAAGCTGCAGTCGTTGCT 000000100
                ||||||||||||||||||||||||||||||||||||||||||||||||||
HIT   000000051 AGATGGTAAGCTCTATTATTAATACTTCTTTTGAAGCTGCAGTCGTTGCT 000000100
                ################################################## source organi
                ################################################## CDS codon_sta
(...)

Example

$ cat ~/jeter.blastn.xml 
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
(...)
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gi|14971104|gb|AF338247.1|</Hit_id>
  <Hit_def>Human rotavirus A strain M clone M1 NSP3 genes, complete cds</Hit_def>
  <Hit_accession>AF338247</Hit_accession>
  <Hit_len>2032</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_num>1</Hsp_num>

$ java -jar dist/biostar3654.jar ~/jeter.blastn.xml 2> /dev/null  | cut -c-${COLUMNS} 

QUERY: No definition line
       ID:Query_186611 Len:980
>Human rotavirus A strain M clone M1 NSP3 genes, complete cds
 AF338247
 id:gi|14971104|gb|AF338247.1| len:2032

   e-value:0 gap:0 bitScore:1764.98

QUERY 000000001 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGC 000000050
                ||||||||||||||||||||||||||||||||||||||||||||||||||
HIT   000000001 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGC 000000050
                ################################################## source organi
                ##################################                 5'UTR
                                                  ################ CDS codon_sta

QUERY 000000051 AGATGGTAAGCTCTATTATTAATACTTCTTTTGAAGCTGCAGTCGTTGCT 000000100
                ||||||||||||||||||||||||||||||||||||||||||||||||||
HIT   000000051 AGATGGTAAGCTCTATTATTAATACTTCTTTTGAAGCTGCAGTCGTTGCT 000000100
                ################################################## source organi
                ################################################## CDS codon_sta
(...)

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