jvarkit

Biostar160470

Getting untranslated nucleotide sequences on tblastn standalone

Usage

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

Usage: java -jar dist/jvarkit.jar biostar160470  [options] Files

Usage: biostar160470 [options] Files
  Options:
    -p, --bindir
      Blast binaries path
    -d, --db
      Blast db name
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• blasn
• blast
• translation
• protein

See also in Biostars

• https://www.biostars.org/p/160470

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar160470.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 biostar160470 ? 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

Makefile:

bin.dir=/commun/data/packages/ncbi/ncbi-blast-2.2.28+/bin

all: blastdb.nin
	cat roxan.fa | ${bin.dir}/tblastn -db blastdb -outfmt 5 | java -jar jvarkit.jar biostar160470 -p ${bin.dir} -d blastdb| xmllint --format - 

blastdb.nin: mysequences.fa
	${bin.dir}/makeblastdb -dbtype nucl -in $< -out blastdb

ouput:

              <Hsp>
                <Hsp_num>5</Hsp_num>
                <Hsp_bit-score>31.9574</Hsp_bit-score>
                <Hsp_score>71</Hsp_score>
                <Hsp_evalue>0.000226217</Hsp_evalue>
                <Hsp_query-from>520</Hsp_query-from>
                <Hsp_query-to>575</Hsp_query-to>
                <Hsp_hit-from>1711</Hsp_hit-from>
                <Hsp_hit-to>1860</Hsp_hit-to>
                <Hsp_query-frame>0</Hsp_query-frame>
                <Hsp_hit-frame>1</Hsp_hit-frame>
                <Hsp_identity>16</Hsp_identity>
                <Hsp_positive>27</Hsp_positive>
                <Hsp_gaps>6</Hsp_gaps>
                <Hsp_align-len>56</Hsp_align-len>
                <Hsp_qseq>MGEFRLCDRLQKGKACPDGDKCRCAHGQEELNEWLDRREVLKQKLAKARKDMLLCP</Hsp_qseq>
                <Hsp_hseq>VGSYYLCKDMINKQDCKYGDNCTFAYHQEEIDVWTEERK------GTLNRDLLFDP</Hsp_hseq>
                <Hsp_midline>+G + LC  +   + C  GD C  A+ QEE++ W + R+          +D+L  P</Hsp_midline>
                <Hsp_hit-DNA>GTGGGCTCCTACTACCTGTGCAAAGACATGATTAACAAGCAGGACTGTAAGTACGGGGATAACTGCACCTTCGCCTACCATCAGGAGGAGATCGACGTGTGGACCGAGGAGCGGAAG------------------CTGCTCTTCGACCCG</Hsp_hit-DNA>
              </Hsp>
              <Hsp>
                <Hsp_num>6</Hsp_num>
                <Hsp_bit-score>22.3274</Hsp_bit-score>
                <Hsp_score>46</Hsp_score>
                <Hsp_evalue>0.215374</Hsp_evalue>
                <Hsp_query-from>22</Hsp_query-from>
                <Hsp_query-to>62</Hsp_query-to>
                <Hsp_hit-from>3316</Hsp_hit-from>
                <Hsp_hit-to>3435</Hsp_hit-to>
                <Hsp_query-frame>0</Hsp_query-frame>
                <Hsp_hit-frame>1</Hsp_hit-frame>
                <Hsp_identity>15</Hsp_identity>
                <Hsp_positive>19</Hsp_positive>
                <Hsp_gaps>1</Hsp_gaps>
                <Hsp_align-len>41</Hsp_align-len>
                <Hsp_qseq>HEAPWTNLTPSWRRPTHRTTVPLAVLRNQPPRQSPACPTLP</Hsp_qseq>
                <Hsp_hseq>HQAAPSPLRPCPSSPHHRPGVRTQAHVLQPP-EAPLKPGLP</Hsp_hseq>
                <Hsp_midline>H+A  + L P    P HR  V       QPP ++P  P LP</Hsp_midline>
                <Hsp_hit-DNA>CATCAGGCAGCCCCCAGCCCCCTGAGGCCCTGTCCATCTTCTCCCCACCACCGCCCCGGTGTGCGTACCCAGGCGCACGTGCTGCAGCCCCCG---GCCCCGCTGAAACCTGGGCTGCCC</Hsp_hit-DNA>
              </Hsp>

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