Question: Blast converter Format Output
0
gravatar for midox
4.5 years ago by
midox260
Tunisia
midox260 wrote:

hello,
I have a Blast output format.
I would like to convert this output format to the Format of Blast formatType=10.

is there a tool or a program to convert my file?
thanks

converter alignment latest • 2.4k views
ADD COMMENTlink modified 4.5 years ago by 5heikki8.9k • written 4.5 years ago by midox260
1
gravatar for 5heikki
4.5 years ago by
5heikki8.9k
Finland
5heikki8.9k wrote:
blast_formatter ships with blast+
ADD COMMENTlink written 4.5 years ago by 5heikki8.9k

for blast_formatter I don't understand the input format file!

I have a format "blast" like this:

Query= channel_109
         (10478 letters)

>NODE_266_length_1072_cov_120960_ID_531
          Length = 1072

 Score = 770 bits (486), Expect = 3.5e-221
 Identities = 881/1045 (84%), Gaps = 74/1045 (7%)
 Strand = Plus / Plus

Query: 6853 ATATTTAGCTTAA--TGGAATTTACCACC-ACTTAGAGCTGCATTCCCAAACAACTCGAC 6909
            ||||||||||| |  |||||||||||||| ||||||||||||||||||||||||||||||
Sbjct: 1    ATATTTAGCTTTAGATGGAATTTACCACCCACTTAGAGCTGCATTCCCAAACAACTCGAC 60

Query: 6910 TCTTCGAAGGCACTTTACAAAGAGACCGCATCA----CACACGGGATCC----CCTCTAT 6961
            |||||||||||||||||||||||  |    ||     |||||||||| |    |||||||
Sbjct: 61   TCTTCGAAGGCACTTTACAAAGAACCGCACTCCTCGCCACACGGGATTCTCACCCTCTAT 120

Query: 6962 GACGTCCTGTTCCAAGGAACA--GACAAGGAACGGCCCCAAAGT--CCCTCTCCAAATTA 7017
            |||||||||||||||||||||  |||||||||||||||||||||  ||||||||||||||
Sbjct: 121  GACGTCCTGTTCCAAGGAACATAGACAAGGAACGGCCCCAAAGTTGCCCTCTCCAAATTA 180

Query: 7018 CAAC--GGGCACTGAAGGTACCAG-TTTCAAATTTGAGCTTT-GCCGCTTCACTCGCCGT 7073
            ||||  |||||| ||||||||||| ||||||||||||||||| |||||||||||||||||
Sbjct: 181  CAACTCGGGCACCGAAGGTACCAGATTTCAAATTTGAGCTTTTGCCGCTTCACTCGCCGT 240

Query: 7074 TACTAAGGCGATCGAGGTTGGTTC--TTTCCTCCATTATTGATACTGCTTAAGTTCAGCG 7131
            ||||||||| |||  ||||||||   ||||||||  |  |     |||||||||||||||
Sbjct: 241  TACTAAGGCAATCCCGGTTGGTTTCTTTTCCTCCGCTTATTGATATGCTTAAGTTCAGCG 300

Query: 7132 GGTATTCCCAGCTGATTTGAGGTCAA--TTTAAGAACATTGTTCGCCTAGGA---CTCTT 7186
            |||| ||| | |||||||||||||||  ||||||||||||||||||||||     |||||
Sbjct: 301  GGTACTCCTACCTGATTTGAGGTCAAACTTTAAGAACATTGTTCGCCTAGACGCTCTCTT 360

Query: 7187 CTTATCGATAACGTTCCAATACGCTCAGTATAAAA---GATTAGCCGCAGTTGGTAAACT 7243
            |||||||||||||||||||||||||||||||||||   ||||||||||||||||||||
Sbjct: 361  CTTATCGATAACGTTCCAATACGCTCAGTATAAAAAAAGATTAGCCGCAGTTGGTAAAAC 420

Query: 7244 AAAACGACCACGTACTTGCATTACCTCCTCAAGCACGCAGAGAAACCTCTCTTTGGAAAA 7303
              ||      |||||||||||||   ||||||||||||||||||||||||||||||||||
Sbjct: 421  CTAAAACGACCGTACTTGCATTATA-CCTCAAGCACGCAGAGAAACCTCTCTTTGGAAAA 479

and I would to convert this type in outfmt=10.

can I do this with blast_formatter because I see the blast_formatter accept just the .asn format.

thanks

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by midox260

Yes, I think you are right, blast_formatter accepts only asn format, you can use BioPerl or BioPython (and maybe also BioJava and BioRuby) to convert standard blast output to tabular format.

ADD REPLYlink written 4.5 years ago by Michael Dondrup47k

I think there are no functions that convert standard blast output to another format.

have you an idea?

thanks

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by midox260

See the Howto's and example scripts for your specific problem: e.g.: http://www.bioperl.org/wiki/HOWTO:SearchIO, https://github.com/bioperl/bioperl-live/blob/master/examples/searchio/custom_writer.pl , https://github.com/bioperl/bioperl-live/blob/master/examples/searchio/resultwriter.pl

There is no function called 'convert', but the main usage pattern is simple:

  • parse file using Bio::SearchIO
  • write the output using Bio::SearchIO using a Bio::SearchIO::Writer subclass in another format
ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by Michael Dondrup47k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2012 users visited in the last hour