Blast converter Format Output

Question

[midox]

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

Answer 1

[5heikki]

blast_formatter ships with blast+

[midox]

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

[Michael]

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.

[midox]

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

have you an idea?

thanks

[Michael]

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