[Bioperl-l] Can't parse blast report written by Bio::SearchIO::Writer::TextResultWriter

Prachi Shah prachi at stanford.edu
Mon May 12 19:17:53 EDT 2008


Thanks Jason for adding the sort_hsps method in
Bio::Search::Hit::GenericHit. I tested it out and it works great.

The other issue I have is the format of HSP start and stop coordinates
when I write a new blast report (with HSPs sorted) using
Bio::SearchIO::Writer::TextResultWriter. Below is an example of the
same HSP alignment as output from BLAST and later when the blast
report is generated by TextResultWriter. Notice, the change in start
and stop coordinates. I would like to keep the start and stop format
as in the first case. How do I specify that? Any indicators are
greatly appreciated.

Thanks,
Prachi

----------------------------------------------------------------------------------------------------
**HSP alignment in blast report generated by BLAST itself:

 Score = 10150 (1529.0 bits), Expect = 0., Sum P(3) = 0.
 Identities = 2120/2345 (90%), Positives = 2120/2345 (90%), Strand =
Minus / Plus

Query:    2364 CATATCCAGATCTATCTTGATGATTCTTATTAGAATATGTATCTGAAGATGTGCCACTTG 2305
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251160 CATATCCAGATCTATCTTGATGATTCTTATTAGAATATGTATCTGAAGATGTGCCACTTG
2251219

Query:    2304 TTGGAGGTGGTGGAGCTCTTCTAGCAGGAATAAGTTCAGATTTATTCATCAAATTATTCA 2245
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251220 TTGGAGGTGGTGGAGCTCTTCTAGCAGGAATAAGTTCAGATTTATTCATCAAATTATTCA
2251279

Query:    2244 ATGGTGAAACGTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC 2185
               ||||||||||||||                                             |
Sbjct: 2251280 ATGGTGAAACGTTTTTAGTATTATTATTGTTAGTGCTGTTGTTATTATTATTATTATTAC
2251339

Query:    2184 CAGAACTAGGTAATGAGCCTGATGATGATGTATGTTGGTGGGAAGAGCCATTTAGTTGTG 2125
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251340 CAGAACTAGGTAATGAGCCTGATGATGATGTATGTTGGTGGGAAGAGCCATTTAGTTGTG
2251399

Query:    2124 TCAAATGATATGGAGTTGGTGGTTTTGGTGCAGCTCGACTAGGTTTGAATTGTGAGACAG 2065
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251400 TCAAATGATATGGAGTTGGTGGTTTTGGTGCAGCTCGACTAGGTTTGAATTGTGAGACAG
2251459

Query:    2064 TAGATTTTGCTGGAGGTTTTACCCATTCTTGTAAATTTGCCTCTTGGACATTGTTTTTGG 2005
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251460 TAGATTTTGCTGGAGGTTTTACCCATTCTTGTAAATTTGCCTCTTGGACATTGTTTTTGG
2251519

Query:    2004 CTGATGAGTAATTGTTAGGGTCATTATTATTATTGTTGGTTTTGGAATTGATCATGGGTG 1945
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251520 CTGATGAGTAATTGTTAGGGTCATTATTATTATTGTTGGTTTTGGAATTGATCATGGGTG
2251579

Query:    1944 ATCCAATTGGAGTTCCAGCAGCAGAATTACCTCCATTTATATCGGAATAAAATTCTAAAA 1885
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251580 ATCCAATTGGAGTTCCAGCAGCAGAATTACCTCCATTTATATCGGAATAAAATTCTAAAA
2251639

Query:    1884 CTTTAATAACAGCAACAGGATCTTTTTTCCAATCCTCATTAGTGATTTTCGAATGTTGTA 1825
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251640 CTTTAATAACAGCAACAGGATCTTTTTTCCAATCCTCATTAGTGATTTTCGAATGTTGTA
2251699


----------------------------------------------------------------------------------------------------
** HSP alignment written by TextResultWriter:

 Score = 1529.0 bits (10150), Expect = 0., P = 0.
 Identities = 2120/2345 (90%)
 Frame =  -1 / +1

Query: 20      CATATCCAGATCTATCTTGATGATTCTTATTAGAATATGTATCTGAAGATGTGCCACTTG -39
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251160 CATATCCAGATCTATCTTGATGATTCTTATTAGAATATGTATCTGAAGATGTGCCACTTG
2251219

Query: -40     TTGGAGGTGGTGGAGCTCTTCTAGCAGGAATAAGTTCAGATTTATTCATCAAATTATTCA -99
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251220 TTGGAGGTGGTGGAGCTCTTCTAGCAGGAATAAGTTCAGATTTATTCATCAAATTATTCA
2251279

Query: -100    ATGGTGAAACGTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC -159
               ||||||||||||||                                             |
Sbjct: 2251280 ATGGTGAAACGTTTTTAGTATTATTATTGTTAGTGCTGTTGTTATTATTATTATTATTAC
2251339

Query: -160    CAGAACTAGGTAATGAGCCTGATGATGATGTATGTTGGTGGGAAGAGCCATTTAGTTGTG -219
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251340 CAGAACTAGGTAATGAGCCTGATGATGATGTATGTTGGTGGGAAGAGCCATTTAGTTGTG
2251399

Query: -220    TCAAATGATATGGAGTTGGTGGTTTTGGTGCAGCTCGACTAGGTTTGAATTGTGAGACAG -279
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251400 TCAAATGATATGGAGTTGGTGGTTTTGGTGCAGCTCGACTAGGTTTGAATTGTGAGACAG
2251459

Query: -280    TAGATTTTGCTGGAGGTTTTACCCATTCTTGTAAATTTGCCTCTTGGACATTGTTTTTGG -339
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251460 TAGATTTTGCTGGAGGTTTTACCCATTCTTGTAAATTTGCCTCTTGGACATTGTTTTTGG
2251519

Query: -340    CTGATGAGTAATTGTTAGGGTCATTATTATTATTGTTGGTTTTGGAATTGATCATGGGTG -399
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251520 CTGATGAGTAATTGTTAGGGTCATTATTATTATTGTTGGTTTTGGAATTGATCATGGGTG
2251579

Query: -400    ATCCAATTGGAGTTCCAGCAGCAGAATTACCTCCATTTATATCGGAATAAAATTCTAAAA -459
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251580 ATCCAATTGGAGTTCCAGCAGCAGAATTACCTCCATTTATATCGGAATAAAATTCTAAAA
2251639

Query: -460    CTTTAATAACAGCAACAGGATCTTTTTTCCAATCCTCATTAGTGATTTTCGAATGTTGTA -519
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2251640 CTTTAATAACAGCAACAGGATCTTTTTTCCAATCCTCATTAGTGATTTTCGAATGTTGTA
2251699


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