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

[Jason Stajich]

that's a very strange bug - I don't quite understand where it is  
coming from.  IF you don't mess with the HSP order and start with a  
report and generate the Text report output, does it also give the  
negative coordinates or are you still reconstituting the Hit/HSP  
objects "manually" in your code?

-jason
On May 12, 2008, at 4:17 PM, Prachi Shah wrote:

> 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