[Bioperl-l] Sorting BLAST hits by score

[Chris Fields]

Lorenzo,

Mind filing this as a bug and attaching the script and BLAST report to that?  Sometimes diagnosing this is easier that way.

http://bioperl.org/wiki/Bugs

chris

On Apr 7, 2011, at 12:00 PM, Lorenzo Carretero wrote:

> Hi,
> 
> My blast -m 8 output looks like this:
> 
> # BLASTP 2.2.18 [Mar-02-2008]
> # Query: AcoGoldSmith_v1.022378m|PACid:18139816
> # Database: Acoerulea_151_cds.pep.blastable
> # Fields: Query id, Subject id, % identity, alignment length, mismatches,
> gap openings, q. start, q. end, s. start, s. end, e-value, bit score
> AcoGoldSmith_v1.022378m|PACid:18139816
> AcoGoldSmith_v1.022378m|PACid:18139816    100.00    772    0    0    1
> 772    1    772    0.0    1542
> AcoGoldSmith_v1.022378m|PACid:18139816
> AcoGoldSmith_v1.024532m|PACid:18155258    35.15    717    422    9    46
> 761    8    682    9e-116     414
> AcoGoldSmith_v1.022378m|PACid:18139816
> AcoGoldSmith_v1.024532m|PACid:18155258    25.34    667    420    15    6
> 647    74    687    7e-53     205
> AcoGoldSmith_v1.022378m|PACid:18139816
> AcoGoldSmith_v1.024532m|PACid:18155258    29.63    378    251    8    5
> 382    174    536    2e-41     167
> AcoGoldSmith_v1.022378m|PACid:18139816
> AcoGoldSmith_v1.024532m|PACid:18155258    33.70    276    172    6    4
> 279    274    538    2e-35     147
> 
> Thanks for the reply,
> Lorenzo
> 
> 
> 
> On Thu, Apr 7, 2011 at 6:34 PM, Dave Messina <David.Messina at sbc.su.se>wrote:
> 
>> Hi Lorenzo,
>> 
>> 
>> 
>>> However, I get the following error message:
>>> Use of uninitialized value in numeric comparison (<=>) at
>>> /Library/Perl//5.10.0/Bio/Search/Result/ResultI.pm line 202, <GEN1> line
>>> 2773.
>>> 
>> 
>> Hmm, I'm not seeing this error message. Could you provide us with your
>> blast -m8 output so I can test with the same data?
>> 
>> 
>> Furthermore, every iteration through the hsps returns the warnig message:
>>> 
>>> --------------------- WARNING ---------------------
>>> MSG: Did not define the number of conserved matches in the HSP; assuming
>>> conserved == identical (152)
>>> 
>> 
>> This is due to the fact that the blast -m8 tabular output doesn't report
>> conserved matches.
>> 
>> You should be able to suppress these warnings by adding
>> 
>>      -verbose => -1
>> 
>> to your Bio::SearchIO->new parameters, but it isn't working for me for some
>> reason. Hmm. Anyway, as it's just a warning, it won't affect your results.
>> 
>> 
>> 
>> Dave
>> 
>> 
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