[Bioperl-l] Sorting BLAST hits by score

[Lorenzo Carretero]

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
>
>