[Bioperl-l] Fwd: BLAST parsing broken
Chris Fields
cjfields at illinois.edu
Sun May 9 20:43:29 UTC 2010
If the patch is against main trunk it isn't a problem, otherwise the diff should be vs. that code.
chris
On May 9, 2010, at 2:23 PM, Razi Khaja wrote:
> Attached (blast.pm.diff) is a patch that fixes Heikki's problem.
> Can someone advise an appropriate way to have this patch applied, given that
> it is an amendment to a previous patch?
> Thanks
> Razi
>
>
> ---------- Forwarded message ----------
> From: Heikki Lehvaslaiho <heikki.lehvaslaiho at gmail.com>
> Date: Wed, May 5, 2010 at 2:11 AM
> Subject: Re: [Bioperl-l] BLAST parsing broken
> To: Razi Khaja <razi.khaja at gmail.com>
>
>
> Hi Raja,
>
> Thanks for trying to fix this.
>
> I am attaching an example output file to this message. I just tested again
> that master from git repository fails to get query ID, but the previous
> version works.
>
> bala ~/src/bioperl-live> git checkout master
> Previous HEAD position was 5e278f5... Robson's patch for buggy blastpgp
> output
> Switched to branch 'master'
>
> When I started using the latest mpiBLAST code a few months ago I did compare
> the 0 output from it to standard NCBI blast and they were identical.
>
>
>
>
> Also, I've noticed a discrepancy between within bioperl blast parsing that
> I have not had time to work on. Would you be interested in having a look?
>
> I am creating output from mpiBLAST in 0 format and then converting it into
> tab-delimited 8 format. I am unable to get 100% similarity for all cases
> when I compare the conversion to the output straight from mpiBLAST in format
> 8. Sometimes the mismatch and gap values are off by one.
>
> I am attaching a script that does the conversion. It is the same one I was
> using when I noticed the problem above. I was going to put the code into
> bioperl but that got delayed when I noticed the discrepancies.
>
>
> Cheers,
>
>
> -Heikki
>
> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
> cell: +966 545 595 849 office: +966 2 808 2429
>
> Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
> 4700 King Abdullah University of Science and Technology (KAUST)
> Thuwal 23955-6900, Kingdom of Saudi Arabia
>
>
>
> On 4 May 2010 20:55, Razi Khaja <razi.khaja at gmail.com> wrote:
>
>> That is odd. Heikki, do you have a blast output file that produces this
>> error?
>> Could you attach the file and either send to the list or myself (if the
>> list
>> does not accept attachments).
>> Thanks,
>> Razi
>>
>>
>> On Mon, May 3, 2010 at 8:08 AM, Chris Fields <cjfields at illinois.edu>
>> wrote:
>>
>>> Odd, I ran tests on that prior to commit. I'll work on fixing that (in
>> svn
>>> of course, until the migration is complete).
>>>
>>> chris
>>>
>>> On May 3, 2010, at 6:45 AM, Heikki Lehvaslaiho wrote:
>>>
>>>> Chris,
>>>>
>>>> latest additions to Bio::SearchIO::blast.pm broke the parsing of
>> normal
>>>> blast output. $result->query_name returns now undef.
>>>>
>>>> (Using the anonymous git now). This change still works:
>>>>
>>>> commit 5e278f5dbb9afc4dc0359cd3fdc8fb0d0f4cad74
>>>> Author: cjfields <cjfields at eb9725d8-4842-0410-9bbb-c0b52e2da49b>
>>>> Date: Sun Dec 20 04:39:58 2009 +0000
>>>>
>>>> Robson's patch for buggy blastpgp output
>>>>
>>>> But this does not:
>>>>
>>>> commit 9a89c3434597104dd50553e3562983d78d14a544
>>>> Author: cjfields <cjfields at eb9725d8-4842-0410-9bbb-c0b52e2da49b>
>>>> Date: Thu Apr 15 04:21:17 2010 +0000
>>>>
>>>> [bug 3031]
>>>>
>>>> patches for catching algorithm ref, courtesy Razi Khaja.
>>>>
>>>> That makes it easy to find the diffs:
>>>>
>>>> $git diff 5e278f5dbb9afc4dc0359cd3fdc8fb0d0f4cad74
>>>> 9a89c3434597104dd50553e3562983d78d14a544 Bio/SearchIO/blast.pm
>>>> diff --git a/Bio/SearchIO/blast.pm b/Bio/SearchIO/blast.pm
>>>> index 378023a..6f7eeeb 100644
>>>> --- a/Bio/SearchIO/blast.pm
>>>> +++ b/Bio/SearchIO/blast.pm
>>>> @@ -209,6 +209,7 @@ BEGIN {
>>>>
>>>> 'BlastOutput_program' => 'RESULT-algorithm_name',
>>>> 'BlastOutput_version' =>
>> 'RESULT-algorithm_version',
>>>> + 'BlastOutput_algorithm-reference' =>
>>> 'RESULT-algorithm_reference',
>>>> 'BlastOutput_query-def' => 'RESULT-query_name',
>>>> 'BlastOutput_query-len' => 'RESULT-query_length',
>>>> 'BlastOutput_query-acc' => 'RESULT-query_accession',
>>>> @@ -504,6 +505,26 @@ sub next_result {
>>>> }
>>>> );
>>>> }
>>>> + # parse the BLAST algorithm reference
>>>> + elsif(/^Reference:\s+(.*)$/) {
>>>> + # want to preserve newlines for the BLAST algorithm
>>> reference
>>>> + my $algorithm_reference = "$1\n";
>>>> + $_ = $self->_readline;
>>>> + # while the current line, does not match an empty line, a
>>> RID:,
>>>> or a Database:, we are still looking at the
>>>> + # algorithm_reference, append it to what we parsed so far
>>>> + while($_ !~ /^$/ && $_ !~ /^RID:/ && $_ !~ /^Database:/) {
>>>> + $algorithm_reference .= "$_";
>>>> + $_ = $self->_readline;
>>>> + }
>>>> + # if we exited the while loop, we saw an empty line, a
>> RID:,
>>> or
>>>> a Database:, so push it back
>>>> + $self->_pushback($_);
>>>> + $self->element(
>>>> + {
>>>> + 'Name' => 'BlastOutput_algorithm-reference',
>>>> + 'Data' => $algorithm_reference
>>>> + }
>>>> + );
>>>> + }
>>>> # added Windows workaround for bug 1985
>>>> elsif (/^(Searching|Results from round)/) {
>>>> next unless $1 =~ /Results from round/;
>>>>
>>>>
>>>> I am not sure why reference parsing messes things up. Maybe it eats too
>>> many
>>>> lines from the result file.
>>>>
>>>> Yours,
>>>>
>>>> -Heikki
>>>>
>>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>>> cell: +966 545 595 849 office: +966 2 808 2429
>>>>
>>>> Computational Bioscience Research Centre (CBRC), Building #2, Office
>>> #4216
>>>> 4700 King Abdullah University of Science and Technology (KAUST)
>>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
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>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
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