[Bioperl-l] Fwd: BLAST parsing broken
Chris Fields
cjfields at illinois.edu
Mon May 10 00:39:33 UTC 2010
Ok, that's fine. It may be something off with revision numbers when using svn with github (git doesn't have incremental revisions, but a SHA). Committed the patch to dev svn, in r16970.
chris
On May 9, 2010, at 6:48 PM, Razi Khaja wrote:
> I checked out bioperl-live from github:
> svn checkout http://svn.github.com/bioperl/bioperl-live.git
>
> I just checked it out again, a few seconds ago and by default I got revision
> 11326.
> Razi
>
>
> On Sun, May 9, 2010 at 5:30 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
>> Then something is wrong, as current trunk is at r16969. Where are you
>> pulling your code from? Our only working anon. server is the sync'ed github
>> one.
>>
>> chris
>>
>> On May 9, 2010, at 4:15 PM, Razi Khaja wrote:
>>
>>> Hi Chris,
>>> The patch is against the main trunk. I checked out version 11326 of the
>>> repository today.
>>> Razi
>>>
>>>
>>> On Sun, May 9, 2010 at 4:43 PM, Chris Fields <cjfields at illinois.edu>
>> wrote:
>>>
>>>> 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
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
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>>>>>>
>>>>> <mpiblast.out><blastparser028.pl
>>>>> <blast.pm.diff>_______________________________________________
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