[Bioperl-l] SearchIO to GFF (was: Getting 'features' from SearchIO?)
Chris Fields
cjfields at illinois.edu
Tue May 12 12:23:35 UTC 2009
Fixed that in svn. We're all still learning the ropes...
chris
On May 12, 2009, at 5:55 AM, Dan Bolser wrote:
> 2009/5/12 Dan Bolser <dan.bolser at gmail.com>:
>> Unfortunately bp_search2gff.pl is giving me errors:
>>
>> bp_search2gff.pl --version 3 -i BlastResults/blast_table_filtered
>> -f
>> blasttable -o BlastResults/blast_table_filtered.gff -t hit
>> --match --target --component
>>
>> --------------------- WARNING ---------------------
>> MSG: Removing score value(s)
>> ---------------------------------------------------
>> Can't locate object method "remove_tags" via package
>> "Bio::SeqFeature::Similarity" at
>> /local/Scratch/dbolser/perl5/lib/perl5/Bio/SeqFeature/Generic.pm line
>> 393, <GEN1> line 5.
>
>
> I'm just learning the ropes...
>
> --- ~/perl5/lib/perl5/Bio/SeqFeature/Generic.pm~ 2009-05-11
> 15:25:55.000000000 +0100
> +++ ~/perl5/lib/perl5/Bio/SeqFeature/Generic.pm 2009-05-12
> 11:52:41.000000000 +0100
> @@ -390,7 +390,7 @@
> }
> if ($self->has_tag('score')) {
> $self->warn("Removing score value(s)");
> - $self->remove_tags('score');
> + $self->remove_tag('score');
> }
> $self->add_tag_value('score',$value);
> }
>
>
>
>
>
>> Anyone seen this before?
>>
>> Cheers,
>> Dan.
>>
>>
>>
>> 2009/5/12 Dan Bolser <dan.bolser at gmail.com>:
>>> Thanks for the info guys, I think I was naively hoping that the
>>> feature would know how to cast itself as a 'SeqFeature' (GFF).
>>>
>>> I think I understand the problem better now, so I'll try to
>>> summarise:
>>>
>>> There is no standard way to encode a HSP as a feature (not least
>>> because there are two choices about which sequence (query or the
>>> hit)
>>> it should be attached to). BioPerl will try, but the result will not
>>> be "well structured" SeqFeatures or "well formed" GFF.
>>>
>>>
>>> From what I read I guess it should be possible to standardize this
>>> mapping (based on something in one of the examples or the
>>> 'search2gff'
>>> script), assuming you specify weather you want features put on the
>>> query or on the hit.
>>>
>>> At some point last year I was trying out the bp_search2gff.pl and my
>>> own code to write a GFF file for loading and viewing by Gbrowse. At
>>> that time I gave up, as nothing seemed to be working. I was hoping
>>> that doing this at a lower level (i.e. never writing any GFF myself)
>>> it would stand a better chance of working.
>>>
>>> Also I was thinking that Gbrowse, if given a SeqFeature::Store,
>>> could
>>> autoconfigure its interface to some degree. I guess its back to the
>>> docs ;-)
>>>
>>>
>>>
>>> I'll keep trying and see if I can get anywhere.
>>>
>>> Thanks again,
>>> Dan.
>>>
>>>
>>>
>>> References for the above:
>>>
>>> 2009/5/11 Jason Stajich <jason at bioperl.org>:
>>>
>>>> otherwise you need to be converting the HSPs into seqfeatures
>>>> with the right associated information (i.e. the tag/value pairs
>>>> that are in the 9th column) in order to have well structured data
>>>> in the database.
>>>
>>>> You can get the individual features from the feature pair with
>>>> $hsp->query or $hsp->hit which can also be passed to a GFF
>>>> writer (or call $hsp->hit->gff_string). Note that since the
>>>> data storage is not structured in a GFF3 like-way this won't
>>>> immediately produce well formed GFF3 for the 9th column.
>>>
>>>
>>> 2009/5/11 Chris Fields <cjfields at illinois.edu>:
>>>
>>>> The main problem is the mapping is subjective based on what your
>>>> reference sequence is within the BLAST run (e.g. whether it is
>>>> the query or the hit), and is something that can't be
>>>> automatically discerned. I ended up rolling my own with
>>>> SeqFeature::Store (just mapped the relevant data to
>>>> Bio::DB::SeqFeatures), but I have long wanted to fix up the
>>>> relevant scripts to integrate my changes in, just haven't had the
>>>> time
>>>
>>
>
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