[Bioperl-l] SearchIO to GFF (was: Getting 'features' from SearchIO?)

[Chris Fields]

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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