[Bioperl-l] Error parsing blast results with blasttable

[Jason Stajich]

Right - but back to my question - what do you want to be getting out?  
Do you want the smallest HSP start position if you are calling 
$hit->start('query')?  Are you hoping for fancy HSP tiling?

I'm pretty sure the problem you are showing has to do with being unable 
to build a single compatible tiling path for a set of HSPs.  I just 
think the code for doing this is just too brittle.  There may also be a 
bug since the blasttable parser has less data available too it and that 
may be the cause as well, so will have to be investigated nonetheless.

-jason
On Jan 7, 2005, at 8:21 AM, michael watson ((IAH-C)) wrote:

> Hi
>
> I submitted a bug which contains some blasttable output, example code,
> and the error produced.
>
> Mick
>
> -----Original Message-----
> From: Jason Stajich [mailto:jason.stajich at duke.edu]
> Sent: 07 January 2005 13:04
> To: michael watson (IAH-C)
> Cc: Bioperl List; Marc Logghe
> Subject: Re: [Bioperl-l] Error parsing blast results with blasttable
>
>
> $hit->start is a convience function which first tiles the HSPs and then
> gives you the smallest start.
>
> If you look at the documentation for the method you see that not giving
> it a type will give you start in the query and hit.
>
>   Usage     : $sbjct->start( [seq_type] );
>   Purpose   : Gets the start coordinate for the query, sbjct, or both
> sequences
>             : in the BlastHit object. If there is more than one HSP, 
> the
>
> lowest start
>             : value of all HSPs is returned.
>   Example   : $qbeg = $sbjct->start('query');
>             : $sbeg = $sbjct->start('hit');
>             : ($qbeg, $sbeg) = $sbjct->start();
>   Returns   : scalar context: integer
>             : array context without args: list of two integers
> (queryStart, sbjctStart)
>             : Array context can be "induced" by providing an argument 
> of
>
> 'list' or 'array'.
>   Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct'
> (default = 'query')
>               ('sbjct' is synonymous with 'hit')
>   Throws    : n/a
>   Comments  : This method requires that all HSPs be tiled. If there is
> more than one
>             : HSP and they have not already been tiled, they will be
> tiled first automatically..
>             : Remember that the start and end coordinates of all HSPs
> are
>             : normalized so that start < end. Strand information can be
>             : obtained by calling $hit->strand().
>
> I don't know why you are seeing concatenated positions unless you are
> somehow getting it in array context and then turning it into a string.
>
>
> I really don't use this, if I want tiled HSPs I use WU-BLAST with the
> -links and build compatible HSP groups.
>
> What are you trying to get - the smallest hit or query start? Just the
> start/end for HSPs?
>
> If this is somehow a blasttable specific problem will try and see if
> can figure out why.
>
> -jason
>
> On Jan 7, 2005, at 5:50 AM, michael watson ((IAH-C)) wrote:
>
>> Hi
>>
>> Having done some more tests with this:
>>
>> $hit->start()
>>
>> Actually returns a string which is the concatenation of query start
>> and subject end!  (btw I'm using the "-m 8" option) - surely this
>> isn't the desired option????
>>
>> If I change it to:
>>
>> $hit->start('query')
>>
>> Then I get the correct start back, but I still get the stack trace
>> error.
>>
>> The two co-ordinate sets which cause the problem (3264-3268 and
>> 3252-3268) are on adjacent lines in the file (3252-3268 is the next
>> line
>> after 3264-3268) and are to the SAME subject, ie they are two HSPs of
>> the same hit (in theory) but they are to two VERY different parts of
>> the
>> query.
>>
>> I'm guessing the way blasttable handles multiple HSPs is causing the
>> trouble.
>>
>> Mick
>>
>> -----Original Message-----
>> From: Marc Logghe [mailto:Marc.Logghe at devgen.com]
>> Sent: 07 January 2005 10:41
>> To: michael watson (IAH-C); Bioperl List
>> Subject: RE: [Bioperl-l] Error parsing blast results with blasttable
>>
>>
>>> while (my $result = $searchio->next_result) {
>>>         while(my $hit = $result->next_hit) {
>>>                 my $start  = $hit->start;
>>>
>>> And it is that call to $hit->start that sets off the whole trace.
>>>
>>> Any ideas?
>>
>>
>> Hi Mick,
>> Have you tried one of these ?:
>>
>> my $start = $hit->start('sbjct');  # or 'query' or 'hit'. Latter is
>> same
>> as 'sbjct'
>>
>> or
>>
>> my $start = $hit->hsp->start('sbjct');
>>
>>
>> I think in all cases it defaults to 'query'. So it should not crash
>> but give you the start position of the query. I am afraid I can't
>> explain the crash, sorry.
>>
>> Marc
>>
>> _______________________________________________
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>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/