[Bioperl-l] Error parsing blast results with blasttable

[michael watson (IAH-C)]

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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>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/