Bioperl: Changing _parse_alignment behaviour in Bio::Tools::Blast?

[Peter van Heusden]

Hi

I'm trying to parse BLAST reports which have oddities in their
description lines which are peculiar to our local BLAST reports
(unfortunately). Unfortunately, there doesn't seem to be a clean way to
over-ride how Bio::Tools::Blast extracts the name from the description
line.

This is how it appears to work:

Bio::Tools::Blast::_get_parse_blast_function's default function
 calls _parse_alignment

Bio::Tools::Blast::_parse_alignment does a 'require
Bio::Tools::Blast::Sbjct' and creates Bio::Tools::Blast::Sbjct objects

Bio::Tools::Blast::Sbjct::_initialise calls _set_id, which
parses the description and sets the name of the hit.

I tried a couple of things (of various levels of hackishness). I can't
sub-class Bio::Tools::Blast, because Bio::Tools::Blast uses a static Blast
object to store state, which isn't inherited (don't ya just love perl's
OO!).

I can't subclass Bio::Tools::Blast::Sbjct, because it is specifically
'require'ed' by Bio::Tools::Blast.

There seem to be two ways out of this mess:

1) Create a way of specifying your own _parse_alignment method (like you
can specify an _exec_func).

2) Move all the global variables used by Bio::Tools::Blast into one place
(e.g. as fields of $Blast), and then use a construct such as:

self->Blast_object(\$Blast); # where $Blast is defined in the module
                             # namespace

...

sub _foo {

my $Blast = $self->Blast_object();

}

In other words, fake class attribute inheritance. *This would involve
quite a significant re-write of Blast.pm*

For now (since I have a deadline of this afternoon), I'm going to just
hack my local Blast.pm. I'd appreciate comments on which way forward
people think is best, though.

Peter
--
Peter van Heusden				pvh@egenetics.com
Electric Genetics

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