[Bioperl-l] SearchIO question

[Jason Stajich]

On Fri, 7 Mar 2003, Shin Enomoto wrote:

> I have been using SearchIO to parse NCBI BLAST reports on five
> different computers with slightly different versions of BioPerl
> installed. I also go back and forth between using Blast.pm and
^^^^ - well there are bug fixes in various versions so I wouldn't expect
things to behave the same.

> PsiBlast.pm. I noticed erratic behavior in some of the parsing results
> from very similar scripts.
>
There are various differences between the implementations of psiblast and
blast parsers and they produce different objects in the end, hence the
variation you see. psiblast is going away very soon as Steve is almost
finished merging his changes to make the blast parser psiblast capable.

> On one machine:
> $hsp->end('hit') with blast  returns hit
> $hsp->hit->end with psiblast returns a large number with a actual
> number embedded within.
>
> $hsp->hit->end with blast returns the correct number.
>
> On this same machine:
> $result->query_description with blast returns blank
> $result->query_name with blast returns name and description as one
> string both of these work with psiblast normally.

> The problem with using psiblast is that I cannot get $hsp->strand to
> give me anything but 0s.
>
> Is there a simple explanation for these erratic behavior? Is there a
> large table of all the methods encoded in the different modules from
> different versions?

not wrt versions but the table of the functions were listed in the HOWTO
recently by Brian Osborne.

> Shin Enomoto
> 295 ASLVM
> 1988 Fitch Ave
> St. Paul, MN 55108
>
> 612-625-7737
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu