[Bioperl-l] SearchIO question

[Shin Enomoto]

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 
PsiBlast.pm. I noticed erratic behavior in some of the parsing results 
from very similar scripts.

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?







Shin Enomoto
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