[Bioperl-l] question about the nature of bioperl

[nkuipers]

>horses for courses.

I am showing my age here.  What does that mean? =)

>is your code available

Regarding the code written by my supervisor, it's not up to me, since that 
integrates rather extensively with our databases and it's not mine to give 
anyway.  As for my own...well, since my work at this time is simple enough, I 
use a series of scripts that I've cobbled together as the need arose.  As 
you've likely guessed, I am somewhat new to Perl, otherwise it would not have 
developed that way.  Anyways, I've been realizing lately the need to unify 
them at some point into a module.  For my current needs, it would do such 
basic things as accept FASTA and strip everything but sequence characters for 
hash operations on redundancy, write back to FASTA, do exact subsequence 
matching with counts versus a flatfile, and provide a simple BLAST parser that 
grabs sequences by user-defined hit-def keywords ('parapoxvirus', 'rhetinoid', 
'7SL RNA' or whatever).  That comes later however; at the moment they work and 
we are pressed for time/results. =)

>a general repository for an ad hoc collection of unsupported scripts and
>modules that don't fit into the central framework?

I love this idea, though I would be in favor of reviews for redundancy (10 
scripts doing exactly the same thing from different people would not be 
beneficial, although maybe 2-3 scripts doing the same thing in procedural and 
OO ways would be useful) and basic quality of the Perl itself.

cheers,
nathanael kuipers