[Bioperl-l] new to bioperl

Jason Stajich jason at cgt.duhs.duke.edu
Tue Jun 8 18:20:25 EDT 2004

On Tue, 8 Jun 2004, [iso-8859-1] aditi gupta wrote:

> hi to all,
>  well,let me put it straight.i'm new to bioperl and i have very
> basic,small knowledge of perl.
> i also don't know how object oriented programming is done in perl.
> and all the modules which i wish to use, are written as objects.
>  and to add more,i've worked on unix before but now i'm forced to work
> on windows, n the ppm is creating some permissions problem and i'm not
> being able to install bioperl because of that........and since i'm not
> an administrator, i'm not allowed to install activeperl again. and i
> even tried using http://www.bioperl.org/Core/Latest/index.shtml but the
> downloaded files are not opening. maybe winzip is required for that,but
> i'm not allowed to install even that.....
>  i've to blast some genes with 30 different species and write output in
> a format which tells query and subject ranges,location on gene and
> chromosome,identities and similarity percentage.

did you just try running blast with -m 8 option which will print out the
data in a tab delimited format.

>  i wish to know whether i can directly include relevant subroutines of
> SearchIO, AlignIO, and SeqIO into the script. will that work?
no.  it won't work. you need all the modules they include and depend on.

>  please reply,my deadline for this work is quite near.
> thanks in advance,
> regards,
> aditi
> Yahoo! India Matrimony: Find your partner online.

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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