Bioperl-guts: Re: your mail

[Zia Khan]

Make sure you have a "use lib" line in your Perl script.
> I'm new to bioperl (and perl) and am having a problem. I tried to write
> a script using SeqIO to read a sequence in from a file:

> $stream = Bio::SeqIO -> new(-file => "/home/brad/seqs/fasta.txt",
> -fmt=> 'Fasta');

Try the following.
$in  = Bio::SeqIO->new(-file => "/home/brad/seqs/fasta.txt" , -format =>
'Fasta');

[Use -format instead of  -fmt.]

If you type "perldoc SeqIO.pm" in the /bioperl-0.5.1/Bio directory you'll
get a manpage showing you the methods in Bio::SeqIO including descriptions
of their arguments.


Zia Khan
zkhan@andrew.cmu.edu or zkhan@transient.net
Carngie Mellon University

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