[Bioperl-l] torturing newbies are we? SeqIO HowTo question

[Brian Osborne]

Jason,

Tom must have been talking about the HTML files in the distribution, but
they're updated now.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason Stajich
Sent: Tuesday, September 21, 2004 11:04 AM
To: Thomas J Keller
Cc: BioPerl-List List
Subject: Re: [Bioperl-l] torturing newbies are we? SeqIO HowTo question

Hmm - Where are you getting the HOWTO from? The website versions of
them don't seem to have these bugs.

What version of bioperl?  I don't get that error for bioperl 1.4 branch
CVS code or main trunk CVS code but haven't tried it with the 1.4
release that is on CPAN.
You said you are using genbank as input format, but what output format?

It may be that you should be passing in the STDOUT like this
-fh => \*STDOUT
not
-fh =>*STDOUT

Although I don't think it make much of a difference.  But this is all
guessing since I can't really make it happen on my machine right now.
-j
On Sep 20, 2004, at 8:29 PM, Thomas J Keller wrote:

> Greetings,
>
> in the Bio::SeqIO HOWTO examples:
>
> the first example (getaccs)
> while (my $seq = $inseq->next_seq) {
>       print $seq->accession_no, "\n";         ###<- wrong method name
> }
>
> should read:
> while (my $seq = $inseq->next_seq) {
>       print $seq->accession_number, "\n";
> }
>
> Also,
> in a later example from this HOWTO (in2out.pl) there's a typo:
> while (my $inseq = $seqin->next_seq) {
>       $outseq->write_seq($inseq);                     ### should be
> $seqout->write_seq($inseq);
> }
>
> But what I really want to know is why, when I run this example
> (in2out.pl), while it gives the correctly formatted output, it gives
> the warnings:
> Argument "*main::STDOUT" isn't numeric in numeric eq (==) at
> /Library/Perl/5.8.1/Bio/Root/IO.pm line 483.
> .. repeated 6 times for a single genbank input file.
> I may be slow, but I catch on eventually, you meanies ;-)
>
> I hope it's clear that while the typos are real, I'm kidding about the
> torture. I really appreciate the help I've gotten from the gurus who
> monitor this list.
>
> Thanks,
> Tom Keller
>
>
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> Bioperl-l at portal.open-bio.org
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>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

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