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

Brian Osborne brian_osborne at cognia.com
Thu Sep 23 19:10:33 EDT 2004


Thanks for pointing these out. The typos were corrected in the *sgml files
(and online) a while back but the HTML files in bioperl-live are not

I'll take a look at that other error...

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 Thomas J Keller
Sent: Monday, September 20, 2004 8:30 PM
To: BioPerl-List
Subject: [Bioperl-l] torturing newbies are we? SeqIO HowTo question


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";

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

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.

Tom Keller

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