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

Thomas J Keller kellert at ohsu.edu
Mon Sep 20 20:29:34 EDT 2004


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 $seqout->write_seq($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.

Tom Keller

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