[Bioperl-l] Should be simple accession number script, but it's not.

[Jamie Hatfield]

Is '@anum = "<SEQ>";' a legal construct?  I've personally never seen
that before.  You can do '@anum = <SEQ>;', though, and it will work.
Or, just use the <SEQ> down in your loop, 

e.g.,
foreach my $accession ( <SEQ> ) {

Should work also.  (or 'while (my $accession = <SEQ>)', etc.  TMTOWTDI,
IMHO, YMMV)  :-)

Sorry.  It's Friday.  Blame it on that.

Ok, but in testing his script, I came up with the following:  I print
out the requested accession number, then print out the id returned from
the DB lookup IF it was successful.
	my $seq = $db->get_Seq_by_acc($accession);
	print "$accession : ";
	print $seq->id() if ($seq);
	print "\n";

Funny thing is, two separate invocations, I get different
successes/failures!!

Accession.txt
=============================
AP005198
AP005244
AP005246
AP005247
AP005252
AP005258
AP005292
AP005296
AP005301
=============================

Testprog.pl
=============================
#!/usr/local/bin/perl -w

use Bio::DB::GenBank;


open SEQ, "<accession.txt";
@anum = <SEQ>;

my $db = new Bio::DB::GenBank;

foreach my $accession ( @anum ) {
	# just get things by accession number
	chomp($accession);
	my $seq = $db->get_Seq_by_acc($accession);
	print "$accession : ";
	print $seq->id() if ($seq);
	print "\n";
	#print $seq->seq();
}
=============================

Output 1
=============================
AP005198 : 
AP005244 : AP005244
AP005246 : 
AP005247 : AP005247
AP005252 : AP005252
AP005258 : AP005258
AP005292 : AP005292
AP005296 : 
AP005301 : 
=============================

Output 2
=============================
AP005198 : AP005198
AP005244 : AP005244
AP005246 : AP005246
AP005247 : 
AP005252 : AP005252
AP005258 : AP005258
AP005292 : AP005292
AP005296 : AP005296
AP005301 : 
=============================

What's with that??


----------------------------------------------------------------------
Jamie Hatfield                              Room 541H, Marley Building
Systems Programmer                          University of Arizona
Arizona Genomics Computational              Tucson, AZ  85721
  Laboratory (AGCoL)                        (520) 626-9598

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]
On Behalf Of Agrin, Nathan
Sent: Friday, December 13, 2002 1:24 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Should be simple accession number script, but it's
not.


I'm writing a simple script:
1) I want it to take a list of accession numbers in a .txt file,
2) pull out the entries from GenBank,
3) and output the names and sequences to a new .txt file.

The problem is that when I write something like;

$seq = $db->get_Seq_by_acc($accession);
print $seq->seq();

I get an error saying cannot preform command on an undefined variable.
Anyone had similar problems?  What's really wierd is that it seems to
work some of the time.  Below is the code so far:

#!perl

use Bio::DB::GenBank;


open SEQ, "<accession.txt";
@anum = "<SEQ>";

my $db = new Bio::DB::GenBank;

foreach my $accession ( @anum ) {
	# just get things by accession number
	my $seq = $db->get_Seq_by_acc($accession);
	print $seq->seq();
}

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