[Bioperl-l] questions

Marco Landwehr tarowas at gmx.de
Thu May 27 14:42:59 EDT 2004

I am new to the list. And even more new to coding. I worked through a
basic Perl learning book and thougt now I could go for using bioperl. But it

 is quite harder than I thought. Because there are countless small error
messages that drive me crazy. ;-) I do not now if this is the right place
for questions, but I will give it a try. Right now I try to understand the
very basics of Bio::SeqIO. I am running bioperl under Windows. (Have also an
installation under cygwin). 
I) I just have problems with the very first working example from the
http://bioperl.org/HOWTOs/html/SeqIO.html . I downloaded a sample fasta file
and while running the script: "test.pl testinput.txt fasta" I am getting the
following error: 
Can't locate object method "accession_no" via package "Bio::Seq" at test.pl
line 38, <GEN0> line 1.
This message is independant of the format (tried different ones) and the
II) next problems while using the Bio::Structure::IO

#!/usr/bin/perl -w
use Bio::Structure::IO;
$structio = Bio::Structure::IO->new(-file => "1cam.pdb", 
    				      -format => 'PDB');
$struc = $structio->next_structure; # returns an Entry object
$pseq = $struc->seqres;             # returns a PrimarySeq object, thus
$partial_sequence=$pseq->subseq(1,20); # returns a sequence string
print "Sequence from 1 to 20 is: $partial_sequence\n";

This is my output:
Sequence from 1 to 20 is: XSHHWGYGKHNGPEHWHKDF
        (in cleanup) Can't call method "CLEAR" on an undefined value at
F:/Perl/site/lib/Bio/Structure/Entry.pm line 776, <GEN0> line 2431 during
global destruction.
I am wondering about the second position "S", this resisue is not defined in
the crystal structure. What does the error message mean? And how to get rid
of it?
III) How to get the atoms at a certain residue? Just adding these two lines:
@atoms = $struc->get_atoms(20);   # Atom objects, given a Residue
print "Atoms at residue 20 are: @atoms\n";
give me a bunch of error messages....

Thanks for comment and/or help


P.S. The idea of bioperl ist great and I have to say thank you to all
contributors. Only the learning curve is quite steep, because there are so
few well documented examples...

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