Bioperl: Two newbie questions

[philipp.pagel@cmp.yale.edu]

		Hi!

Disclaimer: I am not at all experienced with perl in general and just start
with bioperl...

And I am trying to find my way around in the examples and documentation,
because I want to write a litte script to do something usefull for me :-)

I have two questions that I could not figure out with the documentation:

1) I read from a file: 

	$in = Bio::SeqIO->new( '-format' => $informat , -file => $file);
	
	while ($seq = $in->next_seq();){
		...
	}
This works fine for the fasta files included in the bioperl distribution.
But my Sequence happens to come in gcg format - so i just set $informat to
"gcg". Ok - my files include only one single sequence, but anyway... I
expected it to work nevertheless. But this turns out to be an endless loop
delivering the same sequence over and over again. Why is that?

2) I played with run_blast_remote.pl and copuld not get it to work. I just
tried the first example the script returns when evoked with -eg. Here is what 
I get:
------------------------snip--------------------------
Use of uninitialized value at ./run_blast_remote.pl line 114.

-------------------- WARNING --------------------
MSG: /usr/lib/perl5/site_perl/5.005/Bio/Tools/Blast/Run/Webblast.pm:1205
Seq::type - deprecated method. You should use $obj->moltype in preference
(notice that
moltype returns lowercase strings)
-------------------------------------------------
Use of uninitialized value at
/usr/lib/perl5/site_perl/5.005/Bio/PrimarySeqI.pm
line 847.
Use of uninitialized value at
/usr/lib/perl5/site_perl/5.005/Bio/PrimarySeqI.pm
line 848.
Use of uninitialized value at
/usr/lib/perl5/site_perl/5.005/Bio/PrimarySeqI.pm
line 849.

-------------------- WARNING --------------------
MSG: /usr/lib/perl5/site_perl/5.005/Bio/Tools/Blast/Run/Webblast.pm:1206
Seq::seq_len - deprecated method. You should use $obj->length in preference
-------------------------------------------------
Use of uninitialized value at
/usr/lib/perl5/site_perl/5.005/Bio/PrimarySeqI.pm
line 717.
Use of uninitialized value at
/usr/lib/perl5/site_perl/5.005/Bio/Tools/Blast/Run/Webblast.pm line 1228.

The sequence length of  (0) too short for blasting: min length = 15


*** Trouble creating Blast object:

-------------------- EXCEPTION --------------------
MSG: Blast failed: No file created or a error occured upon submission.
CONTEXT: Error in uNKNOWN CONTEXT
SCRIPT: ./run_blast_remote.pl
STACK:
Bio::Tools::Blast::Run::Webblast::_blast(1147)
Bio::Tools::Blast::Run::Webblast::blast_remote(560)
Bio::Tools::Blast::_run_remote(1244)
Bio::Tools::Blast::run(1174)
Bio::Tools::SeqAnal::_initialize(279)
Bio::Root::Object::new(462)
main::create_blast(555)
main::./run_blast_remote.pl(131)
---------------------------------------------------
 


        main::create_blast called at ./run_blast_remote.pl line 131
        eval {...} called at ./run_blast_remote.pl line 130
----------------------snip---------------------------

What am I doing wrong?

cu and thanks for any hints

	Philipp


-- 
Dr. Philipp Pagel
Cellular and Molecular Physiology         phone: (203) 785-6835	
SHM BE-30
Yale University
333 Cedar ST
New Haven, CT 06520

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