[Bioperl-l] help with parsing meme output

[James Wasmuth]

Does this behave itself? 

while    (my %header=$psmIO->header) {
	for (my $i=0; $i<=$#{$header{instances}};$i++)	{
		print $header{instances}->[$i],"\t",$header{lengths}->[$i],"\n";
	}
}


I don't use these modules but having looked at the docs this should work. Although the notes in Bio::Matrix::PSM::IO for this method say it should be obsolete.

If you still get no joy then attach a copy of the output file to an email. This should provide people with an example.









Nandita Mullapudi wrote:

>ok i've got to be missing something here.
>
>this is my code:
>
>use strict;
>use warnings;
>use Bio::Matrix::PSM::IO;
>use Bio::Matrix::PSM::InstanceSite;
>
>my $psmIO = new Bio::Matrix::PSM::IO(    -file => 'memeout.txt',
>                                         -format => 'meme');
>
>while    (my %header=$psmIO->header) {
>    foreach my $seqid (@{$header{instances}}) {
> print "$header->length";
>
>}
>}
>
>
>and the error i get is " Global symbol "$header" requires
>explicit package name at parsememe2.pl line 15.
>Execution of parsememe2.pl aborted due to compilation errors.
>
>
>thanks for your help.
>-n
>
>
>
>
>---- Original message ----
>  
>
>>Date: Thu, 23 Jun 2005 20:51:48 +0100
>>From: James Wasmuth <james.wasmuth at ed.ac.uk>  
>>Subject: Re: [Bioperl-l] help with parsing meme output  
>>To: Nandita Mullapudi <nandita at uga.edu>
>>Cc: bioperl-l at bioperl.org
>>
>>Nandita
>>
>>The BioPerl module $header->length() comes from is
>>    
>>
>PSM/PsmHeader.pm
>  
>
>>This should be inherited when you "use Bio::Matrix::PSM::IO"
>>
>>have a look 
>>http://doc.bioperl.org/releases/bioperl-1.4/Bio/Matrix/PSM/IO.html
>>
>>What you want should be covered there. Otherwise shout and
>>    
>>
>someone will 
>  
>
>>answer
>>
>>-james
>>
>>
>>
>>Nandita Mullapudi wrote:
>>
>>    
>>
>>>thanks James,
>>>
>>> 
>>>
>>>      
>>>
>>>>Is it the length from the input sequence that you want?
>>>>
>>>>my %length= $header->length();
>>>>Function: Returns the length of the input sequence or motifs
>>>>   
>>>>
>>>>        
>>>>
>>>as a hash, indexed
>>> 
>>>
>>>      
>>>
>>>>by a sequence ID (motif id or accession number)
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>yes, i want the length from the input sequence. I am not sure
>>>i can use the above without specifying which module / package
>>>it refers to? 
>>>
>>>also , where can i find this info? :)
>>>thanks,
>>>-nandita
>>>
>>>
>>> 
>>>
>>>      
>>>
>>>>james
>>>>
>>>>
>>>>Nandita Mullapudi wrote:
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>>>Hi,
>>>>>I am trying to use  Bio::Matrix::PSM::IO to parse meme output.
>>>>>I need to extract the values corresponding to length of the
>>>>>sequence, seq id, and motif id, start and significance/score.
>>>>>I can get the last three using 
>>>>>
>>>>>foreach my $instance (@{ $instances }) {
>>>>>      my $start = $instance -> start;
>>>>>      my $score = $instance -> score;
>>>>>
>>>>>But i cannot find out how to get the seq id and seq length.
>>>>>any ideas?
>>>>>thanks
>>>>>-nandita
>>>>>
>>>>>***************************************************
>>>>>Graduate Student, Kissinger Lab.
>>>>>Dept. of Genetics
>>>>>UGA, Athens GA 30602 USA
>>>>>lab phone: 706-542-6563
>>>>>cell phone: 706-254-2444
>>>>>Lab add: C318 Life Sciences
>>>>>****************************************************
>>>>>_______________________________________________
>>>>>Bioperl-l mailing list
>>>>>Bioperl-l at portal.open-bio.org
>>>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>-- 
>>>>http://www.nematodes.org/~james
>>>>
>>>>"Until man duplicates a blade of grass, nature can laugh at
>>>>   
>>>>
>>>>        
>>>>
>>>his so-called scientific knowledge...."
>>> 
>>>
>>>      
>>>
>>>>          --Thomas Edison 
>>>>
>>>>Blaxter Nematode Genomics Group   |
>>>>Institute of Evolutionary Biology |
>>>>Ashworth Laboratories, KB         | tel: +44 131 650 7403
>>>>University of Edinburgh           | web: www.nematodes.org
>>>>Edinburgh                         |
>>>>EH9 3JT                           |
>>>>UK                                |	
>>>>
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>***************************************************
>>>Graduate Student, Kissinger Lab.
>>>Dept. of Genetics
>>>UGA, Athens GA 30602 USA
>>>lab phone: 706-542-6563
>>>cell phone: 706-254-2444
>>>Lab add: C318 Life Sciences
>>>****************************************************
>>> 
>>>
>>>      
>>>
>>-- 
>>http://www.nematodes.org/~james
>>
>>"Until man duplicates a blade of grass, nature can laugh at
>>    
>>
>his so-called scientific knowledge...."
>  
>
>>           --Thomas Edison 
>>
>>Blaxter Nematode Genomics Group   |
>>Institute of Evolutionary Biology |
>>Ashworth Laboratories, KB         | tel: +44 131 650 7403
>>University of Edinburgh           | web: www.nematodes.org
>>Edinburgh                         |
>>EH9 3JT                           |
>>UK                                |	
>>
>>
>>    
>>
>
>***************************************************
>Graduate Student, Kissinger Lab.
>Dept. of Genetics
>UGA, Athens GA 30602 USA
>lab phone: 706-542-6563
>cell phone: 706-254-2444
>Lab add: C318 Life Sciences
>****************************************************
>  
>

-- 
http://www.nematodes.org/~james

"Until man duplicates a blade of grass, nature can laugh at his so-called scientific knowledge...."
            --Thomas Edison 

Blaxter Nematode Genomics Group   |
Institute of Evolutionary Biology |
Ashworth Laboratories, KB         | tel: +44 131 650 7403
University of Edinburgh           | web: www.nematodes.org
Edinburgh                         |
EH9 3JT                           |
UK                                |