[Bioperl-l] help with parsing meme output

[James Wasmuth]

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                                |