[Bioperl-l] help with parsing meme output

[Stefan Kirov]

The error you get is because you did not declare $header prior to usage 
with 'my' (or you can use it as a global, but then you should do 
something like $main::header). Another way is not to use strict, but 
this is not generally recommended if you want to write something reliable.
And yes, $instance->length will give back the hit length, so you may 
need what James suggested.
Stefan

Nandita Mullapudi wrote:

>i should've tried to be clearer, i'm looking for for length of
>the input sequence. i tried James' suggestion of print
>"$header->length"; but the error i get back is 
>
>Global symbol "$header" requires explicit package name at
>parsememe2.pl line 15.
>
>
>altho i am using use Bio::Matrix::PSM::IO;
>
>thanks for your help
>-nandita
>
>---- Original message ----
>  
>
>>Date: Thu, 23 Jun 2005 15:55:53 -0400
>>From: Stefan Kirov <skirov at utk.edu>  
>>Subject: Re: [Bioperl-l] help with parsing meme output  
>>To: Nandita Mullapudi <nandita at uga.edu>
>>Cc: bioperl-l at portal.open-bio.org
>>
>>$instance->accession_number to get the sequence id
>>and
>>lenght is given by $instance->length
>>Stefan
>>
>>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
>>> 
>>>
>>>      
>>>
>
>***************************************************
>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
>****************************************************
>  
>