[Bioperl-l] help with parsing meme output

James Wasmuth james.wasmuth at ed.ac.uk
Thu Jun 23 15:33:04 EDT 2005

Hi Nandita

does "my $id=$instance->primary_id;" do what you want?

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)


Nandita Mullapudi wrote:

>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?
>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


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

Blaxter Nematode Genomics Group   |
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