[Bioperl-l] help with parsing meme output

[James Wasmuth]

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)



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
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>Lab add: C318 Life Sciences
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