[Bioperl-l] help with parsing meme output
James Wasmuth
james.wasmuth at ed.ac.uk
Thu Jun 23 17:23:15 EDT 2005
It would appear that $psmIO->header is not implemented in PSM/IO.pm.
Does anyone know if this is to be done?
Nandita Mullapudi wrote:
>thanks James,
>this one gives the error
>
>Can't use an undefined value as an ARRAY reference at
>/usr/lib/perl5/site_perl/5.6.1/Bio/Matrix/PSM/IO/meme.pm line
>159, <GEN0> line 43.
>
>i've attached the text output i am trying to parse
>
>-nandita
>
>
>---- Original message ----
>
>
>>Date: Thu, 23 Jun 2005 21:36:03 +0100
>>From: James Wasmuth <james.wasmuth at ed.ac.uk>
>>Subject: Re: [Bioperl-l] help with parsing meme output
>>To: Nandita Mullapudi <nandita at uga.edu>
>>Cc: bioperl-l at portal.open-bio.org
>>
>>Does this behave itself?
>>
>>while (my %header=$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 |
>>
>>
>>
>>
>
>***************************************************
>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
>****************************************************
>
>
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