[Bioperl-l] help with parsing meme output
Nandita Mullapudi
nandita at uga.edu
Thu Jun 23 22:40:44 EDT 2005
Thanks Stefan,
the line that didn't make sense was mine, not James'. :p
but i see what was wrong. i'll try this now.
-nandita
>James,
>while you were correct in your first suggestion (to use
>$psmIO->length), but quite incorrect at your next suggestion:
>the code
>while (my %header=$psmIO->header) {
>makes no sense.
>What you probably want to do is:
>while (my $psm=$psmIO->next_psm) {
>my %header=$psm->header; #Bio::Matrix::PSM::Psm method
>#Do something with the has
>}
>But header has different purpose- it contains data about particular
>prediction, such as number of sites, width of the motif, etc.
>If you need the initial sequences lengths it is precisely as you suggested:
>my %lengths=$psmIO->length;
>foreach my $id (keys %lengths) {
>print "Initial sequence $id length is ",$lengths{$id},"\n";
>}
>C'est tout!
>To get a length of a particular hit (that is the sequence, on which
>a predicted motif is based):
>while (my $psm=$psmIO->next_psm) {
>my $instances=$psm->instances;
>foreach my..... {
>print "Hits ... is long", $instance->length....
>}
>Let me know if there are further questions
>Stefan
>
>James Wasmuth wrote:
>
>>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
>>>****************************************************
>>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
--
****************************************************
Nandita Mullapudi
Graduate student, Kissinger Lab.
Dept. of Genetics. UGA Athens GA 30602
Lab Address: C-318 Life Sciences.
Lab phone: 706-542-6563 Cell phone: 706-254-2444
****************************************************
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