[Bioperl-l] help with parsing meme output
Stefan Kirov
skirov at utk.edu
Thu Jun 23 23:13:58 EDT 2005
Sorry James :-[ ... I thought it was your suggestion...
Nandita let me know if you have more questions.
Stefan
Nandita Mullapudi wrote:
> 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
>>
>
>
More information about the Bioperl-l
mailing list