[Bioperl-l] problem with swissprot parsin

Hilmar Lapp hlapp at gmx.net
Fri Oct 15 13:27:45 EDT 2004


The RG/RA issue has been fixed on the main trunk I believe.

Aside from that, different versions of perl will also lead to things  
being complained about or remaining silent. Generally, *always* add the  
version of bioperl you are using if you report a problem.

	-hilmar

On Friday, October 15, 2004, at 09:55  AM, Siddhartha Basu wrote:

> Hi Brian,
> I retested it again. The good part is that i can fetch the seq obj and  
> the sequence now. The warnings are still there. I will try to index  
> the entire swissprot data file and see what happens.
>
> Now,as mentioned by one of the earlier mail in the list that it has to  
> with the absence of RA records in recent swissprot files and the  
> swiss.pm modules spewing out warnings when the variable $au  is not  
> getting the data. Since you are even getting the warnings what version  
> of bioperl you are running.
>
> -siddhartha
>
>
>
>
>
> Brian Osborne wrote:
>> Siddhartha,
>> Changing @files to @ARGV makes your script index without warnings on  
>> my
>> machine, using your Swissprot file or mine. It also retrieves a  
>> sequence.
>> Below...
>> Brian O.
>> #!/usr/bin/perl -w
>> use strict;
>> use Bio::DB::Flat;
>> die "no files\n" unless @ARGV;
>> my $LOCATION = ".";
>> my $db = Bio::DB::Flat->new( -directory => $LOCATION,
>> 									  -dbname => "swissall",
>> 									  -format => "swiss",
>> 									  -index => "bdb",
>> 									  -write_flag => 1,
>> 									) or die "can't create BioFlat indexes\n";
>> $db->build_index(@ARGV);
>> print "Done indexing\n";
>> my $seq = $db->get_Seq_by_acc("P41932");
>> print $seq->seq;
>> -----Original Message-----
>> From: bioperl-l-bounces at portal.open-bio.org
>> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Siddhartha  
>> Basu
>> Sent: Thursday, October 14, 2004 4:54 PM
>> To: Brian Osborne
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] problem with swissprot parsin
>> Hi Brian,
>> Changed it, problem persists.
>> -siddhartha
>> Brian Osborne wrote:
>>> Siddhartha,
>>>
>>> Change @files to @ARGV in the build_index line. Does that fix it?
>>>
>>> Brian O.
>>>
>>> -----Original Message-----
>>> From: Siddhartha Basu [mailto:basu at pharm.sunysb.edu]
>>> Sent: Thursday, October 14, 2004 4:15 PM
>>> To: Brian Osborne
>>> Cc: bioperl-l at bioperl.org
>>> Subject: Re: [Bioperl-l] problem with swissprot parsin
>>>
>>> Hi Brian,
>>> Here is the code that started to give the following error. I presume  
>>> i
>>> am using Bio::DB::Flat::BDB though i haven't called it directly. I am
>>> trying to index swissprot/trembl files here.
>>>
>>> #!/usr/bin/perl -w
>>> use strict;
>>> use Bio::DB::Flat;
>>>
>>> die "no files\n" unless @ARGV;
>>> my $LOCATION = "/home/basu/odbaindex";
>>>
>>> my $db = Bio::DB::Flat->new( -directory => $LOCATION,
>>>                                 -dbname => "swissall",
>>>                                 -format => "swiss",
>>>                                 -index => "bdb",
>>>                                 -write_flag => 1,
>>>                              ) or die "can't create BioFlat  
>>> indexes\n";
>>> $db->build_index(@files);
>>> print "Done indexing\n";
>>>
>>> exit;
>>>
>>>
>>> I get the following warinings.
>>>   
>>> ===================================================================== 
>>> =
>>> Use of uninitialized value in substitution (s///) at
>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>> line
>>>  18676877.
>>>  Use of uninitialized value in substitution (s///) at
>>>  /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>> line
>>>  18676916.
>>>  Use of uninitialized value in substitution (s///) at
>>>  /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>> line
>>>  18676956.
>>>  Use of uninitialized value in substitution (s///) at
>>>  /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>> line
>>>  18677002.
>>>  Use of uninitialized value in substitution (s///) at
>>>  /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>> line
>>> ===================================================================== 
>>> ====
>>>
>>> I have done a small test with Bio::SeqIO module using a small test
>>> file(swiss.test). Here is the code.
>>>
>>> #!/usr/bin/perl -w
>>> #
>>> use strict;
>>> use Bio::SeqIO;
>>>
>>> my $seq = Bio::SeqIO->new(-file => $ARGV[0], -format => "swiss");
>>>
>>> while (my $in = $seq->next_seq) {
>>>    print $in->id,"\n";
>>> }
>>>
>>> exit;
>>>
>>>
>>> It gives the same error
>>> Use of uninitialized value in substitution (s///) at
>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN0>  
>>> line
>> 28.
>>> 1433_CAEEL
>>> Use of uninitialized value in substitution (s///) at
>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN0>  
>>> line
>> 87.
>>> A4_CAEEL
>>> Use of uninitialized value in substitution (s///) at
>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN0>  
>>> line
>> 171.
>>> AATC_CAEEL
>>>
>>> I have also attached the test file.
>>>
>>> Hope this will give some clue for the problem.
>>> Thanks for the response.
>>>
>>> siddhartha
>>>
>>>
>>>
>>> Brian Osborne wrote:
>>>
>>>
>>>> Siddhartha,
>>>>
>>>> Bio::DB::Flat::BinarySearch or Bio::DB::Flat::BDB? Also, please  
>>>> show your
>>>> code when you ask a question, it simplifies matters. For example,  
>>>> it would
>>>> tell me which module you used, which file format, and so on. It  
>>>> also helps
>>>> to attach the actual sequence files, or some smaller test file that  
>>>> shows
>>>> the same error. What happens occasionally is that a question will  
>>>> get
>>>> ignored for the simple reason that no one knows how to answer,  
>>>> there's not
>>>> enough information given in the letter.
>>>>
>>>> Brian O.
>>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at portal.open-bio.org
>>>> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of  
>>>> Siddhartha Basu
>>>> Sent: Thursday, October 14, 2004 2:51 PM
>>>> To: bioperl-l at bioperl.org
>>>> Subject: [Bioperl-l] problem with swissprot parsin
>>>>
>>>> Hi,
>>>> I have already described this problem in this mailing list but  
>>>> haven't
>>>> got anybodies attention yet. I had also asked the author of this  
>>>> module
>>>> but nothing back yet. Anyway i really could'nt figure out how to  
>>>> solve
>>>> this and so i am writing again. I have also tried by replacing the
>>>> swiss.pm module from the bioperl-live version. But the problem  
>>>> persists.
>>>> I understand that this is a maintained module and i am not getting
>>>> ignored because of maintenance issue.
>>>>
>>>> I am trying to make a flat file index of swissprot/trembl files  
>>>> using
>>>> Bio::DB::Flat module. However, i am getting the following consistent
>>>> warnings during the indexing process.
>>>> ==================================================================== 
>>>> ==
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18676877.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18676916.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18676956.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18677002.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18677045.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18677091.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18677136.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18677178.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18677209.
>>>> Use of uninitialized value in substitution (s///) at
>>>> /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1>  
>>>> line
>>>> 18677249.
>>>> ==================================================================== 
>>>> ====
>>>> Though, the indexing get completed, i could'nt fetch any data from  
>>>> there
>>>> as it does not return any seq obj.
>>>> I also get the same warnings when i try to read the swissprot file  
>>>> using
>>>> the Bio::SeqIO module.
>>>> I am using bioperl-1.4 and understand it has something to do with  
>>>> the
>>>> swissprot parser in Seq::IO module.
>>>> So, does any fix or solution available for this problem.
>>>>
>>>> Thanks in  advance.
>>>>
>>>> -siddhartha
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at portal.open-bio.org
>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>
>>>
>>>
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>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------




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