[Bioperl-l] problem with swissprot parsin
Siddhartha Basu
basu at pharm.sunysb.edu
Fri Oct 15 09:55:16 EDT 2004
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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