[Bioperl-l] problem with swissprot parsin
Brian Osborne
brian_osborne at cognia.com
Fri Oct 15 08:25:11 EDT 2004
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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