[Bioperl-l] Errors using Bio::Assembly

[nkuipers]

I did forget that information, didn't I.  Typing phrap -v told me:

phrap version 0.990329

Thoughts on this?

Nathanael Kuipers



>===== Original Message From Andy Nunberg <anunberg at oriongenomics.com> =====
>Curious, what version of phrap did you use to create the file? if your file
>in the 'new' format?
>Andy
>At 01:32 PM 1/31/2003 -0800, you wrote:
>>I just started using this module today, and had no problems...admittedly, my
>>script is MUCH lighter than yours but no errors were thrown with the
>>next_assembly() call anyways.  I am using Linux Red Hat 8.0, Perl 5.8.0,
>>bioperl 1.2.
>>
>># # # # # #
>>
>>use strict;
>>use warnings;
>>
>>use lib qw(/home/nkuipers/lib);
>>use Bio::Assembly::IO;
>>use Fcntl ":flock";
>>
>>my $input = shift;
>>my $io = new Bio::Assembly::IO(-file   => "$input",
>>			       -format => "ace");
>>
>>my $assembly = $io->next_assembly;
>>
>>#collection of Bio::Assembly::Contig objects
>>my $contigs = $assembly->{_contigs};
>>
>>open CLUSTERS, ">>entropyFiltered.clust" or die "Could not open for
>>append.\n";
>>flock(CLUSTERS, LOCK_EX)		or die "LOCK_EX refused.\n";
>>
>>for my $id (sort {$a <=> $b} keys %$contigs)
>>{
>>	#this format is easy to split into a hash of arrays later on
>>
>>	print CLUSTERS "$id=[qw(";
>>	my $elemref = $contigs->{$id}->{_elem};
>>	print CLUSTERS "$_ " for sort {$a <=> $b} keys %$elemref;
>>	print CLUSTERS ")]\n";
>>}
>>
>>__END__
>>
>>
>>>===== Original Message From Andy Nunberg <anunberg at oriongenomics.com> =====
>>>I have tried the new Bio::Assembly module and I get a few errors...
>>>using RH Linux 7.2 with Perl 5.6
>>>
>>>first here is the script i am using...
>>>use lib '/loginhome/anunberg/bioperl-1.2';
>>>use strict;
>>>use Bio::Assembly::IO;
>>>use Bio::Assembly::ContigAnalysis;
>>>use Carp qw(cluck);
>>>my $in=Bio::Assembly::IO->new(-file=>$ARGV[0], -format=>'ace');
>>>my $assembly=$in->next_assembly;
>>>my @contigs=$assembly->all_contigs;
>>>
>>>foreach my $contig(@contigs){
>>>
>>>	my $analysis=Bio::Assembly::ContigAnalysis->new(-contig=>$contig);
>>>	my @hqd=$analysis->high_quality_discrepancies;
>>>	my @ss=$analysis->single_strand;
>>>	my @lcd=$analysis->low_consensus_quality;
>>>	my $id=$contig->id;
>>>	print "$id\t";
>>>	print scalar @hqd."\t";
>>>	print scalar @lcd."\n";
>>>}
>>>
>>>My first error is when calling the next_assembly method.  Some parsing
>>>error occurs, I think.  I got mutlitiple warnings all the same
>>>Argument "" isn't numeric in numeric comparison (<=>) at
>>>/loginhome/anunberg/bioperl-1.2/Bio/SeqFeature/Collection.pm line 436,
>>><GEN0> line 54.
>>>the lines correspond to the QA tag lines in the ace file.  Sometimes the
>>>same complaint occurs one line above it if its blank, but not all blank
>>>lines above the QA tag produce this warning
>>>
>>>when using the method high_quality_discrepancies, i get this warning
>>>Argument "" isn't numeric in numeric comparison (<=>) at
>>>/loginhome/anunberg/bioperl-1.2/Bio/SeqFeature/Collection.pm line 436,
>>><GEN0> line 358.
>>>which is a blank line at the end of the ace file.
>>>
>>>I may be using the method wrong, but using an ace file where i know to have
>>>a high quality descrepancie, i still get 0 .
>>>The documentation is a little off for this method.  The description says
>>>that a Bio::SeqFeature::Collection is returned, but the code and the
>>>example has an array of Bio::SeqFeature::Generic objects being returned(if
>>>i am reading the code correctly).
>>>
>>>
>>>
>>>the single_strand method gives me the following exception
>>>------------- EXCEPTION Bio::Root::NotImplemented -------------
>>>MSG: Abstract method
>>>"Bio::Assembly::ContigAnalysis::_merge_overlapping_features" is not
>>>implemented by package Bio::Assembly::ContigAnalysis.
>>>This is not your fault - author of Bio::Assembly::ContigAnalysis should be
>>>blamed!
>>>
>>>STACK Bio::Root::RootI::throw_not_implemented
>>>/loginhome/anunberg/bioperl-1.2/Bio/Root/RootI.pm:529
>>>STACK Bio::Assembly::ContigAnalysis::_merge_overlapping_features
>>>/loginhome/anunberg/bioperl-1.2/Bio/Assembly/ContigAnalysis.pm:476
>>>STACK Bio::Assembly::ContigAnalysis::single_strand
>>>/loginhome/anunberg/bioperl-1.2/Bio/Assembly/ContigAnalysis.pm:442
>>>STACK toplevel ../testing_BioAssembly.pl:31
>>>
>>>---------------------------------------------------------------
>>>
>>>Thanks to anyone who can help.
>>>Andy
>>>
>>>*******************************************************************
>>>Andy Nunberg, Ph.D
>>>Computational Biologist
>>>Orion Genomics, LLC
>>>(314) 615-6989
>>>http://www.oriongenomics.com
>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l at bioperl.org
>>>http://bioperl.org/mailman/listinfo/bioperl-l
>>
>>_______________________________________________
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>
>*******************************************************************
>Andy Nunberg, Ph.D
>Computational Biologist
>Orion Genomics, LLC
>(314) 615-6989
>http://www.oriongenomics.com