[Bioperl-l] Bio::Assembly::IO problems reading .ace files

[Florent Angly]

Would this issue cause an excessive memory usage? Because I was getting 
a high memory usage when parsing some TIGR Assembler files and was 
wondering if the tigr parser was responsible for that or the parent 
assembly IO module.
I'd definitely be interested in a fix of the Bio::Assembly 
implementation if it's the assembly IO module's fault....
Florent

Chris Fields wrote:
> This seems similar to the 'too many open filehandles issue' documented  
> here:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2320
>
> It unfortunately is due to having an open DB_File for every contig,  
> and is a problem with the Bio::Assembly implementation that isn't  
> easily fixed.  Changing the open filehandle limit using ulimit is the  
> only known fix:
>
> ulimit -n 10000
>
> chris
>
> On Dec 3, 2007, at 6:49 PM, Smithies, Russell wrote:
>
>   
>> Hi all,
>>
>> It' trying to read .ace files but keep getting an error that I don't
>> know the cause of.
>> Really basic example code:
>>
>> 	#!/usr/local/bin/perl -w
>>
>> 	use lib "/data/home/smithiesr/bioperl-live";
>> 	use Bio::Assembly::IO;
>> 	use Data::Dumper;
>>
>> 	$ace = "CLP0001001240-cE15_20030319.ace";
>>
>> 	$io = new Bio::Assembly::IO(-file=>$ace,-format=>"ace");
>> 	$assembly = $io->next_assembly;
>>
>> 	foreach $contig ($assembly->all_contigs) {
>>      		print Dumper $contig;
>> 	}
>>
>> Gives this error;
>> 	[smithiesr at impala ace_phrap]$ perl bp_read_ace.pl
>> 	Can't call method "get_consensus_sequence" on an undefined value
>> at /data/home/smithiesr/bioperl-live/Bio/Assembly/IO/ace.pm line 170,
>> <GEN0> line 42.
>>
>> Which relates to this bit in ace.pm:
>> 	# Loading contig qualities... (Base Quality field)
>> 	/^BQ/ && do {
>> 	    my $consensus = $contigOBJ->get_consensus_sequence()->seq();
>>
>> Is this caused by a dud ace file or a problem with  
>> Bio::Assembly::IO:ace
>> or is the Contig object not getting created?
>> Any ideas?
>>
>> Thanx,
>>
>> Russell Smithies
>>
>> Bioinformatics Software Developer
>> T +64 3 489 9085
>> E  russell.smithies at agresearch.co.nz
>>
>> Invermay  Research Centre
>> Puddle Alley,
>> Mosgiel,
>> New Zealand
>> T  +64 3 489 3809
>> F  +64 3 489 9174
>> www.agresearch.co.nz
>>
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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