[Bioperl-l] Bio::Assembly::IO problems - FIXED!

Florent Angly florent.angly at gmail.com
Tue Feb 26 00:37:20 EST 2008


As far as I know, there really isn't a specification of the ACE file 
format, that would rule if it is legal to have the kind of contig name 
(non capitalized), other that its original implementation in Phrap.
According to the spirit of the ACE file format, my guess is that any 
contig name should be allowed. For example, on this webpage 
http://www.cbcb.umd.edu/research/contig_representation.shtml, the contig 
name is just a number.
So please Russel file this as a bug so that the developers can keep 
track of this bug,
Regards,
Florent


Smithies, Russell wrote:
> I solved the problem :-)
> The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142:
> 	(/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found!
>
> e.g:
> 	CO contig00001 711 12 6 U 
> instead of:
> 	CO Contig00001 711 12 6 U
>
> Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future.
>
>
> 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 
>
>
>
>
>
>
>
>
>   
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-
>> bio.org] On Behalf Of Smithies, Russell
>> Sent: Tuesday, 26 February 2008 11:13 a.m.
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Bio::Assembly::IO problems
>>
>> Is the Bio::Assembly::IO stuff working?
>> I want to parse some .ace files but keep getting errors:
>>
>> 	[smithiesr at impala ace_phrap]$ perl 454_read_ace.pl
>> 	Can't call method "get_consensus_sequence" on an undefined value at
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, <GEN0> line 20.
>>
>> My code is:
>>
>> 	#!perl -w
>>
>> 	use Bio::Assembly::IO;
>> 	use Data::Dumper;
>>
>> 	my $in = "454Contigs.ace";
>>
>> 	$io = new Bio::Assembly::IO(-file=>$in,-format=>"ace");
>> 	$ass = $io->next_assembly;
>>
>> 	print Dumper $ass;
>> 	exit;
>>
>> 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
>>
>>
>> =============================================================
>> ==========
>> Attention: The information contained in this message and/or attachments
>> from AgResearch Limited is intended only for the persons or entities
>> to which it is addressed and may contain confidential and/or privileged
>> material. Any review, retransmission, dissemination or other use of, or
>> taking of any action in reliance upon, this information by persons or
>> entities other than the intended recipients is prohibited by AgResearch
>> Limited. If you have received this message in error, please notify the
>> sender immediately.
>> =============================================================
>> ==========
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>     
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   



More information about the Bioperl-l mailing list