[Bioperl-l] Bio::DB::CUTG problem

Mark A. Jensen maj at fortinbras.us
Thu Mar 4 08:10:06 EST 2010


Thanks, Csaba - change made and commited at r16898
MAJA
----- Original Message ----- 
From: "Csaba Ortutay" <csaba.ortutay at uta.fi>
To: <bioperl-l at lists.open-bio.org>
Sent: Thursday, March 04, 2010 4:57 AM
Subject: [Bioperl-l] Bio::DB::CUTG problem


> Hello,
>
> We would use Bio::DB::CUTG module to get codon usage data for a large number
> of genomes.
>
> We have noticed that the module cannot findcertain organisms which are
> otherwise in the database. It happens when the name contains some non-
> alphabetic characters.
>
> A few examples:
>
> Streptococcus agalactiae 2603V/R
> Shigella flexneri 5 str. 8401
>
> I have located the corresponding part in the CUTG.pm code, and I would suggest
> a change:
>
> 222c222
> <       my $nameparts =  join "+", $self->sp =~ /(\w+)/g;
> ---
>>       my $nameparts =  join "+", $self->sp =~ /(\S+)/g;
>
>
> With this I can now access the wanted tables.
>
> Best regards,
> Csaba
>
> -- 
> Csaba Ortutay PhD
> Docent of Bioinformatics
> IMT Bioinformatics
> University of Tampere
> Finland
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 



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