[Bioperl-l] ace.pm

[Marc Logghe]

> -----Original Message-----
> From: Wes Barris [mailto:wes.barris at csiro.au]
> Sent: dinsdag 17 februari 2004 0:19
> To: Bioperl Mailing List
> Subject: [Bioperl-l] ace.pm
> 
> 
> Hi,
> 
> ACE files generated by an application called tgicl have "CO"
> lines of the form:
> 
> CO CL15Contig2 794 4 0 U
> 
> This line is not parsed properly by the ace.pm bioperl module.
> Notice this line from Bio/Assembly/IO/ace.pm .
> 
>          (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New 
> contig found!
> 
A long time ago I've adapted the code in order to handle tgicl (cap3) generated ACE files. Don't know however, if it made it to CVS. I'll have a look,  I'll send you the patch as soon as I traced it 
HTH,
Marc