[Bioperl-l] ace.pm

[Peter van Heusden]

Marc Logghe wrote:

>  
>
>>-----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
>  
>
Modern versions of phrap can generate two types of ACE files: I think 
the one with the CO instead of Contig is generated when you pass phrap 
the -old_ace command line parameter. The CO/Contig difference is only 
one of many, but I assume your code deals with the other changes as 
well. I know we had to handle these different formats in stackPACK.

Peter