[Bioperl-l] ace.pm

Jason Stajich jason at cgt.duhs.duke.edu
Mon Feb 16 21:14:28 EST 2004

People write code and modules to support the work they are doing,
sometimes for a specific data set - so I suspect Robson wrote this to
support phrap ace format which has a convention of them being ContigXX.

You are welcome to make changes to code on your local system to get it
working and then post the diffs so they can be incorporated back in.  Why
not try changing the code as you have noticed and seeing if it works.  It
is a collaborative project and these modules are newish, so give a try
fixing things and then getting feedback on your fixes.


On Tue, 17 Feb 2004, Wes Barris wrote:

> 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!
> Bioperl expects the second "word" in the line to be "Contig\d+" where
> the number is used as the "contigID".  Is there a reason why
> "contigID" must be a number?  Why can't it be the whole second
> "word" of the "CO" line?

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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