[Bioperl-l] ace.pm

[Marc Logghe]

The thread (including patch) can be found here:
http://bioperl.org/pipermail/bioperl-l/2002-December/010677.html
The patch should still work, cvs version of the package did not change in bioperl.
HTH,
Marc


> -----Original Message-----
> From: Wes Barris [mailto:wes.barris at csiro.au]
> Sent: dinsdag 17 februari 2004 4:36
> To: Jason Stajich
> Cc: Bioperl Mailing List
> Subject: Re: [Bioperl-l] ace.pm
> 
> 
> Jason Stajich wrote:
> 
> > 
> > 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.
> 
> I have modified one line in Bio/Assembly/IO/ace.pm as shown below:
> 
>          # Loading contig sequence (COntig sequence field)
> #       (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # 
> New contig 
> found!
>          (/^CO (\w+) (\d+) (\d+) (\d+) (\w+)/) && do { # New 
> contig found!
> 
> The change will cause the contigID to be whatever the second field of
> this line is (CO CL15Contig1 794 4 0 U).  In this case, it would be
> set to "CL15Contig1".
> 
> 
> > 
> > -jason
> > 
> > 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
> > 
> 
> 
> -- 
> Wes Barris
> E-Mail: Wes.Barris at csiro.au
> 
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