[Bioperl-l] ace.pm

[Wes Barris]

Marc Logghe wrote:

> 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.

Will these changes make their way into the bioperl distribution?

> 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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>  > Bioperl-l at portal.open-bio.org
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>  >
> 


-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au