[Bioperl-l] reverse complement - and features

Roy Chaudhuri roy at colibase.bham.ac.uk
Thu Nov 16 11:49:49 EST 2006


> that method sounds promising, although the documentation seems to be
> copy-and-paste from the trunc_with_features() method.
Yes, I was a bit lazy with that. It has been fixed in CVS (thanks Chris) 
and will be included in the new 1.5.2 release.

> I included in my script, although it doesn't complaint but no being
> there, it doesn't do anything with the file.
> I looked at the version of bioperl in the server where I'm running,
> and it is 1.5.0 and the SeqUtils.pm does not include the
> revcom_with_features().
> Do you know if I can install the SeqUtils.pm module in my directory,
> and call it with use lib "/home/xxxx/xxxx/lib/perl"; ?

Yes, that should work. You can download the most recent version from:
http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioperl-live/Bio/SeqUtils.pm?rev=HEAD&content-type=text/plain

You can put that file in the directory /home/xxxx/xxxx/lib/perl/Bio/ and 
it should then be recognised as the preferred Bio::SeqUtils module if 
you use lib as you say.

Good luck with it.
Roy.

--
Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, U.K.

http://xbase.bham.ac.uk


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