[Bioperl-l] Yet another 'what version's supposed to work?'
jason.stajich at duke.edu
Wed Sep 28 18:42:14 EDT 2005
Exonerate works fine, I don't think this is the problem The tests
pass for me on exonerate 1.0.0 and with the latest code in CVS -- I
spent more than a few hours on this on Monday so you need to make
sure you've got .
$ exonerate --version
exonerate from exonerate version 1.0.0
Using glib version 1.2.10
Built on May 4 2005
Branch: unnamed branch
[jes12 at head2 run]$ make test_Exonerate
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib/
perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0 -e 'use
Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/
All tests successful.
Please be sure you have the latest code from CVS for both bioperl-
live and bioperl-run, I checked in changes to Bio/SearchIO/
exonerate.pm so that it properly parses VULGAR and CIGAR. So
You may want to subscribe to bioperl-guts-l to see the changes as
they come in if you are going to be working on the bleeding edge/
fixing bugs that other folks are working on too.
If you are wanting verify things, run exonerate with --showtargetgff
yes --showquerygff yes
and you'll see GFF (although note that reverse strand features will
be in reverse coordinates, see posts to the mailiing list about this)
On Sep 28, 2005, at 6:24 PM, George Hartzell wrote:
> I'm digging into bioperl-run on FreeBSD.
> I've built a port for exonerate-1.0.0, and it passes all of it's tests
> (but not with --enable-assertions, I've asked Guy about that...).
> t/Exonerate.t blows up all over the place, but I think that the
> problem is that the cDNA<->genomic alignments that are coming back
> aren't quite what the test expect to see. They seem reasonable
> though, leading and/or trailing hsp's seem to have been broken into
> smaller parts.
> Sim4 gives answers that generally agree with both the test expected
> and the calculated data.
> Actually, looking at the exonerate text output and what I'm seeing in
> the perl debugger, it looks like some part of the current bioperl
> parser is treating this:
> 4 : GTTGTGCT-
> GGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCGGCCC : 64
> |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
> 29 :
> GTTGTGCTGGGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCGGCCC : 90
> As two hsps, one from 4->11/29->36, then 12->/38->.... The exonerate
> expected data expects it as a single HSP.
> Does anyone out there have any experience with the exonerate and how
> well it works?
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