[Bioperl-l] Bio::AlignIO::Mase

[Tristan Lefebure]

Thanks again. Based on your comments, would you mind considering the
following patch?

[tristan at picodon bioperl-live] diff -u Bio/AlignIO/mase_original.pm
Bio/AlignIO/mase.pm
--- Bio/AlignIO/mase_original.pm        2011-06-09 09:12:47.929957767 +0200
+++ Bio/AlignIO/mase.pm 2011-06-09 09:12:11.029903646 +0200
@@ -109,7 +109,7 @@

        while( $entry = $self->_readline) {
            $entry =~ /^;/ && last;
-           $entry =~ s/[^A-Za-z\.\-]//g;
+           $entry =~ s/[^A-Za-z\d\.\-]//g;
            $seq .= $entry;
        }
        if( $end == -1) {

[tristan at picodon bioperl-live] prove -lv t/AlignIO/mase.t
t/AlignIO/mase.t ..
1..3
ok 1 - use Bio::AlignIO::mase;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - mase input test
ok
All tests successful.
Files=1, Tests=3,  0 wallclock secs ( 0.03 usr  0.00 sys +  0.14 cusr
0.01 csys =  0.18 CPU)
Result: PASS
[tristan at picodon bioperl-live]


I see that the Bio::AlignIO::Mase write_aln method is yet to be
implemented. Is that on someone's todo list? I may try to do this...

--
Tristan

On Wed, Jun 8, 2011 at 10:35 PM, Chris Fields <cjfields at illinois.edu> wrote:
>
> On Jun 8, 2011, at 10:05 AM, Tristan Lefebure wrote:
>
> > Thanks all for your answers. I didn't know about [^] (always
> > something new to learn with perl...).
> >
> > ...
> > (Chris, how do you run this:
> >       ./Build test --test-files t/AlignIO/mase.t --verbose
> >
> > The only thing I manage to do is:
> >
> > [tristan at picodon bioperl-live] ./Build.PL test --test-files
> > t/AlignIO/mase.t --verbose
> > Too early to specify a build action 'test'.  Do 'Build test'
> > instead.
> > )
>
> Note the lack of '.PL' on './Build test --test-files t/AlignIO/mase.t --verbose'.  You must run 'perl Build.PL' first.
>
> Arguably a better general way to run tests is to use 'prove -lv t/AlignIO/mase.t', which adds the local 'lib' directory while testing.  Just running the tests using 'perl t/AlignIO.mase.t' doesn't do this (it can be done with '-I./lib'), but 'prove' has more flexibility that simply using perl directly.
>
> chris