[gt-users] python tests and splitfasta

[Gordon Gremme]

Hi Brent,

> hi, i'm attaching a patch to update the python tests for recent change
> to use create_new() rather than __init__()
> i also added a property for attribs as i think that's convenient.

thanks, but it leads to a test failure on my machine (Darwin i386):

488: gtpython: AnnotationSketch bindings (FeatureNode(Iterator)) : failed
     [ problem: unexpected return code: 2 != 0
       in: /Users/gordon/work/genometools/testsuite/stest_testsuite/test488 ]

Any ideas?


> i would like to add an option to the splitfasta command-line tool so
> that the targetsize can be specified in basepairs rather
> than MB, and another option to allow overlapping of sequences-- so it
> can take a huge chromosome and e.g. split it into
> 1megabase chunks with 10Kbp overlapping at the ends.
>
> i think the syntax would look like:
>
> gt splitfasta -splitbp -targetsize 1000000  -overlap 10000
>
> so splitbp is bool flag to tell it not to bp rather than mb.
> does this seem reasonable and/or would a patch be accepted for adding that?

Seems like a good idea to me! But I would rather not change the
meaning of -targetsize with an additonal option. I think it would be
better to use an additional option instead which excludes the usage of
-targetsize (analog to -numfiles and -splitdesc). Something like that:

gt splitfasta -splitbp 1000000 -overlap 10000

Bonus points if -overlap works with -targetsize, too ;-)

Gordon