[Biopython] Cross_match

[Chris Fields]

On May 31, 2010, at 4:24 PM, Peter wrote:

> On Mon, May 31, 2010 at 10:05 PM, Chris Fields  wrote:
>> 
>> On May 31, 2010, at 3:54 PM, Peter wrote:
>> 
>>> On Mon, May 31, 2010 at 9:48 PM, Alvaro F Pena Perea wrote:
>>>> Hi all,
>>>> I'm working on small RNA sequences from NGS. In this regard, I
>>>> made an alignment between the sequences and the genome with
>>>> cross match with the tags option. I wonder if there is some method
>>>> in bioperl to parse cross_match alignments.
>>> 
>>> I think BioPerl's SearchIO supports cross_match, but Biopython
>>> doesn't (yet).
>>> 
>>> Peter
>> 
>> Yes, BioPerl does.
>> 
>> perldoc Bio::SearchIO::cross_match
>> 
>> chris
>> 
> 
> I thought it was actually a Biopython/BioPerl typo in the first place,
> but since we are talking about it, I guess there are some example
> files in the BioPerl unit tests we could usefully borrow...
> 
> Peter

Yes, but only one file:

http://github.com/bioperl/bioperl-live/blob/master/t/data/testdata.crossmatch

chris