[Biopython] Cross_match
Chris Fields
cjfields at illinois.edu
Mon May 31 22:08:27 UTC 2010
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
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