[Biopython-dev] [Biopython (old issues only) - Bug #2905] (Closed) Short read alignment format SAM / BAM

[redmine at redmine.open-bio.org]

Issue #2905 has been updated by Peter Cock.

Description updated
Status changed from New to Closed
% Done changed from 0 to 100

I'm going to make this as closed. The Python wrappers for the samtools later htslib C API do a fine job: pysam https://github.com/pysam-developers/pysam

Thanks all.

Peter

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Bug #2905: Short read alignment format SAM / BAM
https://redmine.open-bio.org/issues/2905#change-15342

* Author: Osvaldo Zagordi
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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Hi again,
is there any plan to develop some parsers for alignment of short reads? There's a lot of formats around, and the most serious proposal for a format I've seen is SAM (http://samtools.sourceforge.net/). I should start writing something to parse this output soon. Any suggestion on where to start from (in order not to depend on some module that will be soon obsolete)?

Thanks,
    Osvaldo

---Files--------------------------------
SamBamIO.py (9.06 KB)


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