- Python 2.6.5 or greater
- Cython (download from http://cython.org/)
- Pysam (download from http://code.google.com/p/pysam/)
Bare minimum:
python sam2counts.py sample_1.sam sample_2.sam
This produces a tab-delimited file named counts.txt that contains the counts for each reference. If you prefer to have it named something else:
python sam2counts.py -o s1_to_s2.txt sample_1.sam sample_2.sam
Or use a different delimiter:
python sam2counts.py -o s1_to_s2.csv -d, sample_1.sam sample_2.sam
Currently there is code to indicate if mapped reads map with 0 quality (i.e. map to multiple locations). The best output for this is still being decided, and this is not entirey implemented
Furthermore, this code was tested fairly heavily, but I make no guarantees.
If you have questions regarding this code, please contact Vince Buffalo at vsbuffaloAAAAA@gmail.com (with the poly-A tail removed). All code copyright Vince Buffalo, 2010.
License: GNU General Public License