example code
python methratio.py -d /Volumes/NGS\ Drive/Oyster\ Genome/oyster.v9_M.fa -z -u -o /Volumes/AquaculX/armina/OUTzu_methratioBSMAP_v9_M_A.txt -s /Volumes/Bay3/Software/samtools /Volumes/AquaculX/armina/BSMAP_output_trimmed_v9_M.sam

actual code
genefish:bsmap-2.73 Steven$ python methratio.py -d /Users/Shared/data/oyster.v9_M.fa -z -u -o /Volumes/web/cnidarian/OUTzu_methratioBSMAP_v9_M_ce.txt -s /Users/Shared/Apps/bsmap-2.73/samtools /Users/Shared/data/Claire/bsmapoutput_112012.sam

 
@ Thu Nov 22 04:38:21 2012: reading reference /Users/Shared/data/oyster.v9_M.fa ...
@ Thu Nov 22 04:38:25 2012: reading /Users/Shared/data/Claire/bsmapoutput_112012.sam ...
[samopen] SAM header is present: 60 sequences.


total 25432398 valid mappings, 17734335 covered cytosines, average coverage: 8.10 fold.


OUTPUT:
http://eagle.fish.washington.edu/cnidarian/OUTzu_methratioBSMAP_v9_M_ce.txt