bam read counts

i've been thinking about organization and the database a lot and i think i've come up with a working plan for not only getting the data i want from the sam/bam files, but putting it in the right place for future access. i've also been reading/researching how to query and update mongoDB and utilize pysam and pymongo, so that implementation of this plan is as smooth as possible.


PLAN OF ATTACK:

• open BAMFILE (one per individual)
• query mongoDB for all documents that contain BAMFILE in "individuals" value array
• foreach mongoDB document returned
• query BAMFILE for locus (samfile.fetch)
• count reads that align to locus 
• push count to Individual in locus in mongoDB

i.e., a document that looks like this:
{
"locus" : "loc010",
"individuals" : [
"R01" 
"R02"
"R03"
   ],
"length" : 332
}

will be:
{
"locus" : "loc010",
"individuals" : [
"R01" : 3 ,
"R02" : 15 ,
"R03" : 6
   ],
"length" : 332
}

thus, each element of the individuals array is now a key/value pair. (right?) now i just need to figure out how to do each step. it's going to be a fun week!