stats.py

# Thanks for Andreas Klosterman for dask suggestion
import sys
import md5
import hashlib
import re
import argparse
from collections import defaultdict

import sqlite3
import logging

logging.basicConfig()
logger = logging.getLogger('poretools')

def run(parser, args):
	conn = sqlite3.connect(args.db, check_same_thread=False, timeout=30)
	c = conn.cursor()

	uuiddb = set()

	if args.group_by_asic:
		statscache = defaultdict(lambda : defaultdict(int))

		c.execute("pragma temp_store = 2")
		c.execute("PRAGMA cache_size = 10000000")

		statement = """select asic_id, trackedfiles.uuid, template
                               from basecall
                               join basecaller using (basecaller_id) 
                               join trackedfiles using (filepath) 
                               join experiment using (experiment_id)
                               join flowcell using (asic_id)
                               where basecaller.name = 'ONT Sequencing Workflow'"""
		n = 0
		for r in c.execute(statement):
			n += 1
			if n % 1000 == 0: print n
			template = r[2]
			uuid = r[1]

			if template:
				if uuid in uuiddb:
					continue
				else:
					uuiddb.add(uuid)

				a,b,c,d,e = template.split("\n")
				l = len(b.strip())
				statscache[r[0]]['reads'] += 1
				statscache[r[0]]['bases'] += l

		"""
		trackedfiles = {}
		n = 0
		statement = "select asic_id, filepath FROM trackedfiles JOIN experiment USING (experiment_id)"
		for r in c.execute(statement):
			if n % 1000 == 0: print n

			n += 1
			trackedfiles[r[1]] = r[0]

		statement = "select asic_id, template FROM basecall join trackedfiles using (filepath) join experiment using (experiment_id)"
		statement = "select template, filepath from basecall"
		n = 0
		for r in c.execute(statement):
			if r[0]:
				a,b,c,d,e = r[0].split("\n")
				l = len(b.strip())

				statscache[trackedfiles[r[1]]]['reads'] += 1
				statscache[trackedfiles[r[1]]]['bases'] += l
			n += 1
			if n % 1000 == 0: print n
		"""


		for asic, stats in statscache.iteritems():
			print "%s\t%s\t%s" % (asic, stats['reads'], stats['bases'])