aggregate_logs.py

#! /usr/bin/env python3

import sys, argparse
from lib.version import VERSION

parser = argparse.ArgumentParser(description = 'given a list of UMI-dedup log files, aggregate the numbers into one table\nexpects they all have the same fields in the same order')
parser.add_argument('--version', action = 'version', version = VERSION)
parser.add_argument('log_files', nargs = '*')
args = parser.parse_args()

fields = []
values = []
first_file = True

# parse input
for log_file in args.log_files:
	try:
		i = 0
		for line in open(log_file):
			if '\t' in line:
				value, field = line.rstrip().split('\t')
				if first_file:
					assert len(fields) == len(values) == i
					fields += [field]
					values += [[value]]
				else:
					assert fields[i] == field
					values[i] += [value]
				i += 1
		first_file = False
	except (ValueError, AssertionError):
		pass # will catch these later

# write output
print('\t'.join(['library'] + fields))
for i in range(len(args.log_files)):
	try:
		print('\t'.join([args.log_files[i]] + [value_list[i] for value_list in values]))
	except IndexError:
		print('bad format in %s' % args.log_files[i], file = sys.stderr)