import os

import glob

import re

import sys

import socket

import couchdb

import logging

import argparse

import yaml

import json

import distance

import operator

try:

import ConfigParser

except ImportError:

import configparser

CONFIG = {}

logger = logging.getLogger(__name__)

def setupServer(conf):

db_conf = conf['statusdb']

url="https://{0}:{1}@{2}".format(db_conf['username'], db_conf['password'], db_conf['url'])

return couchdb.Server(url)

def load_yaml_config(config_file):

raise e

class Indexes:

print("{} {} {} {} {}".format(index_seq, index_seq_check, fake_index, hamming_dist, kit_type))

def get_FC_type(FCid):

return FC_type

import time

from datetime import date

def check_single_sample_lanes(instrument_type):

print("")

def find_undetermined_index_over_time(index_to_be_searched, instrument_type):

print("{}_{} {}".format(FCid, lane[0], lane[1]))

def undet_index_to_projects(index_to_be_searched, instrument_type, min_occurences=0):

sys.stdout.write('\n')

def fetch_undermined_stats():

print("{}\t{}\t{}".format(twenty_most_occuring_undet[0], twenty_most_occuring_undet[1], twenty_most_occuring_undet[1]/float(lanes_MiSeq_num)))

def fetch_pooled_projects(instrument_type):

print("\t{}".format(pool))

def main(args):

fetch_pooled_projects(args.instrument_type)

if __name__ == '__main__':

parser = argparse.ArgumentParser("""This scripts queries statusdb x_flowcell_db and fetch informaiton about runs.

The following operations are supported:

- check_undet_index: given a specific index checks all FCs and prints all FC and lanes where the indx appears as undetermined

- most_undet: outputs a summary about undetermiend indexes, printing the most 20 most occurring indexes for each instrument type

- single_sample_lanes: prints stats about HiSeqX lanes run with a single sample in it

- workset_undet: prints for each workset the FC, lanes and samples where the specified index has been found in undet. For each sample the plate position is printed.

""")

parser.add_argument('--config', help="configuration file", type=str, required=True)

parser.add_argument('--indexes', help="yamls file containing indexes we want to analyse", type=str)

parser.add_argument('--min_occurences', help="minimum number of occurences in undet in workset_undet mode", type=int, default=0)

parser.add_argument('--mode', help="define what action needs to be executed", type=str, required=True, choices=('check_undet_index', 'most_undet', 'single_sample_lanes', 'workset_undet', 'fetch_pooled_projects'))

parser.add_argument('--index', help="a specifc index (e.g., CTTGTAAT) to be searched across lanes and FCs", type=str)

parser.add_argument('--instrument-type', help="type of instrument", type=str, default=None, choices=('HiSeqX', 'MiSeq', 'HiSeq2500'))

args = parser.parse_args()

main(args)