#!/usr/bin/env python
'''
Module for NGS580 Targetted Exome Analysis using Igor's sns-wes variant calling pipeline
This script will check for the completion of NGS580 demultiplexing, and conditionally run the
'start_NGS580_WES_analysis.sh' script to start the analysis
copy of the script here:
https://github.com/NYU-Molecular-Pathology/protocols/blob/c90653b31d2a65d6df357984e156279ff7f5895c/NGS580/start_NGS580_WES_analysis.sh
'''
# ~~~~~ LOGGING ~~~~~~ #
from util import log
import logging
import os
script_timestamp = log.timestamp()
scriptdir = os.path.dirname(os.path.realpath(__file__))
scriptname = os.path.basename(__file__)
logdir = os.path.join(scriptdir, 'logs')
file_timestamp = log.timestamp()
log_file = os.path.join(scriptdir, logdir,
'{0}.{1}.log'.format(scriptname, file_timestamp))
# add a per-module timestamped logging file handler
logger = log.build_logger(name="NGS580_analysis")
logger.addHandler(
log.create_main_filehandler(log_file=log_file, name="NGS580_analysis"))
# make the file handler global for use elsewhere
main_filehandler = log.get_logger_handler(logger=logger,
handler_name='NGS580_analysis')
logger.debug("loading NGS580_analysis module")
# -*- coding: utf-8 -*-
"""
Runs a series of analysis tasks
Originally designed as an extension to the sns pipeline output, with the flexibility of added ad hoc extra analysis tasks for downstream processing
"""
# ~~~~~ LOGGING ~~~~~~ #
import os
from util import log
import logging
# path to the script's dir
scriptdir = os.path.dirname(os.path.realpath(__file__))
scriptname = os.path.basename(__file__)
script_timestamp = log.timestamp()
# path to parent dir 2 levels above this script
snsxt_parent_dir = os.path.realpath(os.path.dirname(os.path.dirname(__file__)) )
# /ifs/data/molecpathlab/scripts/snsxt/
# dir for logs
log_dir = os.path.join(snsxt_parent_dir, 'logs')
# timestamped subdir for logs
# log_subdir = os.path.join(snsxt_parent_dir, 'logs', script_timestamp)
# set a timestamped log file for debug log
log_file = os.path.join(log_dir, '{0}.{1}.log'.format(scriptname, script_timestamp))
email_log_file = os.path.join(log_dir, '{0}.{1}.email.log'.format(scriptname, script_timestamp))
def logpath():
"""
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
unit tests for the find module
'''
import unittest
import os
from NGS580_demultiplexing import NextSeqRun
from util import log
script_timestamp = log.timestamp()
scriptdir = os.path.dirname(os.path.realpath(__file__))
fixture_dir = os.path.join(scriptdir, "fixtures")
sequencer_dir = os.path.join(fixture_dir, 'NextSeq_runs')
samplesheet_source_dir = os.path.join(fixture_dir, 'to_be_demultiplexed',
'NGS580')
samplesheet_processed_dir = os.path.join(fixture_dir, 'to_be_demultiplexed',
'processed')
configs = {}
configs['sequencer_dir'] = sequencer_dir
configs['email_recipients'] = 'bar'
configs['reply_to_servername'] = 'baz'
configs['scriptdir'] = scriptdir
configs['logdir'] = os.path.join(scriptdir, 'logs')
configs['script_timestamp'] = log.timestamp()
configs['samplesheet_source_dir'] = samplesheet_source_dir
configs['demultiplex_580_script'] = 'zzzzz'
configs['samplesheet_processed_dir'] = samplesheet_processed_dir
configs['seqtype'] = 'NGS580'