def _prepare():
from std_logger import logger
from helpers import measure_time
import os
import argparse
import time
parser = argparse.ArgumentParser(description='Prepare experiment data for ivi tool')
parser.add_argument('--out', action="store", help='path of output file', type=str,)
parser.add_argument('--unmatched', action="store", help='path of file for writing unmatched'
' hits', type=str,)
parser.add_argument('--tolerance.mz', dest="mztol", action='store', default=20.0, type=float,
help="tolerance in ppm for matching peptide hits and MS2 spectra")
parser.add_argument('--tolerance.rt', dest="rttol", action='store', default=5.0, type=float,
help="tolerance in seconds for matching peptide hits and MS2 spectra")
parser.add_argument('experiment_root_path')
args = parser.parse_args()
root = args.experiment_root_path
out_file = args.out
if out_file is None:
out_file = os.path.join(root, "collected.ivi")
if not out_file.endswith(".ivi"):
raise Exception("please provide file extension .ivi for OUT argument")
unmatched_hits_file = args.unmatched
if unmatched_hits_file is not None:
if not unmatched_hits_file.endswith(".txt"):
raise Exception("please provide file extension .txt for UNMATCHED argument")
mz_tolerance = args.mztol
rt_tolerance = args.rttol
logger.info("got argument mz_tolerance=%.2f ppm" % mz_tolerance)
logger.info("got argument rt_tolerance=%.2f seconds" % rt_tolerance)
logger.info("got argument experiment_root_path=%s" % root)
logger.info("got argument out=%s" % out_file)
logger.info("got argument unmatched=%s" % (unmatched_hits_file or "(None)"))
def _create_dir_for(path):
dirname = os.path.dirname(os.path.abspath(path))
if not os.path.exists(dirname):
logger.info("create directory %s" % dirname)
os.makedirs(dirname)
_create_dir_for(out_file)
if unmatched_hits_file is not None:
_create_dir_for(unmatched_hits_file)
from lib import CollectHitsData
from lib.compress_io import CompressedDataReader
smiles = r"""
_____ _____ _____ _____
.' '. .' '. .' '. .' '.
/ o o \ / o o \ / o o \ / o o \
| | | | | | | |
| \ / | | \ / | | \ / | | \ / |
\ '---' / \ '---' / \ '---' / \ '---' /
jgs '._____.' '._____.' '._____.' '._____.' """.split("\n")
collector = CollectHitsData(root)
collector.collect(out_file, unmatched_hits_file, mz_tolerance, rt_tolerance)
logger.info("")
logger.info("")
for line in smiles:
logger.info(" %s" % line)
logger.info("")
logger.info("")
logger.info("=" * 80)
logger.info("you can inspect your data now running")
logger.info("")
logger.info("ivi %s" % out_file)
logger.info("")
logger.info("from your commandline")
logger.info("=" * 80)
logger.info("")
def _create_dir_for(path):
dirname = os.path.dirname(os.path.abspath(path))
if not os.path.exists(dirname):
logger.info("create directory %s" % dirname)
os.makedirs(dirname)
def measure_time(job_description):
start_at = time.time()
logger.info("start %s" % job_description)
yield
needed = time.time() - start_at
logger.info("%s needed %s" % (job_description, format_seconds(needed)))