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171 lines (157 loc) · 8.44 KB
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from PRIMeval import PRIMeval
import urllib3
import json
import yaml
import os
__author__ = "Rick Conzemius"
__copyright__ = "Copyright 2019, Rick Conzemius"
__license__ = "MIT"
__maintainer__ = "Rick Conzemius"
__version__ = "1.0"
__email__ = "rick.conzemius.fl@ait.ac.at"
__status__ = "Production"
key = "publickey"
update_url = "http://update_url/"
upload_url = "http://upload_url/"
run_folder = os.getcwd() + "/runs/"
def primer_run(run_id):
params_file = run_folder + str(run_id) + "/params.txt"
with open(params_file, 'r') as stream:
try:
params = yaml.load(stream)
except yaml.YAMLError as exc:
return False
primer_mismatches = params['primerMismatchesTotal']
probe_mismatches = params['probeMismatchesTotal']
max_product_size = params['productLength']
cross_check = params['crossCheck']
dimer_check = params['dimerCheck']
probes_only = params['checkProbesOnly']
method = params['method']
primerMonovalentCations = params['primerMonovalentCations']
primerDivalentCations = params['primerDivalentCations']
primerDNTPs = params['primerDNTPs']
primerConcentration = params['primerConcentration']
primerAnnealingTemp = params['primerAnnealingTemp']
probeMonovalentCations = params['probeMonovalentCations']
probeDivalentCations = params['probeDivalentCations']
probeDNTPs = params['probeDNTPs']
probeConcentration = params['probeConcentration']
probeAnnealingTemp = params['probeAnnealingTemp']
dbs = params['dbs']
pe = PRIMevalRun(run_id, primer_mismatches, probe_mismatches, max_product_size, cross_check, probes_only, method, dimer_check,
primerMonovalentCations, primerDivalentCations, primerDNTPs, primerConcentration, primerAnnealingTemp,
probeMonovalentCations, probeDivalentCations, probeDNTPs, probeConcentration, probeAnnealingTemp, dbs)
return pe.run_analysis()
def upload_results(runid):
update_status(runid, "Upload", "Queued", 0, 1)
update_status(runid, "Upload", "Upload", 1, 0)
http = urllib3.PoolManager()
file1 = run_folder + str(runid) + "/output/all_hits.csv"
file2 = run_folder + str(runid) + "/output/results.csv"
file3 = run_folder + str(runid) + "/output/results_wobbled.csv"
file4 = run_folder + str(runid) + "/output/results_dimers.xlsx"
with open(file1) as fp1:
file_data1 = fp1.read()
with open(file2) as fp2:
file_data2 = fp2.read()
with open(file3) as fp3:
file_data3 = fp3.read()
if os.path.isfile(file4):
with open(file4, "rb") as fp4:
file_data4 = fp4.read()
try:
if os.path.isfile(file4):
r = http.request("POST", upload_url + str(runid), fields={'hits': ('all_hits.csv', file_data1),
'results_all': ('results.csv', file_data2),
'results_wob': ('results_wobbled.csv', file_data3),
'results_dimer': ('results_dimers.xlsx', file_data4),
'runid': runid, })
else:
r = http.request("POST", upload_url + str(runid), fields={'hits': ('all_hits.csv', file_data1),
'results_all': ('results.csv', file_data2),
'results_wob': ('results_wobbled.csv', file_data3),
'runid': runid, })
success = json.loads(r.data.decode("utf-8"))
if success['upload_is_valid'] == False:
update_status(runid, "Upload", "Upload", 0, 0)
return False
except:
update_status(runid, "Upload", "Upload", 0, 0)
return False
update_status(runid, "Upload", "Upload", 0, 1)
return True
def update_status(run_id, step, substep, running, finished, error_msg = ""):
http = urllib3.PoolManager()
http.request('GET', update_url + str(run_id) + "/" + str(step) + "/" + str(substep) + "/" + str(running) + "/" + str(finished) + "/" + error_msg, retries=10)
print("Status updated for step " + str(step) + "/" + str(substep) + " for run " + str(run_id) + ".")
class PRIMevalRun(PRIMeval):
def run_analysis(self):
self._prepare_folders()
update_status(self.run_id, "PRIMEval", "PreparingFolders", 0, 1)
update_status(self.run_id, "PRIMEval", "ImportingSequences", 1, 0)
self._import_sequences()
update_status(self.run_id, "PRIMEval", "ImportingSequences", 0, 1)
if self.dimer_check == True:
update_status(self.run_id, "PRIMEval", "DimerCheck", 1, 0)
self._run_cross_dimer_check()
self._run_hairpin_check()
self._analyze_cross_dimer_dataframe()
self._save_dimer_checks()
update_status(self.run_id, "PRIMEval", "DimerCheck", 0, 1)
if self.method == "blast":
update_status(self.run_id, "PRIMEval", "CreatingBLASTDB", 1, 0)
self._create_blast_db()
update_status(self.run_id, "PRIMEval", "CreatingBLASTDB", 0, 1)
update_status(self.run_id, "PRIMEval", "RunningBLAST", 1, 0)
self._blast_call()
update_status(self.run_id, "PRIMEval", "RunningBLAST", 0, 1)
if self.method == "bowtie":
update_status(self.run_id, "PRIMEval", "CreatingBowtieIndex", 1, 0)
self._create_bowtie_index()
update_status(self.run_id, "PRIMEval", "CreatingBowtieIndex", 0, 1)
update_status(self.run_id, "PRIMEval", "RunningBowtie", 1, 0)
self._bowtie_call()
self._check_prebuilt_indexes()
self._specificity_calls()
update_status(self.run_id, "PRIMEval", "RunningBowtie", 0, 1)
update_status(self.run_id, "PRIMEval", "ConvertingBowtieHits", 1, 0)
self._multiprocess_convert_bowtie_to_blast()
update_status(self.run_id, "PRIMEval", "ConvertingBowtieHits", 0, 1)
if self.method == "aho-corasick":
update_status(self.run_id, "PRIMEval", "AddOligosToAhoCorasickAutomaton", 1, 0)
self._add_oligos_to_automaton()
update_status(self.run_id, "PRIMEval", "AddOligosToAhoCorasickAutomaton", 0, 1)
update_status(self.run_id, "PRIMEval", "RunningAhoCorasickStringSearch", 1, 0)
self._multiprocess_string_search()
update_status(self.run_id, "PRIMEval", "RunningAhoCorasickStringSearch", 0, 1)
update_status(self.run_id, "PRIMEval", "SplittingOutputFiles", 1, 0)
self._split_output()
update_status(self.run_id, "PRIMEval", "SplittingOutputFiles", 0, 1)
update_status(self.run_id, "PRIMEval", "ProcessingOutputFiles", 1, 0)
self._multiprocess_split_files()
update_status(self.run_id, "PRIMEval", "ProcessingOutputFiles", 0, 1)
if self.probes_only == True:
update_status(self.run_id, "PRIMEval", "ProcessingProbesOnly", 1, 0)
self._process_probes_only()
update_status(self.run_id, "PRIMEval", "ProcessingProbesOnly", 0, 1)
else:
update_status(self.run_id, "PRIMEval", "ProcessingHits", 1, 0)
self._multiprocess_hits()
update_status(self.run_id, "PRIMEval", "ProcessingHits", 0, 1)
update_status(self.run_id, "PRIMEval", "SaveAllResults", 1, 0)
self._save_results()
update_status(self.run_id, "PRIMEval", "SaveAllResults", 0, 1)
update_status(self.run_id, "PRIMEval", "ParseWobbledResults", 1, 0)
self._parse_results_to_wobbled()
update_status(self.run_id, "PRIMEval", "ParseWobbledResults", 0, 1)
update_status(self.run_id, "PRIMEval", "SaveWobbledResults", 1, 0)
self._save_wobbled_results()
update_status(self.run_id, "PRIMEval", "SaveWobbledResults", 0, 1)
update_status(self.run_id, "PRIMEval", "CleanUpFolders", 1, 0)
self._clean_up_folders()
update_status(self.run_id, "PRIMEval", "CleanUpFolders", 0, 1)
update_status(self.run_id, "PRIMEval", "Run", 0, 1)
return True