def setUp(self):
if FileUtils.fileExists(settings.TESTDBNAME): os.remove(settings.TESTDBNAME)
settings.DBNAME = settings.TESTDBNAME
init_database()
Session = sessionmaker(bind=settings.ENGINE)
self.session = Session()
def __init__(self, deltafile, refseqs, qryseqs):
self.deltafile = deltafile
self.refseqs = refseqs
self.qryseqs = qryseqs
if not FileUtils.fileExists(self.deltafile):
raise Exception(
"Can't parse Mummer delta file. File [%s] doesn't exist" %
self.deltafile)
def setUp(self):
if FileUtils.fileExists(settings.TESTDBNAME):
os.remove(settings.TESTDBNAME)
settings.DBNAME = settings.TESTDBNAME
init_database()
#input_files = ['pog1.fa','pog2.fa','pog3.fa']
#input_types = ['fasta','fasta','fasta']
#self.ana = Analysis("FastQC")
self.input_files = ["testdata/FoxP2_SL167.fastq"]
self.input_types = ['fastq']
Session = sessionmaker(bind=settings.ENGINE)
self.session = Session()
def testRunMummer(self):
mummer = Mummer()
self.assertTrue(mummer)
self.assertTrue(AnalysisUtils.setInputFiles(mummer,self.input_files,['fasta','fasta']))
runner = AnalysisRunner(mummer)
self.assertTrue(runner.run())
self.assertTrue(len(mummer.output_strings) == 1)
self.assertTrue(mummer.output_strings[0].output_string.index('4: FINISHING DATA') > 0)
self.assertTrue(FileUtils.fileExists('../testout/mummer.delta'))
def checkBinary(self,binfile):
return FileUtils.fileExists(binfile)
def tearDown(self):
deltafile = '../testout/mummer.delta'
if FileUtils.fileExists(deltafile):
os.remove(deltafile)
"""Unit test for Analysis.py"""
import os
import sys
import unittest
import logging
sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/../")
from config import settings
from datamodel.FileUtils import FileUtils
from datamodel.database.DB import Analysis, init_database
from datamodel.database.AnalysisUtils import AnalysisUtils
from sqlalchemy.orm import sessionmaker
if FileUtils.fileExists(settings.TESTLOGFILE): os.remove(settings.TESTLOGFILE)
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
fh = logging.FileHandler(settings.TESTLOGFILE, 'a')
fh.setFormatter(formatter)
log = logging.getLogger() # root logger
for hdlr in log.handlers: # remove all old handlers
log.removeHandler(hdlr)
log.addHandler(fh) # set the new handler
class DBAnalysisTest(unittest.TestCase
def getCommands(self):
if self.commands and len(self.commands) > 0:
return self.commands
logging.info(" ========> Analysis %20s Getting commands" % (self.name))
self.commands = []
self.expected_output_files = []
self.temp_output_files = []
outdir = self.output_dir
tmpdir = self.working_dir
btbin = self.bowtiebindir + self.bowtiebinname
stbin = self.samtoolsbindir + self.samtoolsbinname
self.calculateSpaceNeeded()
if FileUtils.fileExists(btbin) == False:
raise Exception("Binary file [%s] doesn't exist = can't continue" %
btbin)
if FileUtils.fileExists(stbin) == False:
raise Exception("Binary file [%s] doesn't exist = can't continue" %
stbin)
if AnalysisUtils.checkInputFiles(self) == False:
raise Exception("Input files [%s] don't exist = can't continue" %
(self.input_files))
AnalysisUtils.checkDiskSpace(self)
for fobj in self.input_files:
f = fobj.input_file
try:
if f.endswith(".gz"):
# f = "<( zcat -c " + f + " )"
tmpf = f.replace(".gz", "")
fparts = FileUtils.getFileParts(tmpf)
command = "gunzip -c " + f + " > " + tmpdir + "/" + fparts[
'basename']
self.commands.append(command)
self.temp_output_files.append(tmpf)
f = tmpdir + "/" + fparts['basename']
fparts = FileUtils.getFileParts(f)
fstub = fparts['filestub']
bowtieoutfile = tmpdir + "/" + fstub + ".sam"
samtoolsoutfile = tmpdir + "/" + fstub + ".bam"
if self.param == None:
raise Exception(
"No parameters entered for bowtie = needs -x <genomeindex>"
)
command1 = btbin + " " + self.param + " " + f + " | " + stbin + " view -bS - | " + stbin + " sort - " + tmpdir + "/" + fstub
logging.info(" ========> Analysis %20s command 1 : %s" %
(self.name, command1))
#command2 = stbin + " view -bS " + bowtieoutfile + "| " + stbin + " sort - " + tmpdir + "/" + fstub
# logging.info(" ========> Analysis %20s command 2 : %s" % (self.name,command2))
command2 = stbin + " index " + samtoolsoutfile
logging.info(" ========> Analysis %20s command 3 : %s" %
(self.name, command2))
# self.expected_output_files.append(fstub + ".sam")
self.expected_output_files.append(
AnalysisExpectedOutputFile(expected_output_file=fstub +
".bam"))
self.expected_output_files.append(
AnalysisExpectedOutputFile(expected_output_file=fstub +
".bam.bai"))
self.commands.append(AnalysisCommand(command=command1))
self.commands.append(AnalysisCommand(command=command2))
#self.commands.append(command3)
except Exception as e:
logging.info(
" ========> Analysis %20s Failed building command list [%s]"
% (self.name, e))
raise
return self.commands