def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd, cmd_args = comp.make_cmd()
cmd_args = ' '.join(map(str, cmd_args))
#The actual resulting command:
real_command = component_reqs.requirements['R'] + ' --no-save --args'
real_command_args = [
'/share/lustre/dgrewal/Miscellaneous/component_tests/plot_titan/component_test/infile',
'./component_test/plots', '1', '1', '1', '<',
os.path.abspath('./component_seed') + '/plot_titan.R'
]
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd,
'Please recheck the cmd variable in make_cmd')
print cmd_args
print real_command_args
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
for val in real_command_args:
if not val in cmd_args:
self.assertEqual(
True, False,
'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd, cmd_args = comp.make_cmd(chunk=None)
cmd_args = ' '.join(map(str, cmd_args))
#The actual resulting command:
real_command = os.path.join(os.path.abspath('./component_seed'),
'classify.py')
real_command_args = []
print '*' * 50
print cmd_args
print '*' * 50
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd,
'Please recheck the cmd variable in make_cmd')
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
for val in real_command_args:
if not val in cmd_args:
self.assertEqual(
True, False,
'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd, cmd_args = comp.make_cmd(chunk=None)
cmd_args = ' '.join(map(str, cmd_args))
#The actual resulting command:
real_command = component_reqs.requirements[
'python'] + ' ' + os.path.join(os.path.abspath('./component_seed'),
'split_fastq.py')
real_command_args = [
'--input /share/lustre/dgrewal/Miscellaneous/component_tests/split_fastq/component_test/infile',
'--output ./component_test/output', '--range 0:3999'
]
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd,
'Please recheck the cmd variable in make_cmd')
print cmd_args
print real_command_args
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
for val in real_command_args:
if not val in cmd_args:
self.assertEqual(
True, False,
'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd,cmd_args = comp.make_cmd()
cmd_args = ' '.join(map(str,cmd_args))
#The actual resulting command:
real_command = component_reqs.requirements['R']+' --no-save --args'
real_command_args = ['1','./component_test/infile',
'./component_test/cnfile',
'/share/lustre/dgrewal/Miscellaneous/component_tests/test_bam/GRCh37-lite.map.ws_1000.wig',
'1','4','2','./component_test/outfile',
'./component_test/params',
'0','TRUE','1','map','5','1e-300','1e9','1e9','2500','20000','8', 'TRUE',
'./component_test/obj',
'<',os.path.abspath('./component_seed')+'/titan.R']
real_command_args = ' '.join(real_command_args)
print cmd_args
print real_command_args
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd, 'Please recheck the cmd variable in make_cmd')
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
self.assertEqual(real_command_args, cmd_args , 'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd, cmd_args = comp.make_cmd(chunk=None)
cmd_args = ' '.join(map(str, cmd_args))
#The actual resulting command:
real_command = component_reqs.requirements['java'] +' -Xmx4G -jar ' +\
component_reqs.requirements['MarkDuplicates']
real_command_args = [
'INPUT=/sample/path/checks/make_cmd/input.bam',
'OUTPUT=/sample/path/checks/make_cmd/output.bam',
'METRICS=/sample/path/checks/make_cmd/metrics',
'ASSUME_SORTED=TRUE',
'READ_NAME_REGEX="[a-zA-Z0-9]+_[0-9]+:[0-9]+:([0-9]+):([0-9]+):([0-9]+).*"',
'OPTICAL_DUPLICATE_PIXEL_DISTANCE=16',
'MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000',
'VALIDATION_STRINGENCY=LENIENCY',
'TMP_DIR=/sample/path/checks/make_cmd/tmp_dir'
]
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd,
'Please recheck the cmd variable in make_cmd')
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
for val in real_command_args:
if not val in cmd_args:
self.assertEqual(
True, False,
'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd, cmd_args = comp.make_cmd(chunk=None)
cmd_args = ' '.join(map(str, cmd_args))
#The actual resulting command:
real_command = 'sh'
real_command_args = [component_reqs.requirements['bowtie2']
'/sample/path/checks/make_cmd/ref.fa',
'/sample/path/checks/make_cmd/1.fastq',
'/sample/path/checks/make_cmd/2.fastq',
'inputformat=bam',
'filename=/sample/path/checks/make_cmd/input.bam',
'exclude=QCFAIL']
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd, 'Please recheck the cmd variable in make_cmd')
print real_command_args
print cmd_args
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
for val in real_command_args:
if not val in cmd_args:
self.assertEqual(True, False, 'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd, cmd_args = comp.make_cmd()
cmd_args = ' '.join(map(str, cmd_args))
#The actual resulting command:
real_command = component_reqs.requirements[
'python'] + ' ' + os.path.abspath(
'./component_seed') + '/transform_vcf_to_counts.py'
real_command_args = [
'--infile ./component_test/infile',
'--outfile ./component_test/outfile'
]
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd,
'Please recheck the cmd variable in make_cmd')
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
for val in real_command_args:
if not val in cmd_args:
self.assertEqual(
True, False,
'Please recheck the cmd_args list in make_cmd')
def setup_component(self, args):
"""
Create uniform Component instances.
"""
component = component_main.Component()
component.requirements = component_reqs.requirements
component.args = args
return component
def test_component(self):
component = component_main.Component()
component.args = self.args
component.run()
import filecmp
filecmp.cmp(self.args.outfile, '/share/lustre/dgrewal/Miscellaneous/component_tests/calc_correctreads_wig/component_test/outfile_ref')
os.remove(self.args.outfile)
def test_component(self):
component = component_main.Component()
component.args = self.args
component.run()
import filecmp
filecmp.cmp('./component_test/outfile', './component_test/outfile_ref')
os.remove(self.args.out)
def test_component(self):
component = component_main.Component()
component.args = self.args
component.run()
import filecmp
filecmp.cmp(
self.args.output,
'/share/lustre/dgrewal/Miscellaneous/component_tests/split_fastq/component_test/output_ref'
)
os.remove(self.args.output)
def setUp(self):
"""
Set a few common variables.
"""
# Obtain component_test directory
current_dir = os.path.dirname(os.path.abspath(__file__))
self.test_dir = current_dir + "/component_test/"
# Create a tmp directory
comp = component_main.Component()
random_num = int(random.random() * 1000)
self.tmp_dir = "/tmp/test_{{}}_{{}}/".format(comp.component_name, random_num)
os.mkdir(self.tmp_dir)
def test_component(self):
component = component_main.Component()
component.args = self.args
component.run()
import filecmp
filecmp.cmp('./component_test/outfile_seg',
'./component_test/outfile.test.seg')
filecmp.cmp('./component_test/outfile_igv',
'./component_test/outfile.test.txt')
os.remove(self.args.outfile)
os.remove(self.args.outigv)
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd, cmd_args = comp.make_cmd(chunk=None)
cmd_args = ' '.join(map(str, cmd_args))
#The actual resulting command:
real_cmd = component_reqs.requirements['python'] + ' ' + os.path.join(
os.path.abspath('./component_seed/'), 'addPrefixToFastq.py')
real_cmd_args = '--infile ' + self.args.input + ' --outfile ' + self.args.output + ' --prefix ' + self.args.prefix
#Ensure that the commands match exactly
self.assertEqual(real_cmd, cmd,
'Please recheck the cmd variable in make_cmd')
#Ensure that each of the args are present in the command args list
self.assertEqual(real_cmd_args, cmd_args,
'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd,cmd_args = comp.make_cmd()
cmd_args = ' '.join(map(str,cmd_args))
#The actual resulting command:
real_command = component_reqs.requirements['R']+' --no-save --args'
real_command_args = ['1', './component_test/tumour.wig',
'./component_test/normal.wig',
'/share/lustre/dgrewal/Miscellaneous/component_tests/calc_correctreads_wig/component_test/gc.wig',
'/share/lustre/dgrewal/Miscellaneous/component_tests/calc_correctreads_wig/component_test/map.wig',
'./component_test/output.txt', '<',
os.path.abspath('./component_seed')+'/correctReads.R']
real_command_args = ' '.join(real_command_args)
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd, 'Please recheck the cmd variable in make_cmd')
self.assertEqual(real_command_args, cmd_args, 'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd,cmd_args = comp.make_cmd(chunk=None)
cmd_args = ' '.join(map(str,cmd_args))
#The actual resulting command:
real_cmd = component_reqs.requirements['python']+' '+ os.path.join(os.path.abspath('./component_seed'),'pygene_annotation.py')
real_cmd_args = ['--infile ./component_test/infile', '--outfile ./component_test/outfile', '--gene_sets_gtf_bin /share/lustre/dgrewal/Miscellaneous/component_tests/annot_pygenes_titan/component_test/Homo_sapiens.GRCh37.73.gtf.gene_models.binary']
print cmd
print real_cmd
#Ensure that the commands match exactly
self.assertEqual(real_cmd, cmd, 'Please recheck the cmd variable in make_cmd')
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
for val in real_cmd_args:
if not val in cmd_args:
self.assertEqual(True, False, 'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd, cmd_args = comp.make_cmd()
cmd_args = ' '.join(map(str, cmd_args))
#The actual resulting command:
real_command = os.path.abspath('./component_seed') + '/readCounter'
real_command_args = '/share/lustre/dgrewal/Miscellaneous/component_tests/test_bam/DG1136a_5Mbp.bam'+\
' -w1000'+' -q0'+' | '+component_reqs.requirements['python']+\
' '+os.path.abspath('./component_seed')+'/filter_chromosomes.py'+\
' ./component_test/outfile'
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd,
'Please recheck the cmd variable in make_cmd')
print cmd_args
print real_command_args
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
self.assertEqual(real_command_args, cmd_args,
'Please recheck the cmd_args list in make_cmd')
def test_make_cmd(self):
comp = component_main.Component()
comp.args = self.args
cmd,cmd_args = comp.make_cmd(None)
cmd_args = ' '.join(map(str,cmd_args))
#The actual resulting command:
real_command = component_reqs.requirements['python'] + ' ' + os.path.abspath('./component_seed')+'/flagPos.py'
real_command_args = ['--infile '+self.args.infile,
'--db '+self.args.db,
'--out '+self.args.out,
'--string '+self.args.string
]
real_command_args = ' '.join(real_command_args)
#Ensure that the commands match exactly
self.assertEqual(real_command, cmd, 'Please recheck the cmd variable in make_cmd')
#Ensure that each of the args are present in the command args list
#Exact match not possible since order can change
self.assertEqual(cmd_args, real_command_args, 'Please recheck the cmd_args variable in make_cmd')
def test_component(self):
component = component_main.Component()
component.args = self.args
component.run()
shutil.rmtree(self.args.outdir)
def setUp(self):
self.component = component_main.Component()
