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()