def test_params_form(self):
# -------------------
# VCF file test
# -------------------
self.assertTrue(self.dataset_vcf.is_vcf_file(), "Should be a VCF file")
self.assertTrue(not self.dataset_vcf.is_fastq_file(),
"Should not be FastQ file")
self.assertEqual(self.dataset_vcf.get_file_patterns(),\
GENTB_VCF_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_vcf)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(
script_directory)
print script_command
self.assertTrue(script_command is not None)
#if script_command is not NOne:
# pipeline_runner.step3_run_command(script_command)
# -------------------
# FastQ file test
# -------------------
self.assertTrue(not self.dataset_fastq.is_vcf_file(),
"Should NOT be a VCF file")
self.assertTrue(self.dataset_fastq.is_fastq_file(),
"Should be a FastQ file")
self.assertEqual(self.dataset_fastq.get_file_patterns(),\
GENTB_FASTQ_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_fastq)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(
script_directory)
print script_command
self.assertTrue(script_command is not None)
