def test_parse_metadata_extra_commas(self):
"""
Tests parsing meta data when extra commas are in the file
Testing the parsing meta data with actual files, instead of mocked files
:return:
"""
sheet_file = path.join(path_to_module, "testValidSheetTrailingCommas",
"SampleSheet.csv")
meta_data = sample_parser.parse_metadata(sheet_file)
correct_metadata = {
"readLengths": "301",
"assay": "TruSeq HT",
"description": "252",
"application": "FASTQ Only",
"investigatorName": "Investigator",
"adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
"adapterread2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
"workflow": "GenerateFASTQ",
"reversecomplement": "0",
"iemfileversion": "4",
"date": "2015-11-12",
"experimentName": "252",
"chemistry": "Amplicon",
"layoutType": "PAIRED_END"
}
self.assertEqual(correct_metadata, meta_data)
def test_build_valid(self):
"""
When given a valid directory, ensure a valid SequencingRun is built with Projects, Samples, ect
:return:
"""
sheet_file = path.join(path_to_module, "fake_ngs_data",
"SampleSheet.csv")
meta_data = sample_parser.parse_metadata(sheet_file)
sequencing_run = sample_parser.build_sequencing_run_from_samples(
sheet_file, meta_data)
# Returns a SequencingRun
self.assertEqual(type(sequencing_run), model.SequencingRun)
# Includes a single project
self.assertEqual(len(sequencing_run.project_list), 1)
# is of type Project
self.assertEqual(type(sequencing_run.project_list[0]), model.Project)
# Project has 3 samples
self.assertEqual(len(sequencing_run.project_list[0].sample_list), 3)
# samples are of type Sample
self.assertEqual(type(sequencing_run.project_list[0].sample_list[0]),
model.Sample)
# samples have SequenceFile
self.assertEqual(
type(sequencing_run.project_list[0].sample_list[0].sequence_file),
model.SequenceFile)
def test_parse_metadata(self):
"""
Testing the parsing meta data with actual files, instead of mocked files
:return:
"""
sheet_file = path.join(path_to_module, "fake_ngs_data",
"SampleSheet.csv")
meta_data = sample_parser.parse_metadata(sheet_file)
correct_metadata = {
"readLengths": "251",
"assay": "Nextera XT",
"description": "Superbug",
"application": "FASTQ Only",
"investigatorName": "Some Guy",
"adapter": "AAAAGGGGAAAAGGGGAAA",
"workflow": "GenerateFASTQ",
"reversecomplement": "0",
"iemfileversion": "4",
"date": "10/15/2013",
"experimentName": "1",
"chemistry": "Amplicon",
"layoutType": "PAIRED_END"
}
self.assertEqual(correct_metadata, meta_data)
def test_parse_metadata_paired_valid(self, mock_csv_reader):
"""
When given a valid directory, ensure valid metadata is built
paired end reads
:return:
"""
h_field_values = ("IEMFileVersion,4\n" +
"Investigator Name,Test Name\n" +
"Experiment Name,Some_Test_Data\n" +
"Date,2015-05-14\n" + "Workflow,GenerateFASTQ\n" +
"Application,FASTQ Only\n" + "Assay,ASDF\n" +
"Description,12-34\n" + "Chemistry,Yes\n")
reads = ("251\n" + "251\n")
d_headers = ("Sample_ID,Sample_Name,Sample_Plate,Sample_Well," +
"I7_Index_ID,index,I5_Index_ID,index2,Sample_Project," +
"Description")
d_field_values = (
"15-0318,,2015-08-05-SE,A01,N701,TAAGGCGA,S502,CTCTCTAT,203\n" +
"15-0455,,2015-08-05-SE,B01,N701,TAAGGCGA,S503,TATCCTCT,203\n" +
"15-0462,,2015-08-05-SE,C01,N701,TAAGGCGA,S505,GTAAGGAG,203\n")
file_contents_str = ("[Header]\n" + "{h_field_values}\n" +
"[Reads]\n" + "{reads}\n" + "[Data]\n" +
"{d_headers}\n" + "{d_field_values}").format(
h_field_values=h_field_values,
reads=reads,
d_headers=d_headers,
d_field_values=d_field_values)
# converts string as a pseudo file / memory file
sample_sheet_file = StringIO(file_contents_str)
# the call to get_csv_reader() inside parse_samples() will return
# items inside side_effect
mock_csv_reader.side_effect = [reader(sample_sheet_file)]
metadata = sample_parser.parse_metadata(None)
# The meta data we care about the most
self.assertEqual(metadata['readLengths'], "251")
self.assertEqual(metadata['layoutType'], "PAIRED_END")
# Other meta data should also be here
self.assertEqual(metadata['iemfileversion'], "4")
self.assertEqual(metadata['investigatorName'], "Test Name")
self.assertEqual(metadata['experimentName'], "Some_Test_Data")
self.assertEqual(metadata['date'], "2015-05-14")
self.assertEqual(metadata['workflow'], "GenerateFASTQ")
self.assertEqual(metadata['application'], "FASTQ Only")
self.assertEqual(metadata['assay'], "ASDF")
self.assertEqual(metadata['description'], "12-34")
self.assertEqual(metadata['chemistry'], "Yes")