def test_setup_analysis_dirs_icell8_atac(self):
"""
setup_analysis_dirs: test create new analysis dir for ICELL8 ATAC
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={"instrument_datestamp": "170901"},
paired_end=True,
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
# Add required metadata to 'projects.info'
projects_info = os.path.join(mockdir.dirn, "projects.info")
with open(projects_info, "w") as fp:
fp.write(
"""#Project\tSamples\tUser\tLibrary\tSC_Platform\tOrganism\tPI\tComments
AB\tAB1,AB2\tAlan Brown\tscATAC-seq\tICELL8 ATAC\tHuman\tAudrey Benson\t1% PhiX
""")
# Add ICELL8 ATAC outputs
xlsx_file = os.path.join(mockdir.dirn, "bcl2fastq", "Reports",
"icell8_atac_stats.xlsx")
with open(xlsx_file, 'w') as fp:
fp.write("")
# Expected data
projects = {
"AB": [
"AB1_S1_R1_001.fastq.gz", "AB1_S1_R2_001.fastq.gz",
"AB2_S2_R1_001.fastq.gz", "AB2_S2_R2_001.fastq.gz"
],
"undetermined": [
"Undetermined_S0_R1_001.fastq.gz",
"Undetermined_S0_R2_001.fastq.gz"
]
}
# Check project dirs don't exist
for project in projects:
project_dir_path = os.path.join(mockdir.dirn, project)
self.assertFalse(os.path.exists(project_dir_path))
# Setup the project dirs
ap = AutoProcess(analysis_dir=mockdir.dirn)
setup_analysis_dirs(ap)
# Check project dirs and contents
for project in projects:
project_dir_path = os.path.join(mockdir.dirn, project)
self.assertTrue(os.path.exists(project_dir_path))
# Check README.info file
readme_file = os.path.join(project_dir_path, "README.info")
self.assertTrue(os.path.exists(readme_file))
# Check Fastqs
fastqs_dir = os.path.join(project_dir_path, "fastqs")
self.assertTrue(os.path.exists(fastqs_dir))
for fq in projects[project]:
fastq = os.path.join(fastqs_dir, fq)
self.assertTrue(os.path.exists(fastq))
# Check extra data for ICELL8 ATAC
icell8_atac_xlsx = os.path.join(mockdir.dirn, "AB",
"icell8_atac_stats.xlsx")
self.assertTrue(os.path.exists(icell8_atac_xlsx))
def test_setup_analysis_dirs_with_identifier(self):
"""
setup_analysis_dirs: test create new analysis dirs with an identifier
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={"instrument_datestamp": "170901"},
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
# Check project dirs don't exist
for project in ("AB", "CDE"):
project_dir_path = os.path.join(mockdir.dirn, project)
self.assertFalse(os.path.exists(project_dir_path))
# Add required metadata to 'projects.info'
projects_info = os.path.join(mockdir.dirn, "projects.info")
with open(projects_info, "w") as fp:
fp.write(
"""#Project\tSamples\tUser\tLibrary\tSC_Platform\tOrganism\tPI\tComments
AB\tAB1,AB2\tAlan Brown\tRNA-seq\t.\tHuman\tAudrey Benson\t1% PhiX
CDE\tCDE3,CDE4\tClive David Edwards\tChIP-seq\t.\tMouse\tClaudia Divine Eccleston\t1% PhiX
""")
# Expected data
projects = {
"AB": [
"AB1_S1_R1_001.fastq.gz", "AB1_S1_R2_001.fastq.gz",
"AB2_S2_R1_001.fastq.gz", "AB2_S2_R2_001.fastq.gz"
],
"CDE": [
"CDE3_S3_R1_001.fastq.gz", "CDE3_S3_R2_001.fastq.gz",
"CDE4_S4_R1_001.fastq.gz", "CDE4_S4_R2_001.fastq.gz"
],
"undetermined": [
"Undetermined_S0_R1_001.fastq.gz",
"Undetermined_S0_R1_001.fastq.gz"
]
}
# Setup the project dirs
ap = AutoProcess(analysis_dir=mockdir.dirn)
setup_analysis_dirs(ap, name="test_id")
# Check project dirs and contents
for project in projects:
project_dir_path = os.path.join(mockdir.dirn,
"%s_%s" % (project, "test_id"))
self.assertTrue(os.path.exists(project_dir_path))
# Check README.info file
readme_file = os.path.join(project_dir_path, "README.info")
self.assertTrue(os.path.exists(readme_file))
# Check Fastqs
fastqs_dir = os.path.join(project_dir_path, "fastqs")
self.assertTrue(os.path.exists(fastqs_dir))
for fq in projects[project]:
fastq = os.path.join(fastqs_dir, fq)
self.assertTrue(os.path.exists(fastq))
def test_setup_analysis_dirs_10x_visium(self):
"""
setup_analysis_dirs: test create new analysis dir for 10x Visium
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={"instrument_datestamp": "170901"},
reads=('R1', 'R2', 'R3', 'I1'),
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
print(os.listdir(os.path.join(mockdir.dirn, "bcl2fastq")))
print(os.listdir(os.path.join(mockdir.dirn, "bcl2fastq", "AB")))
# Add required metadata to 'projects.info'
projects_info = os.path.join(mockdir.dirn, "projects.info")
with open(projects_info, "w") as fp:
fp.write(
"""#Project\tSamples\tUser\tLibrary\tSC_Platform\tOrganism\tPI\tComments
AB\tAB1,AB2\tAlan Brown\tscATAC-seq\t10xGenomics Visium\tHuman\tAudrey Benson\t1% PhiX
""")
# Expected data
projects = {
"AB": [
"AB1_S1_R1_001.fastq.gz", "AB1_S1_R2_001.fastq.gz",
"AB1_S1_R3_001.fastq.gz", "AB1_S1_I1_001.fastq.gz",
"AB2_S2_R1_001.fastq.gz", "AB2_S2_R2_001.fastq.gz",
"AB2_S2_R3_001.fastq.gz", "AB2_S2_I1_001.fastq.gz"
],
"undetermined": [
"Undetermined_S0_R1_001.fastq.gz",
]
}
# Check project dirs don't exist
for project in projects:
project_dir_path = os.path.join(mockdir.dirn, project)
self.assertFalse(os.path.exists(project_dir_path))
# Setup the project dirs
ap = AutoProcess(analysis_dir=mockdir.dirn)
setup_analysis_dirs(ap)
# Check project dirs and contents
for project in projects:
project_dir_path = os.path.join(mockdir.dirn, project)
self.assertTrue(os.path.exists(project_dir_path))
# Check README.info file
readme_file = os.path.join(project_dir_path, "README.info")
self.assertTrue(os.path.exists(readme_file))
# Check Fastqs
fastqs_dir = os.path.join(project_dir_path, "fastqs")
self.assertTrue(os.path.exists(fastqs_dir))
for fq in projects[project]:
fastq = os.path.join(fastqs_dir, fq)
self.assertTrue(os.path.exists(fastq))
def test_setup_analysis_dirs_ignore_missing_metadata(self):
"""
setup_analysis_dirs: test create new analysis dirs (ignore missing metadata)
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={"instrument_datestamp": "170901"},
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
# Expected data
projects = {
"AB": [
"AB1_S1_R1_001.fastq.gz", "AB1_S1_R2_001.fastq.gz",
"AB2_S2_R1_001.fastq.gz", "AB2_S2_R2_001.fastq.gz"
],
"CDE": [
"CDE3_S3_R1_001.fastq.gz", "CDE3_S3_R2_001.fastq.gz",
"CDE4_S4_R1_001.fastq.gz", "CDE4_S4_R2_001.fastq.gz"
],
"undetermined": [
"Undetermined_S0_R1_001.fastq.gz",
"Undetermined_S0_R1_001.fastq.gz"
]
}
# Check project dirs don't exist
for project in projects:
project_dir_path = os.path.join(mockdir.dirn, project)
self.assertFalse(os.path.exists(project_dir_path))
# Setup the project dirs
ap = AutoProcess(analysis_dir=mockdir.dirn)
setup_analysis_dirs(ap, ignore_missing_metadata=True)
# Check project dirs and contents
for project in projects:
project_dir_path = os.path.join(mockdir.dirn, project)
self.assertTrue(os.path.exists(project_dir_path))
# Check README.info file
readme_file = os.path.join(project_dir_path, "README.info")
self.assertTrue(os.path.exists(readme_file))
# Check Fastqs
fastqs_dir = os.path.join(project_dir_path, "fastqs")
self.assertTrue(os.path.exists(fastqs_dir))
for fq in projects[project]:
fastq = os.path.join(fastqs_dir, fq)
self.assertTrue(os.path.exists(fastq))