def test_report_projects_custom_fields(self):
"""report: report run in 'projects' mode with custom fields
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={
"source": "testing",
"run_number": 87,
"sequencer_model": "MiSeq"
},
project_metadata={
"AB": {
"User": "******",
"Library type": "RNA-seq",
"Organism": "Human",
"PI": "Audrey Bower",
"Sequencer model": "MiSeq"
},
"CDE": {
"User": "******",
"Library type": "ChIP-seq",
"Organism": "Mouse",
"PI": "Colin Delaney Eccleston",
"Sequencer model": "MiSeq"
}
},
top_dir=self.dirn)
mockdir.create()
# Make autoprocess instance and set required metadata
ap = AutoProcess(analysis_dir=mockdir.dirn)
# Generate projects report
expected = """170901\tMISEQ_170901#87\t87\ttesting\t\tAB\tAlison Bell\tAudrey Bower\tRNA-seq\t\tHuman\tMISEQ\tMiSeq\t2\t\tyes\tAB1-2\t%s
170901\tMISEQ_170901#87\t87\ttesting\t\tCDE\tCharles David Edwards\tColin Delaney Eccleston\tChIP-seq\t\tMouse\tMISEQ\tMiSeq\t2\t\tyes\tCDE3-4\t%s
""" % (ap.params.analysis_dir, ap.params.analysis_dir)
custom_fields = [
'datestamp', 'run_id', 'run_number', 'source', 'null', 'project',
'user', 'PI', 'library_type', 'single_cell_platform', 'organism',
'platform', 'sequencer_model', '#samples', '#cells', 'paired_end',
'samples', 'path'
]
for o, e in zip(
report_projects(ap, fields=custom_fields).split('\n'),
expected.split('\n')):
self.assertEqual(o, e)
def test_report_no_projects(self):
"""report: report run with no projects in 'projects' mode
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={
"source": "testing",
"run_number": 87,
"sequencer_model": "MiSeq"
},
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
# Make autoprocess instance and set required metadata
ap = AutoProcess(analysis_dir=mockdir.dirn)
# Generate projects report
expected = ""
for o, e in zip(report_projects(ap).split('\n'), expected.split('\n')):
self.assertEqual(o, e)
def test_report_projects_single_cell(self):
"""report: report single-cell run in 'projects' mode
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={
"source": "testing",
"run_number": 87,
"sequencer_model": "MiSeq"
},
project_metadata={
"AB": {
"User": "******",
"Library type": "scRNA-seq",
"Organism": "Human",
"PI": "Audrey Bower",
"Single cell platform": "ICELL8",
"Number of cells": 1311,
"Sequencer model": "MiSeq"
},
"CDE": {
"User": "******",
"Library type": "ChIP-seq",
"Organism": "Mouse",
"PI": "Colin Delaney Eccleston",
"Sequencer model": "MiSeq"
}
},
top_dir=self.dirn)
mockdir.create()
# Make autoprocess instance and set required metadata
ap = AutoProcess(analysis_dir=mockdir.dirn)
# Generate projects report
expected = """MISEQ_170901#87\t87\ttesting\t\tAlison Bell\tAudrey Bower\tscRNA-seq\tICELL8\tHuman\tMISEQ\t2\t1311\tyes\tAB1-2
MISEQ_170901#87\t87\ttesting\t\tCharles David Edwards\tColin Delaney Eccleston\tChIP-seq\t\tMouse\tMISEQ\t2\t\tyes\tCDE3-4
"""
for o, e in zip(report_projects(ap).split('\n'), expected.split('\n')):
self.assertEqual(o, e)