def test_report_summary_single_cell(self):
"""report: report single-cell run in 'summary' mode
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={
"source": "testing",
"run_number": 87,
"bcl2fastq_software":
"('/usr/bin/bcl2fastq', 'bcl2fastq', '2.17.1.14')",
"cellranger_software":
"('/usr/bin/cellranger', 'cellranger', '3.0.1')",
"assay": "Nextera"
},
project_metadata={
"AB": {
"User": "******",
"Library type": "scRNA-seq",
"Organism": "Human",
"PI": "Audrey Bower",
"Single cell platform": "ICELL8",
"Number of cells": 1311
},
"CDE": {
"User": "******",
"Library type": "ChIP-seq",
"Organism": "Mouse",
"PI": "Colin Delaney Eccleston",
"Comments": "Repeat of previous run"
}
},
top_dir=self.dirn)
mockdir.create()
# Make autoprocess instance
ap = AutoProcess(analysis_dir=mockdir.dirn)
# Generate summary report
expected = """MISEQ run #87 datestamped 170901
================================
Run name : 170901_M00879_0087_000000000-AGEW9
Reference : MISEQ_170901#87
Platform : MISEQ
Directory : %s
Endedness : Paired end
Bcl2fastq : bcl2fastq 2.17.1.14
Cellranger: cellranger 3.0.1
Assay : Nextera
2 projects:
- 'AB': Alison Bell Human scRNA-seq (ICELL8) 2 samples/1311 cells (PI Audrey Bower)
- 'CDE': Charles David Edwards Mouse ChIP-seq 2 samples (PI Colin Delaney Eccleston)
Additional notes/comments:
- CDE: Repeat of previous run
""" % mockdir.dirn
for o, e in zip(report_summary(ap).split('\n'), expected.split('\n')):
self.assertEqual(o, e)
def test_report_summary(self):
"""report: report run in 'summary' 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": "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",
"Comments": "Repeat of previous run"
}
},
top_dir=self.dirn)
mockdir.create()
# Make autoprocess instance
ap = AutoProcess(analysis_dir=mockdir.dirn)
# Generate summary report
expected = """MISEQ run #87 datestamped 170901
================================
Run name : 170901_M00879_0087_000000000-AGEW9
Reference: MISEQ_170901#87
Platform : MISEQ
Sequencer: MiSeq
Directory: %s
Endedness: Paired end
Bcl2fastq: Unknown
2 projects:
- 'AB': Alison Bell Human RNA-seq 2 samples (PI Audrey Bower)
- 'CDE': Charles David Edwards Mouse ChIP-seq 2 samples (PI Colin Delaney Eccleston)
Additional notes/comments:
- CDE: Repeat of previous run
""" % mockdir.dirn
for o, e in zip(report_summary(ap).split('\n'), expected.split('\n')):
self.assertEqual(o, e)
def test_report_summary_no_projects(self):
"""report: report run with no projects in 'summary' mode
"""
# Make a mock auto-process directory
mockdir = MockAnalysisDirFactory.bcl2fastq2(
'170901_M00879_0087_000000000-AGEW9',
'miseq',
metadata={
"source": "testing",
"run_number": 87,
"processing_software":
"{ 'bcl2fastq': ('/usr/bin/bcl2fastq', 'bcl2fastq', '2.17.1.14'), 'cellranger': ('/usr/bin/cellranger', 'cellranger', '3.0.1') }",
"bcl2fastq_software":
"('/usr/bin/bcl2fastq', 'bcl2fastq', '2.17.1.14')",
"cellranger_software":
"('/usr/bin/cellranger', 'cellranger', '3.0.1')",
"sequencer_model": "MiSeq"
},
top_dir=self.dirn)
mockdir.create(no_project_dirs=True)
# Make autoprocess instance
ap = AutoProcess(analysis_dir=mockdir.dirn)
# Generate summary report
expected = """MISEQ run #87 datestamped 170901
================================
Run name : 170901_M00879_0087_000000000-AGEW9
Reference : MISEQ_170901#87
Platform : MISEQ
Sequencer : MiSeq
Directory : %s
Endedness : Paired end
Bcl2fastq : bcl2fastq 2.17.1.14
Cellranger: cellranger 3.0.1
No projects found; 'bcl2fastq' directory contains the following data:
- 'AB': 2 samples
- 'CDE': 2 samples""" % mockdir.dirn
report = report_summary(ap)
self.assertEqual(len(report.split('\n')), len(expected.split('\n')))
for o, e in zip(report.split('\n'), expected.split('\n')):
self.assertEqual(o, e)