Python BarcodeCounter.analyse Exemples

Exemple #1

 def test_analyse_with_cutoff(self):
     """BarcodeCounter: perform analysis with cutoff
     """
     bc = BarcodeCounter()
     bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
     bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
     bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
     bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
     bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
     analysis = bc.analyse(lane=1,cutoff=0.013)
     self.assertEqual(analysis.cutoff,0.013)
     self.assertEqual(analysis.mismatches,0)
     self.assertEqual(analysis.total_reads,632402)
     self.assertEqual(analysis.coverage,619228)
     self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
                                         "TATGCGCGGTA",
                                         "CATGCGCGGTA"])
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads,325394)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].reads,285302)
     self.assertEqual(analysis.counts["CATGCGCGGTA"].reads,8532)
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,None)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].sample,None)
     self.assertEqual(analysis.counts["CATGCGCGGTA"].sample,None)
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,1)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences,1)
     self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences,1)

Exemple #2

Fichier : test_barcode_analysis.py Projet : fls-bioinformatics-core/auto_process_ngs

 def test_analyse_with_cutoff(self):
     """BarcodeCounter: perform analysis with cutoff
     """
     bc = BarcodeCounter()
     bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
     bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
     bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
     bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
     bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
     analysis = bc.analyse(lane=1,cutoff=0.013)
     self.assertEqual(analysis.cutoff,0.013)
     self.assertEqual(analysis.mismatches,0)
     self.assertEqual(analysis.total_reads,632402)
     self.assertEqual(analysis.coverage,619228)
     self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
                                         "TATGCGCGGTA",
                                         "CATGCGCGGTA"])
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads,325394)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].reads,285302)
     self.assertEqual(analysis.counts["CATGCGCGGTA"].reads,8532)
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,None)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].sample,None)
     self.assertEqual(analysis.counts["CATGCGCGGTA"].sample,None)
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,1)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences,1)
     self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences,1)

Exemple #3

 def test_analyse_with_no_counts(self):
     """BarcodeCounter: perform analysis for zero counts
     """
     bc = BarcodeCounter()
     analysis = bc.analyse()
     self.assertEqual(analysis.cutoff,None)
     self.assertEqual(analysis.mismatches,0)
     self.assertEqual(analysis.total_reads,0)
     self.assertEqual(analysis.coverage,0)
     self.assertEqual(analysis.barcodes,[])

Exemple #4

Fichier : test_barcode_analysis.py Projet : fls-bioinformatics-core/auto_process_ngs

 def test_analyse_with_no_counts(self):
     """BarcodeCounter: perform analysis for zero counts
     """
     bc = BarcodeCounter()
     analysis = bc.analyse()
     self.assertEqual(analysis.cutoff,None)
     self.assertEqual(analysis.mismatches,0)
     self.assertEqual(analysis.total_reads,0)
     self.assertEqual(analysis.coverage,0)
     self.assertEqual(analysis.barcodes,[])

Exemple #5

    def test_report_barcodes_for_no_counts(self):
        """report_barcodes: check output when there are no counts
        """
        bc = BarcodeCounter()
        analysis = bc.analyse()
        reporter = report_barcodes(bc)
        # Check content
        self.assertEqual(str(reporter),
                         """Barcode analysis for all lanes
==============================
No barcodes counted""")

Exemple #6

Fichier : test_barcode_analysis.py Projet : fls-bioinformatics-core/auto_process_ngs

    def test_report_barcodes_for_no_counts(self):
        """report_barcodes: check output when there are no counts
        """
        bc = BarcodeCounter()
        analysis = bc.analyse()
        reporter = report_barcodes(bc)
        # Check content
        self.assertEqual(str(reporter),
                         """Barcode analysis for all lanes
==============================
No barcodes counted""")

Exemple #7

    def test_report_barcodes(self):
        """report_barcodes: check output for mismatches and sample sheet
        """
        # Create sample sheet
        sample_sheet_file = self._make_file("SampleSheet.csv",
                                            """[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,SMPL1,,,,A006,CATGCGCGGTA,,
1,SMPL2,,,,A012,GCTGCGCGGTC,,
""")
        # Set up barcode counts
        bc = BarcodeCounter()
        bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
        bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
        bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
        bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
        bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
        analysis = bc.analyse(lane=1,mismatches=2,
                              sample_sheet=sample_sheet_file)
        ##"CATGCGCGGTA","TATGCGCGGTA","GATGCGCGGTA","GCTGCGCGGTA" = 307008
        ##"GCTGCGCGGTC" = 325394
        self.assertEqual(analysis.cutoff,None)
        self.assertEqual(analysis.mismatches,2)
        self.assertEqual(analysis.total_reads,632402)
        self.assertEqual(analysis.coverage,632402)
        self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
                                            "CATGCGCGGTA"])
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads,325394)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].reads,307008)
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,"SMPL2")
        self.assertEqual(analysis.counts["CATGCGCGGTA"].sample,"SMPL1")
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,1)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences,4)
        # Create report
        reporter = report_barcodes(bc,
                                   lane=1,
                                   mismatches=2,
                                   sample_sheet=sample_sheet_file)
        # Check content
        self.assertEqual(str(reporter),
                         """Barcode analysis for lane #1
============================
Barcodes have been grouped by allowing 2 mismatches

#Rank	Index	Sample	N_seqs	N_reads	%reads	(%Total_reads)
    1	GCTGCGCGGTC	SMPL2	1	325394	51.5%	(51.5%)
    2	CATGCGCGGTA	SMPL1	4	307008	48.5%	(100.0%)""")

Exemple #8

Fichier : test_barcode_analysis.py Projet : fls-bioinformatics-core/auto_process_ngs

    def test_report_barcodes(self):
        """report_barcodes: check output for mismatches and sample sheet
        """
        # Create sample sheet
        sample_sheet_file = self._make_file("SampleSheet.csv",
                                            """[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,SMPL1,,,,A006,CATGCGCGGTA,,
1,SMPL2,,,,A012,GCTGCGCGGTC,,
""")
        # Set up barcode counts
        bc = BarcodeCounter()
        bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
        bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
        bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
        bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
        bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
        analysis = bc.analyse(lane=1,mismatches=2,
                              sample_sheet=sample_sheet_file)
        ##"CATGCGCGGTA","TATGCGCGGTA","GATGCGCGGTA","GCTGCGCGGTA" = 307008
        ##"GCTGCGCGGTC" = 325394
        self.assertEqual(analysis.cutoff,None)
        self.assertEqual(analysis.mismatches,2)
        self.assertEqual(analysis.total_reads,632402)
        self.assertEqual(analysis.coverage,632402)
        self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
                                            "CATGCGCGGTA"])
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads,325394)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].reads,307008)
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,"SMPL2")
        self.assertEqual(analysis.counts["CATGCGCGGTA"].sample,"SMPL1")
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,1)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences,4)
        # Create report
        reporter = report_barcodes(bc,
                                   lane=1,
                                   mismatches=2,
                                   sample_sheet=sample_sheet_file)
        # Check content
        self.assertEqual(str(reporter),
                         """Barcode analysis for lane #1
============================
Barcodes have been grouped by allowing 2 mismatches

#Rank	Index	Sample	N_seqs	N_reads	%reads	(%Total_reads)
    1	GCTGCGCGGTC	SMPL2	1	325394	51.5%	(51.5%)
    2	CATGCGCGGTA	SMPL1	4	307008	48.5%	(100.0%)""")

Exemple #9

    def test_analyse_with_sample_sheet(self):
        """BarcodeCounter: perform analysis with samplesheet
        """
        # Create sample sheet
        sample_sheet_file = self._make_file("SampleSheet.csv",
                                            """[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,SMPL1,,,,A006,CATGCGCGGTA,,
1,SMPL2,,,,A012,GCTGCGCGGTC,,
2,SMPL3,,,,A005,ACAGTGCGGTA,,
2,SMPL4,,,,A019,GTGAAACGGTC,,
""")
        # Set up barcode counts
        bc = BarcodeCounter()
        bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
        bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
        bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
        bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
        bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
        analysis = bc.analyse(lane=1,sample_sheet=sample_sheet_file)
        self.assertEqual(analysis.cutoff,None)
        self.assertEqual(analysis.mismatches,0)
        self.assertEqual(analysis.total_reads,632402)
        self.assertEqual(analysis.coverage,632402)
        self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
                                            "TATGCGCGGTA",
                                            "CATGCGCGGTA",
                                            "GCTGCGCGGTA",
                                            "GATGCGCGGTA"])
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads,325394)
        self.assertEqual(analysis.counts["TATGCGCGGTA"].reads,285302)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].reads,8532)
        self.assertEqual(analysis.counts["GCTGCGCGGTA"].reads,7853)
        self.assertEqual(analysis.counts["GATGCGCGGTA"].reads,5321)
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,"SMPL2")
        self.assertEqual(analysis.counts["TATGCGCGGTA"].sample,None)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].sample,"SMPL1")
        self.assertEqual(analysis.counts["GCTGCGCGGTA"].sample,None)
        self.assertEqual(analysis.counts["GATGCGCGGTA"].sample,None)
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,1)
        self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences,1)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences,1)
        self.assertEqual(analysis.counts["GCTGCGCGGTA"].sequences,1)
        self.assertEqual(analysis.counts["GATGCGCGGTA"].sequences,1)

Exemple #10

Fichier : test_barcode_analysis.py Projet : fls-bioinformatics-core/auto_process_ngs

    def test_analyse_with_sample_sheet(self):
        """BarcodeCounter: perform analysis with samplesheet
        """
        # Create sample sheet
        sample_sheet_file = self._make_file("SampleSheet.csv",
                                            """[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,SMPL1,,,,A006,CATGCGCGGTA,,
1,SMPL2,,,,A012,GCTGCGCGGTC,,
2,SMPL3,,,,A005,ACAGTGCGGTA,,
2,SMPL4,,,,A019,GTGAAACGGTC,,
""")
        # Set up barcode counts
        bc = BarcodeCounter()
        bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
        bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
        bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
        bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
        bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
        analysis = bc.analyse(lane=1,sample_sheet=sample_sheet_file)
        self.assertEqual(analysis.cutoff,None)
        self.assertEqual(analysis.mismatches,0)
        self.assertEqual(analysis.total_reads,632402)
        self.assertEqual(analysis.coverage,632402)
        self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
                                            "TATGCGCGGTA",
                                            "CATGCGCGGTA",
                                            "GCTGCGCGGTA",
                                            "GATGCGCGGTA"])
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads,325394)
        self.assertEqual(analysis.counts["TATGCGCGGTA"].reads,285302)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].reads,8532)
        self.assertEqual(analysis.counts["GCTGCGCGGTA"].reads,7853)
        self.assertEqual(analysis.counts["GATGCGCGGTA"].reads,5321)
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,"SMPL2")
        self.assertEqual(analysis.counts["TATGCGCGGTA"].sample,None)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].sample,"SMPL1")
        self.assertEqual(analysis.counts["GCTGCGCGGTA"].sample,None)
        self.assertEqual(analysis.counts["GATGCGCGGTA"].sample,None)
        self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,1)
        self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences,1)
        self.assertEqual(analysis.counts["CATGCGCGGTA"].sequences,1)
        self.assertEqual(analysis.counts["GCTGCGCGGTA"].sequences,1)
        self.assertEqual(analysis.counts["GATGCGCGGTA"].sequences,1)

Exemple #11

 def test_analyse_groups(self):
     """BarcodeCounter: perform analysis with grouping
     """
     bc = BarcodeCounter()
     bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
     bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
     bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
     bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
     bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
     analysis = bc.analyse(lane=1,mismatches=1)
     ##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
     ##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
     self.assertEqual(analysis.cutoff,None)
     self.assertEqual(analysis.mismatches,1)
     self.assertEqual(analysis.total_reads,632402)
     self.assertEqual(analysis.coverage,632402)
     self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
                                         "TATGCGCGGTA"])
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads,333247)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].reads,299155)
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,None)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].sample,None)
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,2)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences,3)

Exemple #12

Fichier : test_barcode_analysis.py Projet : fls-bioinformatics-core/auto_process_ngs

 def test_analyse_groups(self):
     """BarcodeCounter: perform analysis with grouping
     """
     bc = BarcodeCounter()
     bc.count_barcode("TATGCGCGGTA",lane=1,incr=285302)
     bc.count_barcode("CATGCGCGGTA",lane=1,incr=8532)
     bc.count_barcode("GATGCGCGGTA",lane=1,incr=5321)
     bc.count_barcode("GCTGCGCGGTA",lane=1,incr=7853)
     bc.count_barcode("GCTGCGCGGTC",lane=1,incr=325394)
     analysis = bc.analyse(lane=1,mismatches=1)
     ##"TATGCGCGGTA","CATGCGCGGTA","GATGCGCGGTA" = 299155
     ##"GCTGCGCGGTC","GCTGCGCGGTA" = 333247
     self.assertEqual(analysis.cutoff,None)
     self.assertEqual(analysis.mismatches,1)
     self.assertEqual(analysis.total_reads,632402)
     self.assertEqual(analysis.coverage,632402)
     self.assertEqual(analysis.barcodes,["GCTGCGCGGTC",
                                         "TATGCGCGGTA"])
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].reads,333247)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].reads,299155)
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].sample,None)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].sample,None)
     self.assertEqual(analysis.counts["GCTGCGCGGTC"].sequences,2)
     self.assertEqual(analysis.counts["TATGCGCGGTA"].sequences,3)