From 9e7a861f53c3210981198f530c467cad1af64cd6 Mon Sep 17 00:00:00 2001 From: AroneyS Date: Tue, 17 Dec 2024 14:28:38 +1000 Subject: [PATCH] rename num_binned/assembled/not_found to coverage_binned/assembled/not_found --- singlem/appraiser.py | 6 +++--- test/test_appraise.py | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/singlem/appraiser.py b/singlem/appraiser.py index 0390753b..178cbf44 100644 --- a/singlem/appraiser.py +++ b/singlem/appraiser.py @@ -193,9 +193,9 @@ def print_appraisal(self, appraisal, '''print the Appraisal object overview to STDOUT''' headers = ['sample', 'domain'] - if doing_binning: headers.append('num_binned') - if doing_assembly: headers.append('num_assembled') - headers.append('num_not_found') + if doing_binning: headers.append('coverage_binned') + if doing_assembly: headers.append('coverage_assembled') + headers.append('coverage_not_found') if doing_binning: headers.append('percent_binned') if doing_assembly: headers.append('percent_assembled') output_io.write("\t".join(headers)+"\n") diff --git a/test/test_appraise.py b/test/test_appraise.py index c460b1c6..43aaad5c 100644 --- a/test/test_appraise.py +++ b/test/test_appraise.py @@ -371,7 +371,7 @@ def test_print_appraisal(self): to_print = StringIO() appraiser.print_appraisal(app, packages, True, to_print) - self.assertEqual("sample\tdomain\tnum_binned\tnum_not_found\tpercent_binned\nminimal\td__Archaea\t0\t0\t0.0\nminimal\td__Bacteria\t4\t0\t100.0\nanother\td__Archaea\t0\t0\t0.0\nanother\td__Bacteria\t0\t2\t0.0\ntotal\td__Archaea\t0\t0\t0.0\naverage\td__Archaea\t0.0\t0.0\tnan\ntotal\td__Bacteria\t4\t2\t66.7\naverage\td__Bacteria\t2.0\t1.0\t50.0\n", to_print.getvalue()) + self.assertEqual("sample\tdomain\tcoverage_binned\tcoverage_not_found\tpercent_binned\nminimal\td__Archaea\t0\t0\t0.0\nminimal\td__Bacteria\t4\t0\t100.0\nanother\td__Archaea\t0\t0\t0.0\nanother\td__Bacteria\t0\t2\t0.0\ntotal\td__Archaea\t0\t0\t0.0\naverage\td__Archaea\t0.0\t0.0\tnan\ntotal\td__Bacteria\t4\t2\t66.7\naverage\td__Bacteria\t2.0\t1.0\t50.0\n", to_print.getvalue()) to_print = StringIO() found_otu_table_io = StringIO() @@ -431,7 +431,7 @@ def test_print_assembly_appraise(self): to_print = StringIO() appraiser.print_appraisal(app, packages, True, to_print, doing_assembly=True) - self.assertEqual("sample\tdomain\tnum_binned\tnum_assembled\tnum_not_found\tpercent_binned\tpercent_assembled\nminimal\td__Archaea\t0\t0\t0\t0.0\t0.0\nminimal\td__Bacteria\t0\t4\t0\t0.0\t100.0\nanother\td__Archaea\t0\t0\t0\t0.0\t0.0\nanother\td__Bacteria\t0\t0\t2\t0.0\t0.0\ntotal\td__Archaea\t0\t0\t0\t0.0\t0.0\naverage\td__Archaea\t0.0\t0.0\t0.0\tnan\tnan\ntotal\td__Bacteria\t0\t4\t2\t0.0\t66.7\naverage\td__Bacteria\t0.0\t2.0\t1.0\t0.0\t50.0\n", to_print.getvalue()) + self.assertEqual("sample\tdomain\tcoverage_binned\tcoverage_assembled\tcoverage_not_found\tpercent_binned\tpercent_assembled\nminimal\td__Archaea\t0\t0\t0\t0.0\t0.0\nminimal\td__Bacteria\t0\t4\t0\t0.0\t100.0\nanother\td__Archaea\t0\t0\t0\t0.0\t0.0\nanother\td__Bacteria\t0\t0\t2\t0.0\t0.0\ntotal\td__Archaea\t0\t0\t0\t0.0\t0.0\naverage\td__Archaea\t0.0\t0.0\t0.0\tnan\tnan\ntotal\td__Bacteria\t0\t4\t2\t0.0\t66.7\naverage\td__Bacteria\t0.0\t2.0\t1.0\t0.0\t50.0\n", to_print.getvalue()) to_print = StringIO() found_otu_table_io = StringIO() @@ -517,7 +517,7 @@ def test_print_assembly_appraise_all_binned(self): to_print = StringIO() appraiser.print_appraisal(app, packages, True, to_print, doing_assembly=True) - self.assertEqual("sample\tdomain\tnum_binned\tnum_assembled\tnum_not_found\tpercent_binned\tpercent_assembled\nminimal\td__Archaea\t0\t0\t0\t0.0\t0.0\nminimal\td__Bacteria\t4\t4\t0\t100.0\t100.0\nanother\td__Archaea\t0\t0\t0\t0.0\t0.0\nanother\td__Bacteria\t0\t0\t2\t0.0\t0.0\ntotal\td__Archaea\t0\t0\t0\t0.0\t0.0\naverage\td__Archaea\t0.0\t0.0\t0.0\tnan\tnan\ntotal\td__Bacteria\t4\t4\t2\t66.7\t66.7\naverage\td__Bacteria\t2.0\t2.0\t1.0\t50.0\t50.0\n", to_print.getvalue()) + self.assertEqual("sample\tdomain\tcoverage_binned\tcoverage_assembled\tcoverage_not_found\tpercent_binned\tpercent_assembled\nminimal\td__Archaea\t0\t0\t0\t0.0\t0.0\nminimal\td__Bacteria\t4\t4\t0\t100.0\t100.0\nanother\td__Archaea\t0\t0\t0\t0.0\t0.0\nanother\td__Bacteria\t0\t0\t2\t0.0\t0.0\ntotal\td__Archaea\t0\t0\t0\t0.0\t0.0\naverage\td__Archaea\t0.0\t0.0\t0.0\tnan\tnan\ntotal\td__Bacteria\t4\t4\t2\t66.7\t66.7\naverage\td__Bacteria\t2.0\t2.0\t1.0\t50.0\t50.0\n", to_print.getvalue()) # Check that unbinned is the same as assembled OTUs when no binning is done to_print = StringIO() @@ -1211,7 +1211,7 @@ def test_appraise_default_cutoff(self): cmd = f'{path_to_script} appraise --metagenome-otu-table {f.name} --genome-otu-table {g.name} --imperfect --metapackage {smpkg}' expected_header = "# Appraised using max divergence 2 (97% ANI)\n" - expected = """sample domain num_binned num_not_found percent_binned + expected = """sample domain coverage_binned coverage_not_found percent_binned minimal d__Archaea 0 0 0.0 minimal d__Bacteria 9 4 69.2 total d__Archaea 0 0 0.0