from unittest import TestCase from cogent3.parse.greengenes import ( MinimalGreengenesParser, SpecificGreengenesParser, make_ignore_f, ) # consider project name # remember to add yourself if you make changes class ParseGreengenesRecordsTests(TestCase): def setUp(self): pass def test_MinimalGreengenesParser_mock(self): """Test MinimalGreengenesParser against mock data""" res = MinimalGreengenesParser( mock_data.splitlines(), RecStart="my_starting", RecEnd="my_ending" ) records = list(res) exp = [ {"a": "1", "b": "2", "c": "3", "d": "", "e": "5"}, {"q": "asdasd", "c": "taco"}, ] self.assertEqual(records, exp) def test_MinimalGreengenesParser_real(self): """Test MinimalGreengenesParser against real data""" res = MinimalGreengenesParser(real_data.splitlines()) record1, record2 = list(res) self.assertEqual(record1["G2_chip_tax_string"], "Unclassified") self.assertEqual( record1["authors"], "Hernanandez-Eugenio,G., Silva-Rojas,H.V., Zelaya-Molina,L.X.", ) self.assertEqual(record1["bel3_div_ratio"], "") self.assertEqual(len(record1), 72) self.assertEqual(record2["ncbi_acc_w_ver"], "FJ832719.1") self.assertEqual(record2["timestamp"], "2010-03-23 14:08:27") self.assertEqual( record2["title"], "Developmental Microbial Ecology of the Crop of the Folivorous Hoatzin", ) def test_SpecificGreengenesParser_real(self): """Test SpecificGreengenesParser against real data""" fields = ["prokMSA_id", "journal"] res = SpecificGreengenesParser(real_data.splitlines(), fields) records = list(res) exp = [("604868", ""), ("604867", "ISME J (2010) In press")] self.assertEqual(records, exp) ids = ["604867", "12312312323"] res = SpecificGreengenesParser(real_data.splitlines(), fields, ids) records = list(res) exp = [("604867", "ISME J (2010) In press")] self.assertEqual(records, exp) def test_make_ignore_f(self): """Properly ignore empty records and the start line""" f = make_ignore_f("testing") self.assertFalse(f(["asasdasd", ""])) self.assertFalse(f(["test", ""])) self.assertFalse(f(["testing2", ""])) self.assertFalse(f(["testing", "asd"])) self.assertTrue(f(["", ""])) self.assertTrue(f(None)) self.assertTrue(f(["", ""])) self.assertTrue(f(["testing", ""])) mock_data = """my_starting a=1 b=2 c=3 d= e=5 my_ending my_starting q=asdasd c=taco my_ending """ real_data = """BEGIN G2_chip_tax_string=Unclassified G2_chip_tax_string_format_2=Unclassified HOMD_tax_string= HOMD_tax_string_format_2= Hugenholtz_tax_string=Unclassified Hugenholtz_tax_string_format_2=Unclassified Ludwig_tax_string=Unclassified Ludwig_tax_string_format_2=Unclassified Pace_tax_string=Unclassified Pace_tax_string_format_2=Unclassified RDP_tax_string=Unclassified RDP_tax_string_format_2=Unclassified Silva_tax_string=Unclassified Silva_tax_string_format_2=Unclassified authors=Hernanandez-Eugenio,G., Silva-Rojas,H.V., Zelaya-Molina,L.X. bel3_div_ratio= bellerophon= blast_perc_ident_to_template= clone=51a contact_info=Irrigacion, Universidad Autonoma Chapingo, Carretera Mexico-Texcoco Km 37.5, Texcoco, Mexico 56230, Mexico core_set_member= core_set_member2= country=Mexico: Mexico City create_date=21-NOV-2009 db_name= decision=clone description=Uncultured bacterium clone 51a 16S ribosomal RNA gene, partial sequence email= gold_id= img_oid= isolate= isolation_source=mesophilic anaerobic reactor fed with effluent from the chemical industry journal= longest_insertion= medline_ids= ncbi_acc= ncbi_acc_w_ver=FJ461956.1 ncbi_gi=213390944 ncbi_seq_length=1512 ncbi_tax_id=77133 ncbi_tax_string=Bacteria; environmental samples ncbi_tax_string_format_2=Unclassified non_ACGT_count= non_ACGT_percent= note= organism=uncultured bacterium perc_ident_to_invariant_core= prokMSA_id=604868 prokMSAname=Microbial ecology industrial digestor mesophilic anaerobic reactor fed effluent chemical industry clone 51a pubmed_ids= remark= replaced_by= single_nt_runs_over_7= small_gap_intrusions= source=uncultured bacterium span_aligned=1..2 specific_host= status=0 strain= study_id=38002 sub_species= submit_date=24-OCT-2008 template= timestamp=2010-03-23 14:08:27 title=Microbial ecology of industrial anaerobic digestor unaligned_length= update_date=21-NOV-2009 warning= wigeon95= wigeon99= wigeon_std_dev= aligned_seq=unaligned END BEGIN G2_chip_tax_string=Unclassified G2_chip_tax_string_format_2=Unclassified HOMD_tax_string= HOMD_tax_string_format_2= Hugenholtz_tax_string=Unclassified Hugenholtz_tax_string_format_2=Unclassified Ludwig_tax_string=Unclassified Ludwig_tax_string_format_2=Unclassified Pace_tax_string=Unclassified Pace_tax_string_format_2=Unclassified RDP_tax_string=Unclassified RDP_tax_string_format_2=Unclassified Silva_tax_string=Unclassified Silva_tax_string_format_2=Unclassified authors=Brodie,E.L., Dominguez-Bello,M.G., Garcia-Amado,M.A., Godoy-Vitorino,F., Goldfarb,K.C., Michelangeli,F. bel3_div_ratio= bellerophon= blast_perc_ident_to_template= clone=J3Q101_11C02 contact_info=Biology, University of Puerto Rico, Rio Piedras Campus, PO Box 23360, San Juan, PR 00931-3360, USA core_set_member= core_set_member2= country=Venezuela create_date=10-DEC-2009 db_name= decision=clone description=Uncultured bacterium clone J3Q101_11C02 16S ribosomal RNA gene, partial sequence email= gold_id= img_oid= isolate= isolation_source=crop contents journal=ISME J (2010) In press longest_insertion= medline_ids= ncbi_acc= ncbi_acc_w_ver=FJ832719.1 ncbi_gi=226447371 ncbi_seq_length=1326 ncbi_tax_id=77133 ncbi_tax_string=Bacteria; environmental samples ncbi_tax_string_format_2=Unclassified non_ACGT_count= non_ACGT_percent= note= organism=uncultured bacterium perc_ident_to_invariant_core= prokMSA_id=604867 prokMSAname=Microbial Ecology Crop Folivorous Hoatzin crop contents clone J3Q101_11C02 pubmed_ids= remark= replaced_by= single_nt_runs_over_7= small_gap_intrusions= source=uncultured bacterium span_aligned=1..2 specific_host= status=0 strain= study_id=37901 sub_species= submit_date=16-MAR-2009 template= timestamp=2010-03-23 14:08:27 title=Developmental Microbial Ecology of the Crop of the Folivorous Hoatzin unaligned_length= update_date=10-DEC-2009 warning= wigeon95= wigeon99= wigeon_std_dev= aligned_seq=unaligned END """