"""Unit tests for locuslink-specific classes """ from unittest import TestCase from cogent3.parse.locuslink import ( LinesToLocusLink, LLFinder, _read_accession, _read_accnum, _read_cdd, _read_comp, _read_contig, _read_extannot, _read_go, _read_grif, _read_map, _read_pmid, _read_rell, _read_sts, ) class locuslinkTests(TestCase): """Tests toplevel functions.""" def test_read_accession(self): """_read_accession should perform correct conversions""" self.assertEqual( _read_accession("NP_035835|6755985|na\n"), {"Accession": "NP_035835", "Gi": "6755985", "Strain": "na"}, ) # check that it ignores additional fields self.assertEqual( _read_accession("NG_002740|30172554|na|1|1315\n"), {"Accession": "NG_002740", "Gi": "30172554", "Strain": "na"}, ) def test_read_rell(self): """_read_rell should perform correct conversions""" self.assertEqual( _read_rell("related mRNA|AK090391|n|NM_153775--AK090391\n"), { "Description": "related mRNA", "Id": "AK090391", "IdType": "n", "Printable": "NM_153775--AK090391", }, ) def test_read_accnum(self): """_read_accnum should perform correct conversions""" self.assertEqual( _read_accnum("NG_002740|30172554|na|1|1315\n"), { "Accession": "NG_002740", "Gi": "30172554", "Strain": "na", "Start": "1", "End": "1315", }, ) def test_read_map(self): """_read_map should perform correct conversions""" self.assertEqual( _read_map("10 C1|RefSeq|C|\n"), {"Location": "10 C1", "Source": "RefSeq", "Type": "C"}, ) def test_read_sts(self): """_read_sts should perform correct conversions""" self.assertEqual( _read_sts("RH35858|2|37920|na|seq_map|epcr\n"), { "Name": "RH35858", "Chromosome": "2", "StsId": "37920", "Segment": "na", "SequenceKnown": "seq_map", "Evidence": "epcr", }, ) def test_read_cdd(self): """_read_cdd should perform correct conversions""" self.assertEqual( _read_cdd("Immunoglobulin C-2 Type|smart00408|103|na|4.388540e+01\n"), { "Name": "Immunoglobulin C-2 Type", "Key": "smart00408", "Score": "103", "EValue": "na", "BitScore": "4.388540e+01", }, ) def test_read_comp(self): """_read_comp should perform correct conversions""" self.assertEqual( _read_comp("10090|Map2k6|11|11 cM|26399|17|MAP2K6|ncbi_mgd\n"), { "TaxonId": "10090", "Symbol": "Map2k6", "Chromosome": "11", "Position": "11 cM", "LocusId": "26399", "ChromosomeSelf": "17", "SymbolSelf": "MAP2K6", "MapName": "ncbi_mgd", }, ) def test_read_grif(self): """_read_grif should perform correct conversions""" self.assertEqual( _read_grif("12037672|interaction with pRb\n"), {"PubMedId": "12037672", "Description": "interaction with pRb"}, ) def test_read_pmid(self): """_read_pmid should perform correct conversions""" self.assertEqual( _read_pmid("12875969,12817023,12743034\n"), ["12875969", "12817023", "12743034"], ) def test_read_go(self): """_read_go should perform correct conversions""" self.assertEqual( _read_go("molecular function|zinc ion binding|IEA|GO:0008270|GOA|na\n"), { "Category": "molecular function", "Term": "zinc ion binding", "EvidenceCode": "IEA", "GoId": "GO:0008270", "Source": "GOA", "PubMedId": "na", }, ) def test_read_extannot(self): """_read_extannot should perform correct conversions""" self.assertEqual( _read_extannot("cellular role|Pol II transcription|NR|Proteome|8760285\n"), { "Category": "cellular role", "Term": "Pol II transcription", "EvidenceCode": "NR", "Source": "Proteome", "PubMedId": "8760285", }, ) def test_read_contig(self): """_read_contig should perform correct conversions""" self.assertEqual( _read_contig("NT_011109.15|29800594|na|31124734|31133047|-|19|reference\n"), { "Accession": "NT_011109.15", "Gi": "29800594", "Strain": "na", "From": "31124734", "To": "31133047", "Orientation": "-", "Chromosome": "19", "Assembly": "reference", }, ) def test_LinesToLocusLink(self): """LinesToLocusLink should give expected results on sample data""" fake_file = """>>1 LOCUSID: 1 LOCUS_CONFIRMED: yes LOCUS_TYPE: gene with protein product, function known or inferred ORGANISM: Homo sapiens STATUS: REVIEWED NM: NM_130786|21071029|na NP: NP_570602|21071030 CDD: Immunoglobulin C-2 Type|smart00408|103|na|4.388540e+01 PRODUCT: alpha 1B-glycoprotein ASSEMBLY: AF414429,AK055885,AK056201 CONTIG: NT_011109.15|29800594|na|31124734|31133047|-|19|reference EVID: supported by alignment with mRNA XM: NM_130786|21071029|na XP: NP_570602|21071030|na ACCNUM: AC010642|9929687|na|43581|41119 TYPE: g ACCNUM: AF414429|15778555|na|na|na TYPE: m PROT: AAL07469|15778556 ACCNUM: AK055885|16550723|na|na|na TYPE: m ACCNUM: AK056201|16551539|na|na|na TYPE: m ACCNUM: BC035719|23273475|na|na|na TYPE: m PROT: AAH35719|23273476 ACCNUM: none|na|na|na|na TYPE: p PROT: P04217|23503038 OFFICIAL_SYMBOL: A1BG OFFICIAL_GENE_NAME: alpha-1-B glycoprotein ALIAS_SYMBOL: A1B ALIAS_SYMBOL: ABG ALIAS_SYMBOL: GAB PREFERRED_PRODUCT: alpha 1B-glycoprotein SUMMARY: Summary: The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins. CHR: 19 STS: RH65092|-|10673|na|na|epcr STS: WI-16009|-|52209|na|na|epcr STS: G59506|-|136670|na|na|epcr COMP: 10090|A1bg|na|na|117586|19|A1BG|ncbi_mgd COMP: 10090|A1bg|7|7 cM|117586|19|A1BG|ncbi_mgd BUTTON: unigene.gif LINK: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=390608 UNIGENE: Hs.390608 OMIM: 138670 MAP: 19q13.4|RefSeq|C| MAPLINK: default_human_gene|A1BG BUTTON: snp.gif LINK: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=1 BUTTON: homol.gif LINK: http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=1[loc]&TAXID=9606 BUTTON: ensembl.gif LINK: http://www.ensembl.org/Homo_sapiens/contigview?geneid=NM_130786 BUTTON: ucsc.gif LINK: http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=NM_130786 BUTTON: mgc.gif LINK: http://mgc.nci.nih.gov/Genes/GeneInfo?ORG=Hs&CID=390608 PMID: 12477932,8889549,3458201,2591067 GO: molecular function|molecular_function unknown|ND|GO:0005554|GOA|3458201 GO: biological process|biological_process unknown|ND|GO:0000004|GOA|na GO: cellular component|extracellular|IDA|GO:0005576|GOA|3458201 >>386590 LOCUSID: 386590 LOCUS_CONFIRMED: yes LOCUS_TYPE: gene with protein product, function known or inferred ORGANISM: Danio rerio ACCNUM: AF510108|31323727|na|na|na TYPE: m PROT: AAP47138|31323728 OFFICIAL_SYMBOL: tra1 OFFICIAL_GENE_NAME: tumor rejection antigen (gp96) 1 BUTTON: zfin.gif LINK: http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-031002-1 PMID: 14499652""" records = list(LLFinder(fake_file.split("\n"))) self.assertEqual(len(records), 2) first, second = list(map(LinesToLocusLink, records)) # test the second one first, since it's shorter self.assertEqual(second.LOCUSID, 386590) self.assertEqual(second.LOCUS_CONFIRMED, "yes") self.assertEqual( second.LOCUS_TYPE, "gene with protein product, function known or inferred" ) self.assertEqual(second.ORGANISM, "Danio rerio") self.assertEqual( second.ACCNUM, [ { "Accession": "AF510108", "Gi": "31323727", "Strain": "na", "Start": "na", "End": "na", } ], ) self.assertEqual(second.TYPE, ["m"]) self.assertEqual(second.PROT, [{"Accession": "AAP47138", "Gi": "31323728"}]) self.assertEqual(second.OFFICIAL_SYMBOL, "tra1") self.assertEqual(second.OFFICIAL_GENE_NAME, "tumor rejection antigen (gp96) 1") self.assertEqual(second.BUTTON, ["zfin.gif"]) self.assertEqual( second.LINK, ["http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-031002-1"] ) self.assertEqual(second.PMID, ["14499652"]) # now for the annoying test on the longer record self.assertEqual(first.LOCUSID, 1) self.assertEqual(first.LOCUS_CONFIRMED, "yes") self.assertEqual(first.ORGANISM, "Homo sapiens") self.assertEqual( first.LOCUS_TYPE, "gene with protein product, function known or inferred" ) self.assertEqual(first.STATUS, "REVIEWED") self.assertEqual( first.NM, [{"Accession": "NM_130786", "Gi": "21071029", "Strain": "na"}] ) self.assertEqual(first.NP, [{"Accession": "NP_570602", "Gi": "21071030"}]) self.assertEqual( first.CDD, [ { "Name": "Immunoglobulin C-2 Type", "Key": "smart00408", "Score": "103", "EValue": "na", "BitScore": "4.388540e+01", } ], ) self.assertEqual(first.PRODUCT, ["alpha 1B-glycoprotein"]) self.assertEqual(first.ASSEMBLY, [["AF414429", "AK055885", "AK056201"]]) self.assertEqual( first.CONTIG, [ { "Accession": "NT_011109.15", "Gi": "29800594", "Strain": "na", "From": "31124734", "To": "31133047", "Orientation": "-", "Chromosome": "19", "Assembly": "reference", } ], ) self.assertEqual(first.EVID, ["supported by alignment with mRNA"]) self.assertEqual( first.XM, [{"Accession": "NM_130786", "Gi": "21071029", "Strain": "na"}] ) self.assertEqual( first.XP, [{"Accession": "NP_570602", "Gi": "21071030", "Strain": "na"}] ) self.assertEqual( first.ACCNUM, [ { "Accession": "AC010642", "Gi": "9929687", "Strain": "na", "Start": "43581", "End": "41119", }, { "Accession": "AF414429", "Gi": "15778555", "Strain": "na", "Start": "na", "End": "na", }, { "Accession": "AK055885", "Gi": "16550723", "Strain": "na", "Start": "na", "End": "na", }, { "Accession": "AK056201", "Gi": "16551539", "Strain": "na", "Start": "na", "End": "na", }, { "Accession": "BC035719", "Gi": "23273475", "Strain": "na", "Start": "na", "End": "na", }, { "Accession": "none", "Gi": "na", "Strain": "na", "Start": "na", "End": "na", }, ], ) self.assertEqual(first.TYPE, ["g", "m", "m", "m", "m", "p"]) self.assertEqual( first.PROT, [ {"Accession": "AAL07469", "Gi": "15778556"}, {"Accession": "AAH35719", "Gi": "23273476"}, {"Accession": "P04217", "Gi": "23503038"}, ], ) self.assertEqual(first.OFFICIAL_SYMBOL, "A1BG") self.assertEqual(first.OFFICIAL_GENE_NAME, "alpha-1-B glycoprotein") self.assertEqual(first.ALIAS_SYMBOL, ["A1B", "ABG", "GAB"]) self.assertEqual(first.PREFERRED_PRODUCT, ["alpha 1B-glycoprotein"]) self.assertEqual( first.SUMMARY, [ """Summary: The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins.""" ], ) self.assertEqual(first.CHR, ["19"]) self.assertEqual( first.STS, [ { "Name": "RH65092", "Chromosome": "-", "StsId": "10673", "Segment": "na", "SequenceKnown": "na", "Evidence": "epcr", }, { "Name": "WI-16009", "Chromosome": "-", "StsId": "52209", "Segment": "na", "SequenceKnown": "na", "Evidence": "epcr", }, { "Name": "G59506", "Chromosome": "-", "StsId": "136670", "Segment": "na", "SequenceKnown": "na", "Evidence": "epcr", }, ], ) self.assertEqual( first.COMP, [ { "TaxonId": "10090", "Symbol": "A1bg", "Chromosome": "na", "Position": "na", "LocusId": "117586", "ChromosomeSelf": "19", "SymbolSelf": "A1BG", "MapName": "ncbi_mgd", }, { "TaxonId": "10090", "Symbol": "A1bg", "Chromosome": "7", "Position": "7 cM", "LocusId": "117586", "ChromosomeSelf": "19", "SymbolSelf": "A1BG", "MapName": "ncbi_mgd", }, ], ) self.assertEqual( first.BUTTON, [ "unigene.gif", "snp.gif", "homol.gif", "ensembl.gif", "ucsc.gif", "mgc.gif", ], ) self.assertEqual( first.LINK, [ "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=390608", "http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?locusId=1", "http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=1[loc]&TAXID=9606", "http://www.ensembl.org/Homo_sapiens/contigview?geneid=NM_130786", "http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=NM_130786", "http://mgc.nci.nih.gov/Genes/GeneInfo?ORG=Hs&CID=390608", ], ) self.assertEqual(first.UNIGENE, ["Hs.390608"]) self.assertEqual(first.OMIM, ["138670"]) self.assertEqual( first.MAP, [{"Location": "19q13.4", "Source": "RefSeq", "Type": "C"}] ) self.assertEqual(first.MAPLINK, ["default_human_gene|A1BG"]) self.assertEqual(first.PMID, ["12477932", "8889549", "3458201", "2591067"]) self.assertEqual( first.GO, [ { "Category": "molecular function", "Term": "molecular_function unknown", "EvidenceCode": "ND", "GoId": "GO:0005554", "Source": "GOA", "PubMedId": "3458201", }, { "Category": "biological process", "Term": "biological_process unknown", "EvidenceCode": "ND", "GoId": "GO:0000004", "Source": "GOA", "PubMedId": "na", }, { "Category": "cellular component", "Term": "extracellular", "EvidenceCode": "IDA", "GoId": "GO:0005576", "Source": "GOA", "PubMedId": "3458201", }, ], )