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|
"""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",
},
],
)
|
