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#!/usr/bin/env python
"""Unit tests for locuslink-specific classes
"""
from cogent.parse.locuslink import ll_start,LLFinder,pipes,first_pipe,commas, \
_read_accession, _read_rell, _read_accnum, \
_read_map, _read_sts, _read_comp, _read_grif, _read_pmid, _read_go, \
_read_extannot, _read_cdd, _read_contig, LocusLink, LinesToLocusLink
from cogent.util.unit_test import TestCase, main
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
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 = 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'},
])
if __name__ == '__main__':
main()
|
