exec/testLoadUniprotKBEntries.R
In groupschoof/PhyloFun: Annotates Proteins with Gene Ontology (GO) Terms
require( PhyloFun )
# Accessions of Proteins involved in the following tests:
test.accessions <- c('Q0KFR8','B2AFZ7','Q1LSI9','Protein_1')
# Test extractName
print("Testing extractName(...)")
res.extractName <- extractName(
xmlInternalTreeParse( project.file.path( "Q9ZZX1.xml" ) ),
xpath.prefix='//xmlns:entry/'
)
exp.extractName <- "Q9ZZX1"
checkEquals( res.extractName, exp.extractName )
# With the result of getEntries:
res.extractName <- extractName( getEntries(
readLines( project.file.path( "Q9ZZX1.xml" ) ) )[[ 1 ]] )
exp.extractName <- "Q9ZZX1"
checkEquals( res.extractName, exp.extractName )
# NULL argument should return NULL accession:
checkTrue( is.null( extractName( NULL ) ) )
# Test downloadUniprotDocuments
print("Testing downloadUniprotDocuments(...)")
res.downloadUniprotDocuments <- downloadUniprotDocuments( test.accessions )
# print( res.downloadUniprotDocuments )
checkEquals( length( res.downloadUniprotDocuments ), 3 )
# Test retrieveAnnotationsBiomart
print("Testing retrieveAnnotationsBiomart(...)")
bm.annos <- retrieveAnnotationsBiomart(test.accessions)
# print( bm.annos )
checkEquals( class(bm.annos), 'matrix' )
checkEquals( nrow(bm.annos), 2 )
checkEquals( ncol(bm.annos), 4 )
# print(class(( bm.annos[ 'InterPro', 'Protein_1' ] ) ))
checkEquals( length( unlist( bm.annos[ 'InterPro', 'Protein_1' ] ) ), 0 )
checkEquals( length( unlist( bm.annos[ 'GO', 'Protein_1' ] ) ), 0 )
# print( bm.annos['Q0KFR8', 'InterPro'] )
checkTrue( 'IPR020591' %in% unlist( bm.annos[ 'InterPro', 'Q0KFR8' ] ) )
# print( bm.annos['Q0KFR8', 'GO'] )
checkTrue( 'GO:0005524' %in% unlist( bm.annos[ 'GO', 'Q0KFR8' ] ) )
# Test uniprotkb.url
print("Testing uniprotkb.url(...)")
checkEquals(uniprotkb.url('Q0KFR8'),
'http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprotkb/Q0KFR8/xml')
checkEquals(uniprotkb.url("sp|P34529|DCR1_CAEEL"),
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprotkb/sp%7cP34529%7cDCR1_CAEEL/xml")
checkEquals( uniprotkb.url('Q0KFR8', frmt='fasta'),
'http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprotkb/Q0KFR8/fasta'
)
# Test extractAnnotations
print("Testing extractAnnotations(...)")
d <- xmlInternalTreeParse( project.file.path( "Q9ZZX1.xml" ) )
annos <- extractAnnotations(d, 'InterPro')
# print( d )
# print( annos )
checkTrue(length(annos) > 0)
checkTrue('IPR004860' %in% annos)
annos <- extractAnnotations(d, 'GO')
# print( annos )
checkTrue(length(annos) > 0)
checkTrue('GO:0005739' %in% annos)
annos <- extractAnnotations(d, 'Pfam')
checkTrue(length(annos) > 0)
checkTrue('PF00115' %in% annos)
# Test retrieveAnnotations
print("Testing retrieveAnnotations(...)")
res.retrieveAnnotations <- retrieveAnnotations( d, xpath.prefix='//' )
exp.retrieveAnnotations <- list(
'GO'=c( "GO:0016021", "GO:0005739", "GO:6969696", "GO:0004129",
"GO:0009055", "GO:0004519", "GO:0020037", "GO:0005506",
"GO:0009060", "GO:0006316", "GO:0006397", "GO:0008380" ),
'InterPro'=c( "IPR000883", "IPR023615", "IPR023616", "IPR004860" ),
'Pfam'=c( "PF00115", "PF03161")
)
# print( res.retrieveAnnotations )
# print( exp.retrieveAnnotations )
checkEquals( res.retrieveAnnotations, exp.retrieveAnnotations )
# Test retrieveUniprotAnnotations
# Uniprot constantly changes the annotation of its proteins, hence we
# cannot test for correct annotations.
print("Testing retrieveUniprotAnnotations(...)")
res.retrieveUniprotAnnotations <- retrieveUniprotAnnotations( c( 'sp|Q5ZL72|CH60_CHICK', 'P63039' ) )
checkTrue( ! is.null( res.retrieveUniprotAnnotations ) )
checkEquals( class( res.retrieveUniprotAnnotations ), 'matrix' )
checkEquals( nrow( res.retrieveUniprotAnnotations ), 3 )
checkEquals( rownames( res.retrieveUniprotAnnotations ),
c( 'GO','InterPro','Pfam') )
checkTrue( ncol( res.retrieveUniprotAnnotations ) > 0 )
# Test uniq.annotations
print("Testing uniq.annotations(...)")
fl <- file(project.file.path('test_annotations.tbl'),'r')
an.ma <- unserialize(fl)
close(fl)
u.an.ma <- uniq.annotations(an.ma, 'GO')
checkEquals(u.an.ma, c(NA,"GO:0003688","GO:0005524",
"GO:0005737", "GO:0006270", "GO:0006275","GO:0017111"))
u.an.ma <- uniq.annotations(an.ma, 'GO', T)
checkEquals(u.an.ma, c("GO:0003688","GO:0005524",
"GO:0005737", "GO:0006270", "GO:0006275","GO:0017111"))
# Test sharedAnnotation
print("Testing sharedAnnotation(...)")
f <- file( project.file.path( "test_annotations.tbl" ), "r" )
annos <- unserialize( f )
close( f )
shrd.annos.1 <- sharedAnnotation( annos, "GO:0017111" )
# print( shrd.annos.1 )
checkEquals( class(shrd.annos.1), "matrix" )
checkEquals( nrow(shrd.annos.1), 3 )
checkEquals( ncol(shrd.annos.1), 6 )
checkEquals( shrd.annos.1[[ "GO", "A0LE53" ]], "GO:0017111" )
checkEquals( shrd.annos.1[[ "GO", "A0PKB2" ]], annos[[ "GO", "A0PKB2" ]] )
shrd.annos.2 <- sharedAnnotation( annos, "GO:0005737" )
# print( shrd.annos.2 )
checkEquals( class(shrd.annos.2), "matrix" )
checkEquals( nrow(shrd.annos.2), 3 )
checkEquals( ncol(shrd.annos.2), 2 )
checkEquals( shrd.annos.2[[ "GO", "A0Q3U7" ]], annos[[ "GO", "A0Q3U7" ]] )
# Test getEvidenceCode
ns <- c( xmlns="http://uniprot.org/uniprot" )
db.ref.tag <- '<?xml version="1.0" encoding="UTF-8"?>
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">
<dbReference type="GO" id="GO:0009815">
<property type="term" value="F:1-aminocyclopropane-1-carboxylate oxidase activity"/>
<property type="evidence" value="IEA:UniProtKB-EC"/>
</dbReference>
</uniprot>'
print("Testing getEvidenceCode(...)")
res.getEvidenceCode <- getEvidenceCode(
getNodeSet( xmlInternalTreeParse( db.ref.tag ),
"//xmlns:dbReference", namespace=ns )[[1]]
)
exp.getEvidenceCode <- 'IEA'
checkEquals( res.getEvidenceCode, exp.getEvidenceCode )
db.ref.tag <- '<?xml version="1.0" encoding="UTF-8"?>
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">
<dbReference type="GO" id="GO:0009815">
<property type="term" value="F:1-aminocyclopropane-1-carboxylate oxidase activity"/>
</dbReference>
</uniprot>'
res.getEvidenceCode <- getEvidenceCode(
getNodeSet( xmlInternalTreeParse( db.ref.tag ),
"//xmlns:dbReference", namespace=ns )[[1]]
)
exp.getEvidenceCode <- NA
checkEquals( res.getEvidenceCode, exp.getEvidenceCode )
db.ref.tag <- '<?xml version="1.0" encoding="UTF-8"?>
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">
<dbReference type="GO" id="GO:0009815">
<property type="term" value="F:1-aminocyclopropane-1-carboxylate oxidase activity"/>
<property type="evidence" value="IDA:UniProtKB-EC"/>
</dbReference>
</uniprot>'
res.getEvidenceCode <- getEvidenceCode(
getNodeSet( xmlInternalTreeParse( db.ref.tag ),
"//xmlns:dbReference", namespace=ns )[[1]]
)
exp.getEvidenceCode <- 'IDA'
checkEquals( res.getEvidenceCode, exp.getEvidenceCode )
# Test extractExperimentallyVerifiedGoAnnos
print("Testing extractExperimentallyVerifiedGoAnnos(...)")
rslt <- extractExperimentallyVerifiedGoAnnos(
xmlInternalTreeParse( project.file.path( "A0AEI7.xml" ) )
)
checkTrue( is.null(rslt) )
rslt <- extractExperimentallyVerifiedGoAnnos(
xmlInternalTreeParse( project.file.path( "Q9ZZX1.xml" ) ),
evidence.codes=c( 'EXP', 'IDA', 'IPI', 'IMP', 'IGI', 'IEP' )
)
# print( rslt )
exp.rslt <- read.table( stringsAsFactors=FALSE, text="GO:0004519 IMP Q9ZZX1
GO:0006316 IMP Q9ZZX1" )
checkEquals( exp.rslt, rslt )
# including evidence codes TAS and IC
rslt <- extractExperimentallyVerifiedGoAnnos(
xmlInternalTreeParse( project.file.path( "Q9ZZX1.xml" ) ),
evidence.codes=c( 'EXP', 'IDA', 'IPI', 'IMP', 'IGI', 'IEP', 'TAS', 'IC' )
)
exp.rslt <- read.table( stringsAsFactors=FALSE, text="GO:0005739 TAS Q9ZZX1
GO:6969696 IC Q9ZZX1
GO:0004519 IMP Q9ZZX1
GO:0006316 IMP Q9ZZX1" )
checkEquals( exp.rslt, rslt )
# Test retrieveExperimentallyVerifiedGOAnnotations
print("Testing retrieveExperimentallyVerifiedGOAnnotations(...)")
exper.go.annos <- retrieveExperimentallyVerifiedGOAnnotations( c( "A0AEI7", "Q9ZZX1" ) )
# print( exper.go.annos )
checkEquals( length(
intersect( c( "GO:0004519", "GO:0006316" ), exper.go.annos[, 1] )
), 2 )
checkEquals( ncol(exper.go.annos), 3 )
# Test with 550 accessions, triggering recursive execution:
accs.550 <- as.character( read.table( project.file.path( "550_exp_ver_accs.txt" ) )$V1 )
exper.go.annos.550 <- retrieveExperimentallyVerifiedGOAnnotations( accs.550 )
checkTrue( ! is.null( exper.go.annos.550 ) )
checkEquals( "data.frame", class( exper.go.annos.550 ) )
checkEquals( 3, ncol( exper.go.annos.550 ) )
# Test extractRefSeqAccession
print("Testing extractRefSeqAccession(...)")
res.extractRefSeqAccession <- extractRefSeqAccession( 'gi|444722022|gb|ELW62727.1|' )
exp.extractRefSeqAccession <- 'ELW62727.1'
checkEquals( res.extractRefSeqAccession, exp.extractRefSeqAccession )
groupschoof/PhyloFun documentation built on May 17, 2019, 8:38 a.m.
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require( PhyloFun )
# Accessions of Proteins involved in the following tests:
test.accessions <- c('Q0KFR8','B2AFZ7','Q1LSI9','Protein_1')
# Test extractName
print("Testing extractName(...)")
res.extractName <- extractName(
xmlInternalTreeParse( project.file.path( "Q9ZZX1.xml" ) ),
xpath.prefix='//xmlns:entry/'
)
exp.extractName <- "Q9ZZX1"
checkEquals( res.extractName, exp.extractName )
# With the result of getEntries:
res.extractName <- extractName( getEntries(
readLines( project.file.path( "Q9ZZX1.xml" ) ) )[[ 1 ]] )
exp.extractName <- "Q9ZZX1"
checkEquals( res.extractName, exp.extractName )
# NULL argument should return NULL accession:
checkTrue( is.null( extractName( NULL ) ) )
# Test downloadUniprotDocuments
print("Testing downloadUniprotDocuments(...)")
res.downloadUniprotDocuments <- downloadUniprotDocuments( test.accessions )
# print( res.downloadUniprotDocuments )
checkEquals( length( res.downloadUniprotDocuments ), 3 )
# Test retrieveAnnotationsBiomart
print("Testing retrieveAnnotationsBiomart(...)")
bm.annos <- retrieveAnnotationsBiomart(test.accessions)
# print( bm.annos )
checkEquals( class(bm.annos), 'matrix' )
checkEquals( nrow(bm.annos), 2 )
checkEquals( ncol(bm.annos), 4 )
# print(class(( bm.annos[ 'InterPro', 'Protein_1' ] ) ))
checkEquals( length( unlist( bm.annos[ 'InterPro', 'Protein_1' ] ) ), 0 )
checkEquals( length( unlist( bm.annos[ 'GO', 'Protein_1' ] ) ), 0 )
# print( bm.annos['Q0KFR8', 'InterPro'] )
checkTrue( 'IPR020591' %in% unlist( bm.annos[ 'InterPro', 'Q0KFR8' ] ) )
# print( bm.annos['Q0KFR8', 'GO'] )
checkTrue( 'GO:0005524' %in% unlist( bm.annos[ 'GO', 'Q0KFR8' ] ) )
# Test uniprotkb.url
print("Testing uniprotkb.url(...)")
checkEquals(uniprotkb.url('Q0KFR8'),
'http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprotkb/Q0KFR8/xml')
checkEquals(uniprotkb.url("sp|P34529|DCR1_CAEEL"),
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprotkb/sp%7cP34529%7cDCR1_CAEEL/xml")
checkEquals( uniprotkb.url('Q0KFR8', frmt='fasta'),
'http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprotkb/Q0KFR8/fasta'
)
# Test extractAnnotations
print("Testing extractAnnotations(...)")
d <- xmlInternalTreeParse( project.file.path( "Q9ZZX1.xml" ) )
annos <- extractAnnotations(d, 'InterPro')
# print( d )
# print( annos )
checkTrue(length(annos) > 0)
checkTrue('IPR004860' %in% annos)
annos <- extractAnnotations(d, 'GO')
# print( annos )
checkTrue(length(annos) > 0)
checkTrue('GO:0005739' %in% annos)
annos <- extractAnnotations(d, 'Pfam')
checkTrue(length(annos) > 0)
checkTrue('PF00115' %in% annos)
# Test retrieveAnnotations
print("Testing retrieveAnnotations(...)")
res.retrieveAnnotations <- retrieveAnnotations( d, xpath.prefix='//' )
exp.retrieveAnnotations <- list(
'GO'=c( "GO:0016021", "GO:0005739", "GO:6969696", "GO:0004129",
"GO:0009055", "GO:0004519", "GO:0020037", "GO:0005506",
"GO:0009060", "GO:0006316", "GO:0006397", "GO:0008380" ),
'InterPro'=c( "IPR000883", "IPR023615", "IPR023616", "IPR004860" ),
'Pfam'=c( "PF00115", "PF03161")
)
# print( res.retrieveAnnotations )
# print( exp.retrieveAnnotations )
checkEquals( res.retrieveAnnotations, exp.retrieveAnnotations )
# Test retrieveUniprotAnnotations
# Uniprot constantly changes the annotation of its proteins, hence we
# cannot test for correct annotations.
print("Testing retrieveUniprotAnnotations(...)")
res.retrieveUniprotAnnotations <- retrieveUniprotAnnotations( c( 'sp|Q5ZL72|CH60_CHICK', 'P63039' ) )
checkTrue( ! is.null( res.retrieveUniprotAnnotations ) )
checkEquals( class( res.retrieveUniprotAnnotations ), 'matrix' )
checkEquals( nrow( res.retrieveUniprotAnnotations ), 3 )
checkEquals( rownames( res.retrieveUniprotAnnotations ),
c( 'GO','InterPro','Pfam') )
checkTrue( ncol( res.retrieveUniprotAnnotations ) > 0 )
# Test uniq.annotations
print("Testing uniq.annotations(...)")
fl <- file(project.file.path('test_annotations.tbl'),'r')
an.ma <- unserialize(fl)
close(fl)
u.an.ma <- uniq.annotations(an.ma, 'GO')
checkEquals(u.an.ma, c(NA,"GO:0003688","GO:0005524",
"GO:0005737", "GO:0006270", "GO:0006275","GO:0017111"))
u.an.ma <- uniq.annotations(an.ma, 'GO', T)
checkEquals(u.an.ma, c("GO:0003688","GO:0005524",
"GO:0005737", "GO:0006270", "GO:0006275","GO:0017111"))
# Test sharedAnnotation
print("Testing sharedAnnotation(...)")
f <- file( project.file.path( "test_annotations.tbl" ), "r" )
annos <- unserialize( f )
close( f )
shrd.annos.1 <- sharedAnnotation( annos, "GO:0017111" )
# print( shrd.annos.1 )
checkEquals( class(shrd.annos.1), "matrix" )
checkEquals( nrow(shrd.annos.1), 3 )
checkEquals( ncol(shrd.annos.1), 6 )
checkEquals( shrd.annos.1[[ "GO", "A0LE53" ]], "GO:0017111" )
checkEquals( shrd.annos.1[[ "GO", "A0PKB2" ]], annos[[ "GO", "A0PKB2" ]] )
shrd.annos.2 <- sharedAnnotation( annos, "GO:0005737" )
# print( shrd.annos.2 )
checkEquals( class(shrd.annos.2), "matrix" )
checkEquals( nrow(shrd.annos.2), 3 )
checkEquals( ncol(shrd.annos.2), 2 )
checkEquals( shrd.annos.2[[ "GO", "A0Q3U7" ]], annos[[ "GO", "A0Q3U7" ]] )
# Test getEvidenceCode
ns <- c( xmlns="http://uniprot.org/uniprot" )
db.ref.tag <- '<?xml version="1.0" encoding="UTF-8"?>
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">
<dbReference type="GO" id="GO:0009815">
<property type="term" value="F:1-aminocyclopropane-1-carboxylate oxidase activity"/>
<property type="evidence" value="IEA:UniProtKB-EC"/>
</dbReference>
</uniprot>'
print("Testing getEvidenceCode(...)")
res.getEvidenceCode <- getEvidenceCode(
getNodeSet( xmlInternalTreeParse( db.ref.tag ),
"//xmlns:dbReference", namespace=ns )[[1]]
)
exp.getEvidenceCode <- 'IEA'
checkEquals( res.getEvidenceCode, exp.getEvidenceCode )
db.ref.tag <- '<?xml version="1.0" encoding="UTF-8"?>
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">
<dbReference type="GO" id="GO:0009815">
<property type="term" value="F:1-aminocyclopropane-1-carboxylate oxidase activity"/>
</dbReference>
</uniprot>'
res.getEvidenceCode <- getEvidenceCode(
getNodeSet( xmlInternalTreeParse( db.ref.tag ),
"//xmlns:dbReference", namespace=ns )[[1]]
)
exp.getEvidenceCode <- NA
checkEquals( res.getEvidenceCode, exp.getEvidenceCode )
db.ref.tag <- '<?xml version="1.0" encoding="UTF-8"?>
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">
<dbReference type="GO" id="GO:0009815">
<property type="term" value="F:1-aminocyclopropane-1-carboxylate oxidase activity"/>
<property type="evidence" value="IDA:UniProtKB-EC"/>
</dbReference>
</uniprot>'
res.getEvidenceCode <- getEvidenceCode(
getNodeSet( xmlInternalTreeParse( db.ref.tag ),
"//xmlns:dbReference", namespace=ns )[[1]]
)
exp.getEvidenceCode <- 'IDA'
checkEquals( res.getEvidenceCode, exp.getEvidenceCode )
# Test extractExperimentallyVerifiedGoAnnos
print("Testing extractExperimentallyVerifiedGoAnnos(...)")
rslt <- extractExperimentallyVerifiedGoAnnos(
xmlInternalTreeParse( project.file.path( "A0AEI7.xml" ) )
)
checkTrue( is.null(rslt) )
rslt <- extractExperimentallyVerifiedGoAnnos(
xmlInternalTreeParse( project.file.path( "Q9ZZX1.xml" ) ),
evidence.codes=c( 'EXP', 'IDA', 'IPI', 'IMP', 'IGI', 'IEP' )
)
# print( rslt )
exp.rslt <- read.table( stringsAsFactors=FALSE, text="GO:0004519 IMP Q9ZZX1
GO:0006316 IMP Q9ZZX1" )
checkEquals( exp.rslt, rslt )
# including evidence codes TAS and IC
rslt <- extractExperimentallyVerifiedGoAnnos(
xmlInternalTreeParse( project.file.path( "Q9ZZX1.xml" ) ),
evidence.codes=c( 'EXP', 'IDA', 'IPI', 'IMP', 'IGI', 'IEP', 'TAS', 'IC' )
)
exp.rslt <- read.table( stringsAsFactors=FALSE, text="GO:0005739 TAS Q9ZZX1
GO:6969696 IC Q9ZZX1
GO:0004519 IMP Q9ZZX1
GO:0006316 IMP Q9ZZX1" )
checkEquals( exp.rslt, rslt )
# Test retrieveExperimentallyVerifiedGOAnnotations
print("Testing retrieveExperimentallyVerifiedGOAnnotations(...)")
exper.go.annos <- retrieveExperimentallyVerifiedGOAnnotations( c( "A0AEI7", "Q9ZZX1" ) )
# print( exper.go.annos )
checkEquals( length(
intersect( c( "GO:0004519", "GO:0006316" ), exper.go.annos[, 1] )
), 2 )
checkEquals( ncol(exper.go.annos), 3 )
# Test with 550 accessions, triggering recursive execution:
accs.550 <- as.character( read.table( project.file.path( "550_exp_ver_accs.txt" ) )$V1 )
exper.go.annos.550 <- retrieveExperimentallyVerifiedGOAnnotations( accs.550 )
checkTrue( ! is.null( exper.go.annos.550 ) )
checkEquals( "data.frame", class( exper.go.annos.550 ) )
checkEquals( 3, ncol( exper.go.annos.550 ) )
# Test extractRefSeqAccession
print("Testing extractRefSeqAccession(...)")
res.extractRefSeqAccession <- extractRefSeqAccession( 'gi|444722022|gb|ELW62727.1|' )
exp.extractRefSeqAccession <- 'ELW62727.1'
checkEquals( res.extractRefSeqAccession, exp.extractRefSeqAccession )
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