exec/testPhyloFunTools.R
In groupschoof/PhyloFun: Annotates Proteins with Gene Ontology (GO) Terms
require( PhyloFun )
require( PhyloFun )
# Test parsePhmmerTable
print("Testing parsePhmmerTable(...)")
jr <- project.file.path( 'jackhmmer_out_10_prots.tbl' )
hmmer.tbl <- parsePhmmerTable( jr )
# print( hmmer.tbl[1,] )
checkTrue( ! is.null( hmmer.tbl ) )
checkEquals( class(hmmer.tbl) , 'data.frame' )
checkEquals( nrow(hmmer.tbl), 863 )
checkEquals( colnames(hmmer.tbl), c( "hit.name", "query.name", "bit.score" ) )
checkEquals( hmmer.tbl[ 1, 'hit.name' ], "sp|B5YXA4|DNAA_ECO5E" )
checkEquals( hmmer.tbl[ 1, 'query.name' ], "Protein_1" )
checkEquals( hmmer.tbl[ 1, 'bit.score' ], 697.8 )
phmmer.tbl <- project.file.path( 'phmmer_out.tbl' )
hmmer.tbl <- parsePhmmerTable( phmmer.tbl )
# print( hmmer.tbl[1,] )
checkTrue( ! is.null( hmmer.tbl ) )
checkEquals( class(hmmer.tbl) , 'data.frame' )
checkEquals( nrow(hmmer.tbl), 1174 )
checkEquals( colnames(hmmer.tbl), c( "hit.name", "query.name", "bit.score" ) )
checkEquals( hmmer.tbl[ 1, 'hit.name' ], "Q8LPI7" )
checkEquals( hmmer.tbl[ 1, 'query.name' ], "Medtr1g004990.2" )
checkEquals( hmmer.tbl[ 1, 'bit.score' ], 542.7 )
# Test parseBlastTable
print("Testing parseBlastTable(...)")
res.parseBlastTable <- parseBlastTable( read.table(
project.file.path( 'test_blast_results.tbl' ) )
)
exp.parseBlastTable <- read.table( text=
'"query.name" "hit.name" "bit.score"
"1" "Query_D3Z7J9" "P63039" 289
"2" "Query_D3Z7J9" "P63038" 289
"3" "Query_D3Z7J9" "D3Z2F2" 288
"4" "Query_D3Z7J9" "P10809" 286
"5" "Query_D3Z7J9" "E7EXB4" 285
"6" "Query_D3Z7J9" "E7ESH4" 285
"7" "Query_D3Z7J9" "B7Z712" 285
"8" "Query_D3Z7J9" "Q5ZL72" 283
"9" "Query_D3Z7J9" "Q803B0" 279
"10" "Query_D3Z7J9" "C9JL25" 265' )
# print( res.parseBlastTable )
# print( exp.parseBlastTable )
checkEquals( colnames( res.parseBlastTable ), colnames( exp.parseBlastTable ) )
checkEquals( rownames( res.parseBlastTable ), rownames( exp.parseBlastTable ) )
checkTrue( all( as.logical(
lapply( colnames( exp.parseBlastTable ), function( cn ) {
checkEquals( res.parseBlastTable[ , cn ], exp.parseBlastTable[ , cn ] )
} )
) ) )
# Test extractUniprotAccessionFromUniprotName
print("Testing extractUniprotAccessionFromUniprotName(...)")
uni.acc <- extractUniprotAccessionFromUniprotName( "sp|B5YXA4|DNAA_ECO5E" )
checkEquals( uni.acc, "B5YXA4" )
checkTrue( is.na( extractUniprotAccessionFromUniprotName( NA ) ) )
# Test parseInterProScanTable
print("Testing parseInterProScanTable(...)")
ipr <- scan( file=project.file.path( "interproscan_out.tsv" ),
what=character(), sep="\n" )
ipr.res <- parseInterProScanTable( ipr )
# print( ipr.res )
checkTrue( ! is.null( ipr.res ) )
checkEquals( class(ipr.res), "matrix" )
checkEquals( ncol(ipr.res), 9 )
checkEquals( ipr.res[[ "InterPro", "Protein_5" ]], "IPR011990" )
checkEquals( ipr.res[[ "InterPro", "Protein_4" ]],
c("IPR011650", "IPR017439", "IPR002933")
)
# Test commandLineArguments
print("Testing commandLineArguments(...)")
res.commandLineArguments <- commandLineArguments(
c( '-a', '1', '-b', '2' ), list('b'='0', 'c'='3')
)
exp.commandLineArguments <- list( 'a'='1', 'b'='2', 'c'='3' )
# print( res.commandLineArguments )
checkEquals( res.commandLineArguments, exp.commandLineArguments )
# Test sanitizeUniprotAccession
print("Testing sanitizeUniprotAccession(...)")
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( ' sp|MyAccession|MOUSE_SHEEP ' )
exp.sanitizeUniprotAccession <- 'MyAccession'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# without pipes
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( ' MyAccession ' )
exp.sanitizeUniprotAccession <- 'MyAccession'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# test NULL:
checkTrue( is.null( sanitizeUniprotAccession( NULL ) ) )
# test new format provided, when large numbers of accessions are downloaded:
# … with leading whitespace:
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( ' UNIPROT:YNF5_SCHPO O13633 Uncharacterized J domain-containing protein C17A3.05c ' )
exp.sanitizeUniprotAccession <- 'O13633'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# … without leading whitespace:
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( 'UNIPROT:YNF5_SCHPO O13633 Uncharacterized J domain-containing protein C17A3.05c' )
exp.sanitizeUniprotAccession <- 'O13633'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# … with leading '>':
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( '>UNIPROT:YNF5_SCHPO O13633 Uncharacterized J domain-containing protein C17A3.05c' )
exp.sanitizeUniprotAccession <- 'O13633'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# … with leading '> ':
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( '> UNIPROT:YNF5_SCHPO O13633 Uncharacterized J domain-containing protein C17A3.05c' )
exp.sanitizeUniprotAccession <- 'O13633'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# Test uniqueHomologs
print("Testing uniqueHomologs(...)")
uniqueHomologs( project.file.path( 'non_unique_hmlgs.fasta' ),
'tmp.fasta', FALSE )
res.uniqueHomologs <- readAAStringSet( 'tmp.fasta' )
checkTrue( ! is.null( res.uniqueHomologs ) )
checkEquals( length( res.uniqueHomologs ), 167 )
exp.unique.hmlgs.names <- c( "Q8K4K1", "Q9S744", "Q9FYK2", "Q8VHC5", "Q9SRE6",
"O35648", "Q545L8", "Q9C8Y1", "O88751", "B1AKR1",
"O15182", "P08590", "P02600", "Q9NZU7", "Q8TD86",
"P05976", "Q9NPB3", "P57796", "Q9ZSA2", "P12829",
"Q9SRR7", "Q38868", "Q9NP86", "O23184", "P25070",
"Q9SU00", "Q3E9C0", "Q8RWL2", "A2AVY6", "Q9CQ19",
"Q9FMP5", "Q06850", "Q3THE2", "P18666", "Q8VZ50",
"Q9ZR02", "Q94AZ4", "Q9S9V0", "Q38870", "Q38872",
"Q39016", "Q9ZSA4", "O74435", "P13832", "Q6ZWQ9",
"Q38871", "Q38869", "Q42479", "Q9LE22", "Q5XJC3",
"Q9ZQE6", "P06704", "Q9ZSA3", "Q9M101", "E5RJF8",
"Q38873", "E5RK82", "Q9SSF8", "Q1PFH8", "Q9C9U8",
"Q6NLQ6", "Q99MJ8", "Q99MJ7", "Q09510", "Q42438",
"Q9FI19", "P93759", "P10916", "Q9XVI9", "P08733",
"P51667", "Q9FIH9", "P13833", "P48593", "P63100",
"Q63810", "P40423", "Q9M9V8", "Q95XF6", "O14008",
"Q8W4I7", "E9QNY3", "Q62082", "Q08331", "Q9SVG9",
"Q8CCS7", "Q52K82", "P04466", "P97457", "P22676",
"Q9SS31", "Q24214", "P53141", "P48451", "Q801M3",
"Q9UU93", "P28470", "Q5SVI8", "Q9QVP4", "Q5NCJ7",
"Q86V35", "Q91ZM8", "Q01449", "P19626", "P19625",
"Q5AK12", "P53014", "Q9BUA6", "Q55G87", "Q7XJR9",
"Q09196", "Q9FKW4", "P25296", "Q9BXU9", "P30188",
"E9Q8Y0", "B1AUQ7", "A1BN54", "Q542R1", "Q9JJG7",
"P05094", "F8WHE1", "P61601", "P61602", "Q5PQN0",
"Q6ZM98", "Q8CBJ9", "Q3B7N2", "P12814", "D3YUI7",
"Q7TPR4", "Q9Z1P2", "P09402", "Q9SRE7", "P35609",
"P42324", "D3ZCV0", "Q9JI91", "Q5FW75", "Q9UUG5",
"P42325", "O88990", "Q08043", "P12815", "P20111",
"P04354", "O75340", "P62748", "Q9QXQ0", "P57780",
"Q3ULT2", "O43707", "A8Y589", "E9PV73", "P84074",
"P84075", "P84076", "Q9FDX6", "Q54X77", "A6NER6",
"P18432", "P07171", "A2AS59", "P12658", "P05937",
"P06742", "Q8UUX9" )
checkEquals( names( res.uniqueHomologs ), exp.unique.hmlgs.names )
# clean up:
unlink( 'tmp.fasta' )
# Test msaEqual
print("Testing msaEqual(...)")
msa.a <- readAAStringSet( project.file.path( 'test_msa_equal_A.fasta' ) )
msa.b <- readAAStringSet( project.file.path( 'test_msa_equal_B.fasta' ) )
msa.c <- readAAStringSet( project.file.path( 'test_msa_equal_C.fasta' ) )
checkTrue( msaEqual( msa.a, msa.b ) )
checkTrue( ! msaEqual( msa.a, msa.c ) )
checkTrue( ! msaEqual( msa.b, msa.c ) )
# Test bestHits
print("Testing bestHits(...)")
seq.srch.rslt <- matrix( c( 'Query_A', 'Query_A', 'Query_A', 'Query_B',
'Hit_1', 'Hit_2', 'Hit_3', 'Hit_4', 4, 3, 2, 4 ),
ncol=3, nrow=4,
dimnames=list( c(), c( 'query.name', 'hit.name', 'bit.score' ) )
)
res.bestHits <- bestHits( seq.srch.rslt, 'Query_A', 2 )
exp.bestHits <- matrix( c( 'Query_A', 'Query_A', 'Hit_1', 'Hit_2', 4, 3 ),
nrow=2, ncol=3, dimnames=list( c(),
c( 'query.name', 'hit.name', 'bit.score' ) )
)
checkEquals( res.bestHits, exp.bestHits )
res.bestHits <- bestHits( seq.srch.rslt, 'Query_A', 4 )
exp.bestHits <- matrix( c( 'Query_A', 'Query_A', 'Query_A', 'Hit_1', 'Hit_2', 'Hit_3', 4, 3, 2 ),
nrow=3, ncol=3, dimnames=list( c(),
c( 'query.name', 'hit.name', 'bit.score' ) )
)
checkEquals( res.bestHits, exp.bestHits )
# Test filterMultipleSequenceAlignment
print("Testing filterMultipleSequenceAlignment(...)")
msa <- readAAStringSet( project.file.path( 'test_msa.fasta' ) )
res.filterMultipleSequenceAlignment <- filterMultipleSequenceAlignment( msa, 25 )
exp.filterMultipleSequenceAlignment <- msa[ 1 ]
checkTrue( msaEqual( res.filterMultipleSequenceAlignment, exp.filterMultipleSequenceAlignment ) )
msa.empty <- readAAStringSet( project.file.path( 'test_msa_empty.fasta' ) )
res.filterMultipleSequenceAlignment <- filterMultipleSequenceAlignment( msa.empty, 25 )
exp.filterMultipleSequenceAlignment <- NULL
checkEquals( res.filterMultipleSequenceAlignment, exp.filterMultipleSequenceAlignment )
# Test chooseFilteredAlignment
print("Testing chooseFilteredAlignment(...)")
res.chooseAlignment <- chooseFilteredAlignment( msa )
exp.chooseAlignment <- FALSE
# expected to choose unfiltered MSA
checkTrue( ! exp.chooseAlignment )
res.chooseAlignment <- chooseFilteredAlignment( msa.empty )
exp.chooseAlignment <- FALSE
# expected to choose unfiltered MSA
checkTrue( ! exp.chooseAlignment )
msa.good <- readAAStringSet( project.file.path( 'test_msa_good.fasta' ) )
res.chooseAlignment <- chooseFilteredAlignment( msa.good )
exp.chooseAlignment <- TRUE
# expected to choose FILTERED MSA
checkTrue( exp.chooseAlignment )
# Test sanitizeUniprotAccessions
print("Testing sanitizeUniprotAccessions(...)")
seq.search.rslt.tbl <- read.table( text=
" query.name hit.name bit.score
Query_Q9VIH3 sp|O08601|MTP_MOUSE 226
Query_Q9VIH3 sp|P55158|MTP_MESAU 217
Query_Q9VIH3 sp|P55157|MTP_HUMAN 208
Query_Q9VIH3 sp|Q865F1|MTP_PIG 204
Query_Q9VIH3 sp|P55156|MTP_BOVIN 198
Query_Q9VIH3 tr|Q961S9|Q961S9_DROME 1724
Query_Q9VIH3 tr|B4Q3W8|B4Q3W8_DROSI 1691
Query_Q9VIH3 tr|B4IFI6|B4IFI6_DROSE 1670
Query_Q9VIH3 tr|B3NKW4|B3NKW4_DROER 1617
Query_Q9VIH3 tr|B4P714|B4P714_DROYA 1606
", header=T )
res.sanitizeUniprotAccessions <- sanitizeUniprotAccessions( seq.search.rslt.tbl )
exp.sanitizeUniprotAccessions <- c( 'O08601', 'P55158', 'P55157', 'Q865F1',
'P55156', 'Q961S9', 'B4Q3W8', 'B4IFI6', 'B3NKW4', 'B4P714' )
checkEquals( as.character( res.sanitizeUniprotAccessions[ , 'hit.name' ] ),
exp.sanitizeUniprotAccessions )
# Test mergeQueryPredictionsAndHomologAnnotations
print("Testing mergeQueryPredictionsAndHomologAnnotations(...)")
prot.acc <- 'Protein_1'
pf.preds <- read.table( project.file.path(
'test_phylo_fun_predictions.tbl' ), header=T )
f <- file( project.file.path(
'test_go_type_annotations_R_serialized.txt' ), 'r' )
gt.annos <- unserialize( f )
close( f )
res.merged <- mergeQueryPredictionsAndHomologAnnotations( prot.acc,
pf.preds, gt.annos )
checkTrue( ! is.null( res.merged ) )
checkEquals( class(res.merged), 'list' )
go.types <- c( 'biological_process',
'cellular_component', 'molecular_function' )
checkEquals( names( res.merged ), go.types )
for ( go.type in go.types ) {
res.gt <- res.merged[[ go.type ]]
gt.pf.pred <- as.character( res.gt[ 'GO', prot.acc ][[ 1 ]] )
exp.gt.pf.pred <- as.character(
pf.preds[ which( pf.preds[ , 'term_type' ] == go.type ), 'acc' ]
)
print( checkEquals( gt.pf.pred, exp.gt.pf.pred ) )
go.tp.annos <- res.gt[ ,
setdiff( colnames( res.gt ), prot.acc ), drop=F
]
print( checkEquals( go.tp.annos, gt.annos[[ go.type ]] ) )
}
# Test replaceSelenocysteinInFasta
print("Testing replaceSelenocysteinInFasta(...)")
res.replaceSelenocysteinInFasta <- replaceSelenocysteinInFasta( project.file.path( 'aa_seqs_with_u.fasta'), 'tmp_rslt.fasta' )
aa.seqs.fltrd <- readAAStringSet( 'tmp_rslt.fasta' )
checkEquals( names( aa.seqs.fltrd ), c( 'protein_1', 'protein_2' ) )
checkEquals( toString( aa.seqs.fltrd[[ 1 ]] ), 'xxxxxxxxxxxxxXXXXXXXXXXXXXXXXX' )
checkEquals( toString( aa.seqs.fltrd[[ 2 ]] ), 'MSTVAAYAAMSATExXxXxXPLTKTTITRS' )
unlink( 'tmp_rslt.fasta' )
# Test proteinPairsSharingAnnotation
print("Testing proteinPairsSharingAnnotation(...)")
prots <- read.table( text=
"A A
B B
C C
A B
B C
A D", stringsAsFactors=FALSE )
prot.annos <- read.table( stringsAsFactors=FALSE, text=
"GO:0001234 IEA A
GO:0001234 IEA B
GO:0001234 IEA D" )
res.proteinPairsSharingAnnotation <- proteinPairsSharingAnnotation(
'GO:0001234', prots, prot.annos )
exp.proteinPairsSharingAnnotation <- read.table( stringsAsFactors=FALSE, text=
"A A TRUE
B B TRUE
A B TRUE
B C FALSE
A D TRUE
")
checkEquals(
as.character( unlist( res.proteinPairsSharingAnnotation ) ),
as.character( unlist( exp.proteinPairsSharingAnnotation ) )
)
#################################################################
# The following function is the only one tested that is of file #
# geneOntologySql.R #
#################################################################
# Test selectMostSignificantEvidenceCode
print("Testing selectMostSignificantEvidenceCode(...)")
res.selectMostSignificantEvidenceCode <- selectMostSignificantEvidenceCode( c( 'EXP', 'TAS', 'IEA', 'IDA' ) )
exp.selectMostSignificantEvidenceCode <- 'EXP'
checkEquals( res.selectMostSignificantEvidenceCode, exp.selectMostSignificantEvidenceCode )
res.selectMostSignificantEvidenceCode <- selectMostSignificantEvidenceCode( 'IEA' )
exp.selectMostSignificantEvidenceCode <- 'IEA'
checkEquals( res.selectMostSignificantEvidenceCode, exp.selectMostSignificantEvidenceCode )
res.selectMostSignificantEvidenceCode <- selectMostSignificantEvidenceCode( c( 'IEA', 'IC' ) )
exp.selectMostSignificantEvidenceCode <- 'IC'
checkEquals( res.selectMostSignificantEvidenceCode, exp.selectMostSignificantEvidenceCode )
# Test uniqueGOAnnotationsWithMostSignificantEvidenceCodes
print("Testing uniqueGOAnnotationsWithMostSignificantEvidenceCodes(...)")
clean.up.anno.df <- read.table( stringsAsFactors=FALSE, text=
"GO:0001234 IEA A
GO:0001234 IEA B
GO:0001234 IC B
GO:0001234 IEA D" )
res.uniqueGOAnnotationsWithMostSignificantEvidenceCodes <- uniqueGOAnnotationsWithMostSignificantEvidenceCodes( clean.up.anno.df )
exp.uniqueGOAnnotationsWithMostSignificantEvidenceCodes <- read.table( stringsAsFactors=FALSE, text=
"GO:0001234 IEA A
GO:0001234 IC B
GO:0001234 IEA D" )
rownames( res.uniqueGOAnnotationsWithMostSignificantEvidenceCodes ) <- c()
checkEquals( res.uniqueGOAnnotationsWithMostSignificantEvidenceCodes, exp.uniqueGOAnnotationsWithMostSignificantEvidenceCodes )
groupschoof/PhyloFun documentation built on May 17, 2019, 8:38 a.m.
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require( PhyloFun )
require( PhyloFun )
# Test parsePhmmerTable
print("Testing parsePhmmerTable(...)")
jr <- project.file.path( 'jackhmmer_out_10_prots.tbl' )
hmmer.tbl <- parsePhmmerTable( jr )
# print( hmmer.tbl[1,] )
checkTrue( ! is.null( hmmer.tbl ) )
checkEquals( class(hmmer.tbl) , 'data.frame' )
checkEquals( nrow(hmmer.tbl), 863 )
checkEquals( colnames(hmmer.tbl), c( "hit.name", "query.name", "bit.score" ) )
checkEquals( hmmer.tbl[ 1, 'hit.name' ], "sp|B5YXA4|DNAA_ECO5E" )
checkEquals( hmmer.tbl[ 1, 'query.name' ], "Protein_1" )
checkEquals( hmmer.tbl[ 1, 'bit.score' ], 697.8 )
phmmer.tbl <- project.file.path( 'phmmer_out.tbl' )
hmmer.tbl <- parsePhmmerTable( phmmer.tbl )
# print( hmmer.tbl[1,] )
checkTrue( ! is.null( hmmer.tbl ) )
checkEquals( class(hmmer.tbl) , 'data.frame' )
checkEquals( nrow(hmmer.tbl), 1174 )
checkEquals( colnames(hmmer.tbl), c( "hit.name", "query.name", "bit.score" ) )
checkEquals( hmmer.tbl[ 1, 'hit.name' ], "Q8LPI7" )
checkEquals( hmmer.tbl[ 1, 'query.name' ], "Medtr1g004990.2" )
checkEquals( hmmer.tbl[ 1, 'bit.score' ], 542.7 )
# Test parseBlastTable
print("Testing parseBlastTable(...)")
res.parseBlastTable <- parseBlastTable( read.table(
project.file.path( 'test_blast_results.tbl' ) )
)
exp.parseBlastTable <- read.table( text=
'"query.name" "hit.name" "bit.score"
"1" "Query_D3Z7J9" "P63039" 289
"2" "Query_D3Z7J9" "P63038" 289
"3" "Query_D3Z7J9" "D3Z2F2" 288
"4" "Query_D3Z7J9" "P10809" 286
"5" "Query_D3Z7J9" "E7EXB4" 285
"6" "Query_D3Z7J9" "E7ESH4" 285
"7" "Query_D3Z7J9" "B7Z712" 285
"8" "Query_D3Z7J9" "Q5ZL72" 283
"9" "Query_D3Z7J9" "Q803B0" 279
"10" "Query_D3Z7J9" "C9JL25" 265' )
# print( res.parseBlastTable )
# print( exp.parseBlastTable )
checkEquals( colnames( res.parseBlastTable ), colnames( exp.parseBlastTable ) )
checkEquals( rownames( res.parseBlastTable ), rownames( exp.parseBlastTable ) )
checkTrue( all( as.logical(
lapply( colnames( exp.parseBlastTable ), function( cn ) {
checkEquals( res.parseBlastTable[ , cn ], exp.parseBlastTable[ , cn ] )
} )
) ) )
# Test extractUniprotAccessionFromUniprotName
print("Testing extractUniprotAccessionFromUniprotName(...)")
uni.acc <- extractUniprotAccessionFromUniprotName( "sp|B5YXA4|DNAA_ECO5E" )
checkEquals( uni.acc, "B5YXA4" )
checkTrue( is.na( extractUniprotAccessionFromUniprotName( NA ) ) )
# Test parseInterProScanTable
print("Testing parseInterProScanTable(...)")
ipr <- scan( file=project.file.path( "interproscan_out.tsv" ),
what=character(), sep="\n" )
ipr.res <- parseInterProScanTable( ipr )
# print( ipr.res )
checkTrue( ! is.null( ipr.res ) )
checkEquals( class(ipr.res), "matrix" )
checkEquals( ncol(ipr.res), 9 )
checkEquals( ipr.res[[ "InterPro", "Protein_5" ]], "IPR011990" )
checkEquals( ipr.res[[ "InterPro", "Protein_4" ]],
c("IPR011650", "IPR017439", "IPR002933")
)
# Test commandLineArguments
print("Testing commandLineArguments(...)")
res.commandLineArguments <- commandLineArguments(
c( '-a', '1', '-b', '2' ), list('b'='0', 'c'='3')
)
exp.commandLineArguments <- list( 'a'='1', 'b'='2', 'c'='3' )
# print( res.commandLineArguments )
checkEquals( res.commandLineArguments, exp.commandLineArguments )
# Test sanitizeUniprotAccession
print("Testing sanitizeUniprotAccession(...)")
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( ' sp|MyAccession|MOUSE_SHEEP ' )
exp.sanitizeUniprotAccession <- 'MyAccession'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# without pipes
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( ' MyAccession ' )
exp.sanitizeUniprotAccession <- 'MyAccession'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# test NULL:
checkTrue( is.null( sanitizeUniprotAccession( NULL ) ) )
# test new format provided, when large numbers of accessions are downloaded:
# … with leading whitespace:
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( ' UNIPROT:YNF5_SCHPO O13633 Uncharacterized J domain-containing protein C17A3.05c ' )
exp.sanitizeUniprotAccession <- 'O13633'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# … without leading whitespace:
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( 'UNIPROT:YNF5_SCHPO O13633 Uncharacterized J domain-containing protein C17A3.05c' )
exp.sanitizeUniprotAccession <- 'O13633'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# … with leading '>':
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( '>UNIPROT:YNF5_SCHPO O13633 Uncharacterized J domain-containing protein C17A3.05c' )
exp.sanitizeUniprotAccession <- 'O13633'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# … with leading '> ':
res.sanitizeUniprotAccession <- sanitizeUniprotAccession( '> UNIPROT:YNF5_SCHPO O13633 Uncharacterized J domain-containing protein C17A3.05c' )
exp.sanitizeUniprotAccession <- 'O13633'
checkEquals( res.sanitizeUniprotAccession, exp.sanitizeUniprotAccession )
# Test uniqueHomologs
print("Testing uniqueHomologs(...)")
uniqueHomologs( project.file.path( 'non_unique_hmlgs.fasta' ),
'tmp.fasta', FALSE )
res.uniqueHomologs <- readAAStringSet( 'tmp.fasta' )
checkTrue( ! is.null( res.uniqueHomologs ) )
checkEquals( length( res.uniqueHomologs ), 167 )
exp.unique.hmlgs.names <- c( "Q8K4K1", "Q9S744", "Q9FYK2", "Q8VHC5", "Q9SRE6",
"O35648", "Q545L8", "Q9C8Y1", "O88751", "B1AKR1",
"O15182", "P08590", "P02600", "Q9NZU7", "Q8TD86",
"P05976", "Q9NPB3", "P57796", "Q9ZSA2", "P12829",
"Q9SRR7", "Q38868", "Q9NP86", "O23184", "P25070",
"Q9SU00", "Q3E9C0", "Q8RWL2", "A2AVY6", "Q9CQ19",
"Q9FMP5", "Q06850", "Q3THE2", "P18666", "Q8VZ50",
"Q9ZR02", "Q94AZ4", "Q9S9V0", "Q38870", "Q38872",
"Q39016", "Q9ZSA4", "O74435", "P13832", "Q6ZWQ9",
"Q38871", "Q38869", "Q42479", "Q9LE22", "Q5XJC3",
"Q9ZQE6", "P06704", "Q9ZSA3", "Q9M101", "E5RJF8",
"Q38873", "E5RK82", "Q9SSF8", "Q1PFH8", "Q9C9U8",
"Q6NLQ6", "Q99MJ8", "Q99MJ7", "Q09510", "Q42438",
"Q9FI19", "P93759", "P10916", "Q9XVI9", "P08733",
"P51667", "Q9FIH9", "P13833", "P48593", "P63100",
"Q63810", "P40423", "Q9M9V8", "Q95XF6", "O14008",
"Q8W4I7", "E9QNY3", "Q62082", "Q08331", "Q9SVG9",
"Q8CCS7", "Q52K82", "P04466", "P97457", "P22676",
"Q9SS31", "Q24214", "P53141", "P48451", "Q801M3",
"Q9UU93", "P28470", "Q5SVI8", "Q9QVP4", "Q5NCJ7",
"Q86V35", "Q91ZM8", "Q01449", "P19626", "P19625",
"Q5AK12", "P53014", "Q9BUA6", "Q55G87", "Q7XJR9",
"Q09196", "Q9FKW4", "P25296", "Q9BXU9", "P30188",
"E9Q8Y0", "B1AUQ7", "A1BN54", "Q542R1", "Q9JJG7",
"P05094", "F8WHE1", "P61601", "P61602", "Q5PQN0",
"Q6ZM98", "Q8CBJ9", "Q3B7N2", "P12814", "D3YUI7",
"Q7TPR4", "Q9Z1P2", "P09402", "Q9SRE7", "P35609",
"P42324", "D3ZCV0", "Q9JI91", "Q5FW75", "Q9UUG5",
"P42325", "O88990", "Q08043", "P12815", "P20111",
"P04354", "O75340", "P62748", "Q9QXQ0", "P57780",
"Q3ULT2", "O43707", "A8Y589", "E9PV73", "P84074",
"P84075", "P84076", "Q9FDX6", "Q54X77", "A6NER6",
"P18432", "P07171", "A2AS59", "P12658", "P05937",
"P06742", "Q8UUX9" )
checkEquals( names( res.uniqueHomologs ), exp.unique.hmlgs.names )
# clean up:
unlink( 'tmp.fasta' )
# Test msaEqual
print("Testing msaEqual(...)")
msa.a <- readAAStringSet( project.file.path( 'test_msa_equal_A.fasta' ) )
msa.b <- readAAStringSet( project.file.path( 'test_msa_equal_B.fasta' ) )
msa.c <- readAAStringSet( project.file.path( 'test_msa_equal_C.fasta' ) )
checkTrue( msaEqual( msa.a, msa.b ) )
checkTrue( ! msaEqual( msa.a, msa.c ) )
checkTrue( ! msaEqual( msa.b, msa.c ) )
# Test bestHits
print("Testing bestHits(...)")
seq.srch.rslt <- matrix( c( 'Query_A', 'Query_A', 'Query_A', 'Query_B',
'Hit_1', 'Hit_2', 'Hit_3', 'Hit_4', 4, 3, 2, 4 ),
ncol=3, nrow=4,
dimnames=list( c(), c( 'query.name', 'hit.name', 'bit.score' ) )
)
res.bestHits <- bestHits( seq.srch.rslt, 'Query_A', 2 )
exp.bestHits <- matrix( c( 'Query_A', 'Query_A', 'Hit_1', 'Hit_2', 4, 3 ),
nrow=2, ncol=3, dimnames=list( c(),
c( 'query.name', 'hit.name', 'bit.score' ) )
)
checkEquals( res.bestHits, exp.bestHits )
res.bestHits <- bestHits( seq.srch.rslt, 'Query_A', 4 )
exp.bestHits <- matrix( c( 'Query_A', 'Query_A', 'Query_A', 'Hit_1', 'Hit_2', 'Hit_3', 4, 3, 2 ),
nrow=3, ncol=3, dimnames=list( c(),
c( 'query.name', 'hit.name', 'bit.score' ) )
)
checkEquals( res.bestHits, exp.bestHits )
# Test filterMultipleSequenceAlignment
print("Testing filterMultipleSequenceAlignment(...)")
msa <- readAAStringSet( project.file.path( 'test_msa.fasta' ) )
res.filterMultipleSequenceAlignment <- filterMultipleSequenceAlignment( msa, 25 )
exp.filterMultipleSequenceAlignment <- msa[ 1 ]
checkTrue( msaEqual( res.filterMultipleSequenceAlignment, exp.filterMultipleSequenceAlignment ) )
msa.empty <- readAAStringSet( project.file.path( 'test_msa_empty.fasta' ) )
res.filterMultipleSequenceAlignment <- filterMultipleSequenceAlignment( msa.empty, 25 )
exp.filterMultipleSequenceAlignment <- NULL
checkEquals( res.filterMultipleSequenceAlignment, exp.filterMultipleSequenceAlignment )
# Test chooseFilteredAlignment
print("Testing chooseFilteredAlignment(...)")
res.chooseAlignment <- chooseFilteredAlignment( msa )
exp.chooseAlignment <- FALSE
# expected to choose unfiltered MSA
checkTrue( ! exp.chooseAlignment )
res.chooseAlignment <- chooseFilteredAlignment( msa.empty )
exp.chooseAlignment <- FALSE
# expected to choose unfiltered MSA
checkTrue( ! exp.chooseAlignment )
msa.good <- readAAStringSet( project.file.path( 'test_msa_good.fasta' ) )
res.chooseAlignment <- chooseFilteredAlignment( msa.good )
exp.chooseAlignment <- TRUE
# expected to choose FILTERED MSA
checkTrue( exp.chooseAlignment )
# Test sanitizeUniprotAccessions
print("Testing sanitizeUniprotAccessions(...)")
seq.search.rslt.tbl <- read.table( text=
" query.name hit.name bit.score
Query_Q9VIH3 sp|O08601|MTP_MOUSE 226
Query_Q9VIH3 sp|P55158|MTP_MESAU 217
Query_Q9VIH3 sp|P55157|MTP_HUMAN 208
Query_Q9VIH3 sp|Q865F1|MTP_PIG 204
Query_Q9VIH3 sp|P55156|MTP_BOVIN 198
Query_Q9VIH3 tr|Q961S9|Q961S9_DROME 1724
Query_Q9VIH3 tr|B4Q3W8|B4Q3W8_DROSI 1691
Query_Q9VIH3 tr|B4IFI6|B4IFI6_DROSE 1670
Query_Q9VIH3 tr|B3NKW4|B3NKW4_DROER 1617
Query_Q9VIH3 tr|B4P714|B4P714_DROYA 1606
", header=T )
res.sanitizeUniprotAccessions <- sanitizeUniprotAccessions( seq.search.rslt.tbl )
exp.sanitizeUniprotAccessions <- c( 'O08601', 'P55158', 'P55157', 'Q865F1',
'P55156', 'Q961S9', 'B4Q3W8', 'B4IFI6', 'B3NKW4', 'B4P714' )
checkEquals( as.character( res.sanitizeUniprotAccessions[ , 'hit.name' ] ),
exp.sanitizeUniprotAccessions )
# Test mergeQueryPredictionsAndHomologAnnotations
print("Testing mergeQueryPredictionsAndHomologAnnotations(...)")
prot.acc <- 'Protein_1'
pf.preds <- read.table( project.file.path(
'test_phylo_fun_predictions.tbl' ), header=T )
f <- file( project.file.path(
'test_go_type_annotations_R_serialized.txt' ), 'r' )
gt.annos <- unserialize( f )
close( f )
res.merged <- mergeQueryPredictionsAndHomologAnnotations( prot.acc,
pf.preds, gt.annos )
checkTrue( ! is.null( res.merged ) )
checkEquals( class(res.merged), 'list' )
go.types <- c( 'biological_process',
'cellular_component', 'molecular_function' )
checkEquals( names( res.merged ), go.types )
for ( go.type in go.types ) {
res.gt <- res.merged[[ go.type ]]
gt.pf.pred <- as.character( res.gt[ 'GO', prot.acc ][[ 1 ]] )
exp.gt.pf.pred <- as.character(
pf.preds[ which( pf.preds[ , 'term_type' ] == go.type ), 'acc' ]
)
print( checkEquals( gt.pf.pred, exp.gt.pf.pred ) )
go.tp.annos <- res.gt[ ,
setdiff( colnames( res.gt ), prot.acc ), drop=F
]
print( checkEquals( go.tp.annos, gt.annos[[ go.type ]] ) )
}
# Test replaceSelenocysteinInFasta
print("Testing replaceSelenocysteinInFasta(...)")
res.replaceSelenocysteinInFasta <- replaceSelenocysteinInFasta( project.file.path( 'aa_seqs_with_u.fasta'), 'tmp_rslt.fasta' )
aa.seqs.fltrd <- readAAStringSet( 'tmp_rslt.fasta' )
checkEquals( names( aa.seqs.fltrd ), c( 'protein_1', 'protein_2' ) )
checkEquals( toString( aa.seqs.fltrd[[ 1 ]] ), 'xxxxxxxxxxxxxXXXXXXXXXXXXXXXXX' )
checkEquals( toString( aa.seqs.fltrd[[ 2 ]] ), 'MSTVAAYAAMSATExXxXxXPLTKTTITRS' )
unlink( 'tmp_rslt.fasta' )
# Test proteinPairsSharingAnnotation
print("Testing proteinPairsSharingAnnotation(...)")
prots <- read.table( text=
"A A
B B
C C
A B
B C
A D", stringsAsFactors=FALSE )
prot.annos <- read.table( stringsAsFactors=FALSE, text=
"GO:0001234 IEA A
GO:0001234 IEA B
GO:0001234 IEA D" )
res.proteinPairsSharingAnnotation <- proteinPairsSharingAnnotation(
'GO:0001234', prots, prot.annos )
exp.proteinPairsSharingAnnotation <- read.table( stringsAsFactors=FALSE, text=
"A A TRUE
B B TRUE
A B TRUE
B C FALSE
A D TRUE
")
checkEquals(
as.character( unlist( res.proteinPairsSharingAnnotation ) ),
as.character( unlist( exp.proteinPairsSharingAnnotation ) )
)
#################################################################
# The following function is the only one tested that is of file #
# geneOntologySql.R #
#################################################################
# Test selectMostSignificantEvidenceCode
print("Testing selectMostSignificantEvidenceCode(...)")
res.selectMostSignificantEvidenceCode <- selectMostSignificantEvidenceCode( c( 'EXP', 'TAS', 'IEA', 'IDA' ) )
exp.selectMostSignificantEvidenceCode <- 'EXP'
checkEquals( res.selectMostSignificantEvidenceCode, exp.selectMostSignificantEvidenceCode )
res.selectMostSignificantEvidenceCode <- selectMostSignificantEvidenceCode( 'IEA' )
exp.selectMostSignificantEvidenceCode <- 'IEA'
checkEquals( res.selectMostSignificantEvidenceCode, exp.selectMostSignificantEvidenceCode )
res.selectMostSignificantEvidenceCode <- selectMostSignificantEvidenceCode( c( 'IEA', 'IC' ) )
exp.selectMostSignificantEvidenceCode <- 'IC'
checkEquals( res.selectMostSignificantEvidenceCode, exp.selectMostSignificantEvidenceCode )
# Test uniqueGOAnnotationsWithMostSignificantEvidenceCodes
print("Testing uniqueGOAnnotationsWithMostSignificantEvidenceCodes(...)")
clean.up.anno.df <- read.table( stringsAsFactors=FALSE, text=
"GO:0001234 IEA A
GO:0001234 IEA B
GO:0001234 IC B
GO:0001234 IEA D" )
res.uniqueGOAnnotationsWithMostSignificantEvidenceCodes <- uniqueGOAnnotationsWithMostSignificantEvidenceCodes( clean.up.anno.df )
exp.uniqueGOAnnotationsWithMostSignificantEvidenceCodes <- read.table( stringsAsFactors=FALSE, text=
"GO:0001234 IEA A
GO:0001234 IC B
GO:0001234 IEA D" )
rownames( res.uniqueGOAnnotationsWithMostSignificantEvidenceCodes ) <- c()
checkEquals( res.uniqueGOAnnotationsWithMostSignificantEvidenceCodes, exp.uniqueGOAnnotationsWithMostSignificantEvidenceCodes )
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