Nothing
## require(RUnit)
## require(UniProt.ws)
.check_rect_result <- function(res){
all(checkTrue(dim(res)[1] >1),
checkTrue(dim(res)[2] ==2))
}
## problem?
test_mapUniprot <- function(){
mapUniprot <- UniProt.ws:::mapUniprot
res <- mapUniprot(
from='ACC',to='P_REFSEQ_AC',
query=c('P13368','P20806','Q9UM73','P97793','Q17192')
)
.check_rect_result(res)
checkTrue(res[1,1]=='P13368')
checkTrue(res[1,2]=='NP_511114.2')
## what if I have entrezGene IDs and I want UniProts?
res <- mapUniprot(
from='P_ENTREZGENEID', to='ACC', query=c('1','2','3','9','10')
)
.check_rect_result(res)
checkTrue(res[1,1]=='1')
checkTrue(res[1,2]=='P04217')
## I can then map UniProt accessions to Unigene IDs
res <- mapUniprot(
from='ACC',to='GENENAME',
query=c('P04217','P01023','F5H5R8','P18440','Q400J6')
)
.check_rect_result(res)
## I can catch cases where the server returns results with double tabs
tt <- 'yourlist:M20181018A7434721E10EE6586998A056CCD0537EBF8181F\tisomap:M20181018A7434721E10EE6586998A056CCD0537EBF8181F\tEntry\tEntry name\tStatus\tProtein names\tGene names\tOrganism\tLength\n1\t\tP04217\tA1BG_HUMAN\treviewed\tAlpha-1B-glycoprotein (Alpha-1-B glycoprotein)\tA1BG\tHomo sapiens (Human)\t495\n1\t\tV9HWD8\tV9HWD8_HUMAN\tunreviewed\tEpididymis secretory sperm binding protein Li 163pA\tHEL-S-163pA\tHomo sapiens (Human)\t495\n2\t\tP01023\tA2MG_HUMAN\treviewed\tAlpha-2-macroglobulin (Alpha-2-M) (C3 and PZP-like alpha-2-macroglobulin domain-containing protein 5)\tA2M CPAMD5 FWP007\tHomo sapiens (Human)\t1474\n9\t\tF5H5R8\tF5H5R8_HUMAN\tunreviewed\tArylamine N-acetyltransferase 1\tNAT1\tHomo sapiens (Human)\t352\n9\t\tP18440\tARY1_HUMAN\treviewed\tArylamine N-acetyltransferase 1 (EC 2.3.1.5) (Arylamide acetylase 1) (Monomorphic arylamine N-acetyltransferase) (MNAT) (N-acetyltransferase type 1) (NAT-1)\tNAT1 AAC1\tHomo sapiens (Human)\t290\n9\t\tQ400J6\tQ400J6_HUMAN\tunreviewed\tArylamine N-acetyltransferase 1 (EC 2.3.1.5) (Arylamine N-acetyltrasnferase 1) (Fragment)\tNAT1\tHomo sapiens (Human)\t92\n10\t\tA4Z6T7\tA4Z6T7_HUMAN\tunreviewed\tArylamine N-acetyltransferase 2\tNAT2\tHomo sapiens (Human)\t290\n10\t\tP11245\tARY2_HUMAN\treviewed\tArylamine N-acetyltransferase 2 (EC 2.3.1.5) (Arylamide acetylase 2) (N-acetyltransferase type 2) (NAT-2) (Polymorphic arylamine N-acetyltransferase) (PNAT)\tNAT2AAC2\tHomo sapiens (Human)\t290\n'
res <- UniProt.ws:::.cleanup(tt, from = 'P_ENREZGENEID', to = 'ACC')
.check_rect_result(res)
checkTrue(res[1,1]=='1')
checkTrue(res[1,2]=='P04217')
}
test_getUniprotGoodies <- function(){
query = c('P04217','P30443')
cols = 'sequence'
res <- UniProt.ws:::getUniprotGoodies(query, cols)
checkTrue(is(res, "data.frame"))
checkTrue(dim(res)[1] == 2)
checkTrue(dim(res)[2] == 2)
## can also be used to extract interpro IDs
query = c('P13368','P20806','Q9UM73','P97793','Q17192')
cols = 'database(interpro)'
res <- UniProt.ws:::getUniprotGoodies(query, cols)
checkTrue(is(res, "data.frame"))
checkTrue(dim(res)[1] == 5)
checkTrue(dim(res)[2] == 2)
## OR extract a number of other things...
cols = c('3d','go-id','taxon')
res <- UniProt.ws:::getUniprotGoodies(query, cols)
checkTrue(is(res, "data.frame"))
checkTrue(dim(res)[1] == 5)
checkTrue(dim(res)[2] == 4)
}
## Faster testing:
## BiocGenerics:::testPackage(pattern="^test_serviceAccessors.*\\.R$")
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