In paodan/prideDownloader:

#### run test ####
# speciesFilter is the for species, 9606 is homo sapiens.
cnt = prideCount(query = "breast", speciesFilter = 9606)
cnt
srch = prideSearch(query = "breast", speciesFilter = 9606, show = 1000)
View(srch)

# Quantification
srchEx =prideSearchExtra(srch$accession)
View(srchEx)

lnk = prideLink(rownames(srchEx[srchEx$quantification == "Label free", ]))
prideDownload(lnk[1:30, ], fileMaxSize = 40, fileType = "SEARCH",
              path = "../PXD_Breast/")


lnk = prideLink(srch$accession[1:31])
View(lnk)
prideDownload(lnk[1:50,], fileMaxSize = 4, fileType = "SEARCH",
              path = "")


# available, first 4 files
ava = srchEx[srchEx$quantification != "Not available",]
lnk = prideLink(rownames(ava))
ext3 = substr(lnk$fileName, nchar(lnk$fileName)-2, nchar(lnk$fileName))
ext4 = substr(lnk$fileName, nchar(lnk$fileName)-3, nchar(lnk$fileName))
table(ext3)
table(ext4)
ext = tools::file_ext(lnk$fileName)
id = ext %in% c(".7z", ".gz", ".zip", ".csv", ".rar", ".tsv", ".txt", ".xls", ".xls")
# id = ext3 %in% c(".7z", ".gz") |
#   ext4 %in% c(".zip", ".csv", ".rar", ".tsv", ".txt", ".xls", ".xls")
# id = ext4 %in% c(".zip")
downloadLink = subset(lnk[id, ], fileType == "SEARCH")
downloadLink = downloadLink[order(downloadLink$fileSize, decreasing = T), ]
write.csv(downloadLink, file = "../sampleLink/downloadLink.csv")

prideDownload(prideLinks = downloadLink[downloadLink$fileSize < 10^10, ], fileMaxSize = 60, fileType = "SEARCH",
              path = "../PXD_Breast/")

paodan/prideDownloader documentation built on May 6, 2019, 11:44 a.m.