check_allen.R

library(jaffelab)

## PDF --> Excel using Adobe Acrobat
## Excel --> TSV using Excel
## scan subsequent text file
x = scan("HBA_ISH_GeneList.txt", what = "character", sep = "\n")

## get rows for each table
ind = c(1, grep("Table", x), nrow(x))
names(ind) = gsub("\"", "", gsub(" ", "", ss(x[ind], "\\.", 1)))
names(ind)[c(1, length(ind))] = c("Table1", "Table5")

## get row indicies
indList = split(ind, names(ind))

first = sapply(indList, "[[", 1)
second = c(first[-1] - 1, length(x))
indList2 = mapply(function(x, y)
    x:y, first, second)

## subset
tableList = lapply(indList2, function(ii)
    x[ii])

## manually clean up
tableList$Table1 = tableList$Table1[-(1:3)]
tableList = lapply(tableList, function(x)
    x[-(1:2)])

## read in
datList = lapply(tableList[-3], function(x) {
    read.delim(text = x,
        as.is = TRUE,
        header = TRUE)
})
datList = lapply(datList, function(x) {
    x[, colMeans(is.na(x)) < 1]
})

## fix table 3
tab3 = tableList$Table3
tab3 = tab3[!grepl("Gene", tab3)]
tab3 = tab3[!grepl("Character", tab3)]
tab3 = tab3[!grepl("Table 3", tab3)]
tab3 = tab3[!grepl("System", tab3)]
tab3 = tab3[!grepl("Symbol", tab3)]

dat3 = read.delim(text = tab3,
    as.is = TRUE,
    header = FALSE)
dat3 = dat3[, colMeans(is.na(dat3)) < 1]
colnames(dat3) = c(
    "Gene.Symbol",
    "EntrezID",
    "Gene.Description",
    "Characterized",
    "System",
    "Family" ,
    "Marker.Type"
)
datList$Table3 = dat3

datList = datList[paste0("Table", 1:5)]
dir.create("tables")
for (i in seq(along = datList)) {
    write.table(datList[[i]],
        paste0("tables/allen_HBA_ISH_GeneList_Table", i, ".txt"),
        row.names = FALSE)
}
zip("allen_HBA_ISH_GeneList_Tables.zip",
    files = list.files("tables", full = TRUE))