R/add_ext_read.R

In OchoaLab/genio: Genetics Input/Output Functions

# Tries to fix path when a name is provided but not found, and an extension is expected
# This function simply returns the input path when its guesses don't result in files that exist, doesn't die unless arguments are missing.
#
# Internal function    
add_ext_read <- function(file, ext) {
    # both inputs are mandatory
    if (missing(file))
        stop('Input file is required!')
    if (missing(ext))
        stop('Expected file extension (ext) is required!')
    
    # if "file" was not a character object, then the following manipulations won't work, so just return that and hope for the best
    if (!is.character(file))
        return(file)
    # ditto if file already exists, we're set!
    # (includes all ext cases, even if not matching!)
    # make sure it's not a directory too, which has happened to me!  (in this case we ignore the directory, and we add extension as desired.  Note later tests add extensions already so we don't keep asking if those are directories; it would be exceedingly weird for a directory to have a file extension though it's legal!)
    if ( file.exists(file) && !dir.exists( file ) )
        return(file)
    # now assume file as specified is not found

    # if the file already ends in .gz, don't do anything!
    # this is because .gz must be the final extension, we won't try to fix this path
    if ( grepl('\\.gz$', file) )
        return(file)
    # now assume .gz is missing

    # test presence of expected extension
    # in the absence of .gz, the expected extension must be the last one ("$" in regex below)
    # this can also conveniently handle ext=NA and gz case
    if ( is.na( ext ) || grepl( paste0('\\.', ext, '$'), file) ) {
        # here we already have the expected extension but not .gz, and the file as-is didn't exist, try adding .gz
        fileGz <- paste0(file, '.gz')
        # if the second version exists, use that!
        if (file.exists(fileGz))
            file <- fileGz
        # return file, whatever that is here
        return(file)
    }

    # NOTE: here ext != NA
    # now assume both extensions are missing
    # add extension first
    fileExt <- paste0(file, '.', ext)
    if (file.exists(fileExt)) {
        # if the second version exists, use that!
        # (otherwise stay with file, whatever that is)
        file <- fileExt
    } else {
        # try add gzip extension too
        fileExtGz <- paste0(fileExt, '.gz')
        if (file.exists(fileExtGz))
            file <- fileExtGz
    }
    
    # return whatever file is now (in case of failure it's just input)
    return(file)
}