From ca87357da33d711e45d02fb28995b35d3e2e1a0e Mon Sep 17 00:00:00 2001
From: Taha Ahmed <taha@asks2>
Date: Thu, 16 Feb 2012 21:41:43 +0100
Subject: [PATCH] Changed implementation to dirname(basename()). This should be
 more robust. ...

This should be more robust as the dirname follows a more stringent format
than the filename itself.
---
 ProvideSampleId.R | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/ProvideSampleId.R b/ProvideSampleId.R
index 24a9840..b3a9e99 100644
--- a/ProvideSampleId.R
+++ b/ProvideSampleId.R
@@ -3,7 +3,14 @@ ProvideSampleId <- function (pathexpfile) {
    # with a path to an experimental file.
    ## Note: the sample ID must derive directly from the file or path.
    
-   sampleid <- sub("\\.[\\w]+$", "", basename(pathexpfile), perl = TRUE)
+   # basename(dirname()) returns the name of the lowest sub-directory
+   # split()[[1]][2] splits the dirname at the hyphen and returns the sampleid
+   sampleid <- strsplit(x = basename(dirname(pathexpfile)),
+                        split = "-")[[1]][2]
+   
+#    # basename() returns the filename sans path
+#    # sub() returns the filename sans extension
+#    sampleid <- sub("\\.[\\w]+$", "", basename(pathexpfile), perl = TRUE)
    
    #### The code below is the old ProvideSampleId() function   
    #  ### OBS! Only very rudimentary error-checking.