diff unsorted_uniq.py @ 0:ec66f9d90ef0 draft

initial uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/unsorted_uniq.py	Thu Sep 05 04:58:21 2013 -0400
@@ -0,0 +1,36 @@
+import sys
+import subprocess
+
+"""
+    We only need that file because galaxy do not understand the -t $'\t' term.
+    Otherwise that would be the right XML-only solution:
+    sort -u 
+        $ignore_case
+        $is_numeric
+        -t \$'\t'
+        #if $adv_opts.adv_opts_selector=="advanced":
+            -k$adv_opts.column_start,$adv_opts.column_end
+        #end if
+        -o $outfile
+        $input
+"""
+
+if sys.argv[1].strip() != 'false':
+    ignore_case = sys.argv[1]
+else:
+    ignore_case = ''
+
+if sys.argv[2].strip() != 'false':
+    is_numeric = sys.argv[2]
+else:
+    is_numeric = ''
+
+try:
+    col_start = sys.argv[3]
+    col_end = sys.argv[4]
+    com = "sort -u %s %s -t '	' -k%s,%s -o %s %s" % (is_numeric, ignore_case, col_start, col_end, sys.argv[5], sys.argv[6])
+except:
+    # no advanced options selected
+    com = "sort -u %s %s -t '	' -o %s %s" % (is_numeric, ignore_case, sys.argv[3], sys.argv[4])
+
+subprocess.call(com, shell=True)