diff split_tabular_columns.py @ 0:d43312f961cc draft default tip

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_tabular_columns commit 1d5750b99b90bb1d2730c816a95849e9b9a7d2f9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_tabular_columns.py	Wed Mar 01 14:01:57 2017 -0500
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+"""
+#
+#------------------------------------------------------------------------------
+#                                                 University of Minnesota
+#                 Copyright 2016, Regents of the University of Minnesota
+#------------------------------------------------------------------------------
+# Author:
+#
+#    James E Johnson
+#
+#------------------------------------------------------------------------------
+"""
+
+"""
+Split selected columns on pattern
+and print a line for each item split
+
+For example:
+split_tabular_columns.py -c 3 -c 4 -s '; '
+with input line:
+1	1.3	id1; id2	desc1; desc2	AMDLID
+will be output as:
+1	1.3	id1	desc1	AMDLID
+1	1.3	id2	desc2	AMDLID
+"""
+
+import sys
+import os.path
+import optparse
+from optparse import OptionParser
+
+
+def __main__():
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('-i', '--input', dest='input', default=None, help='Tabular input file')
+    parser.add_option('-o', '--output', dest='output', default=None, help='Tabular output file')
+    parser.add_option('-c', '--column', type='int', action='append', dest='column', default=[], help='column ordinal to split')
+    parser.add_option('-s', '--split_on', dest='split_on', default=' ', help='String on which to split columns')
+    parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
+    (options, args) = parser.parse_args()
+    # Input file
+    if options.input is not None:
+        try:
+            inputPath = os.path.abspath(options.input)
+            inputFile = open(inputPath, 'r')
+        except Exception, e:
+            print >> sys.stderr, "failed: %s" % e
+            exit(2)
+    else:
+        inputFile = sys.stdin
+    # Output file
+    if options.output is not None:
+        try:
+            outputPath = os.path.abspath(options.output)
+            outputFile = open(outputPath, 'w')
+        except Exception, e:
+            print >> sys.stderr, "failed: %s" % e
+            exit(3)
+    else:
+        outputFile = sys.stdout
+    split_cols = [x - 1 for x in options.column]
+    split_on = options.split_on
+    try:
+        for i, line in enumerate(inputFile):
+            fields = line.rstrip('\r\n').split('\t')
+            split_fields = dict()
+            cnt = 0
+            for c in split_cols:
+                if c < len(fields):
+                    split_fields[c] = fields[c].split(split_on)
+                    cnt = max(cnt, len(split_fields[c]))
+            if cnt == 0:
+                print >> outputFile, "%s" % '\t'.join(fields)
+            else:
+                for n in range(0, cnt):
+                    flds = [x if c not in split_cols else split_fields[c][n] for (c, x) in enumerate(fields)]
+                    print >> outputFile, "%s" % '\t'.join(flds)
+    except Exception, e:
+        print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin', e)
+        exit(1)
+
+if __name__ == "__main__":
+    __main__()