diff filter_tabular.py @ 0:6fbd9d25ceef draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_tabular.py	Tue Jul 18 09:06:47 2017 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import json
+import optparse
+import os.path
+import sys
+
+from filters import filter_file
+
+
+def __main__():
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('-i', '--input', dest='input', default=None,
+                      help='Input file for filtering')
+    parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None,
+                      help='JSON array of filter specifications')
+    parser.add_option('-o', '--output', dest='output', default=None,
+                      help='Output file for query results')
+    parser.add_option('-v', '--verbose', dest='verbose', default=False,
+                      action='store_true',
+                      help='verbose')
+    (options, args) = parser.parse_args()
+
+    if options.input is not None:
+        try:
+            inputPath = os.path.abspath(options.input)
+            inputFile = open(inputPath, 'r')
+        except Exception as e:
+            exit('Error: %s' % (e))
+    else:
+        inputFile = sys.stdin
+
+    if options.output is not None:
+        try:
+            outputPath = os.path.abspath(options.output)
+            outputFile = open(outputPath, 'w')
+        except Exception as e:
+            exit('Error: %s' % (e))
+    else:
+        outputFile = sys.stdout
+
+    filters = None
+    if options.jsonfile:
+        try:
+            with open(options.jsonfile) as fh:
+                filters = json.load(fh)
+        except Exception as e:
+            exit('Error: %s' % (e))
+
+    if options.verbose and filters:
+        for f in filters:
+            print('%s  %s' % (f['filter'],
+                  ', '.join(
+                  ['%s: %s' % (k, f[k])
+                   for k in set(f.keys()) - set(['filter'])])),
+                  file=sys.stdout)
+
+    try:
+        filter_file(inputFile, outputFile, filters=filters)
+    except Exception as e:
+        exit('Error: %s' % (e))
+
+
+if __name__ == "__main__":
+    __main__()