diff list-file-cols.py @ 6:f86fec07f392 draft default tip

planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce

--- a/list-file-cols.py	Wed Apr 19 10:00:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-#!/usr/bin/env python
-# vi: fdm=marker
-
-import csv
-import re
-import argparse
-
-# Get file cols {{{1
-################################################################
-
-def get_file_cols(file, preferred):
-
-	cols = []
-
-	with open(file if isinstance(file, str) else file.get_file_name(), 'r') as f:
-
-		# Read file header
-		reader = csv.reader(f, delimiter = "\t", quotechar='"')
-		header = reader.next()
-
-		preferred = preferred.split(',')
-
-		# Determine default value
-		perfect_matches = []
-		partial_matches = []
-		for p in preferred:
-			for c in header:
-				if c == p:
-					perfect_matches.append(c) # Perfect match !
-				elif re.match(p, c):
-					partial_matches.append(c) # Keep this partial match in case we find no perfect match
-
-		ordered_cols = perfect_matches + partial_matches
-		for c in header:
-			if not c in ordered_cols:
-				ordered_cols.append(c)
-		ordered_cols.append('NA')
-
-		default = 0
-		if len(perfect_matches) + len(partial_matches) == 0:
-			default = len(ordered_cols) - 1
-
-		# Build list of cols
-		for i, c in enumerate(ordered_cols):
-			cols.append( (c, c, i == default) )
-
-	return cols
-
-# Main {{{1
-################################################################
-
-if __name__ == '__main__':
-    
-    # Parse command line arguments
-    parser = argparse.ArgumentParser(description='Script for getting column names in a csv file.')
-    parser.add_argument('-f', help = 'CSV File (separator must be TAB)',       dest = 'file',    required = True)
-    parser.add_argument('-p', help = 'List (comma separated values) of preferred column names for default one.',        dest = 'preferred',     required = True)
-    args = parser.parse_args()
-    args_dict = vars(args)
-    
-    print(get_file_cols(**args_dict))