diff list-file-cols.py @ 5:fb9c0409d85c draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/list-file-cols.py	Wed Apr 19 10:00:05 2017 -0400
@@ -0,0 +1,61 @@
+#!/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))