diff converter.py @ 0:aae5945b961e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/converter.py	Tue May 20 03:23:20 2014 -0400
@@ -0,0 +1,41 @@
+# python 2.7
+# MB
+# Convertion multiple .dta files to one .csv file with coordinates
+# and one .csv file with sample names.
+
+from optparse import OptionParser
+from os.path import basename
+
+# Function for merging all files in .csv format 
+# and extracting the headers of the files.
+def main():
+    # extracting the users input
+    parser = OptionParser()
+    parser.add_option("--output")
+    parser.add_option("--output2")
+    parser.add_option("--input_file", action="append", default=[]) # multiple inputfiles
+    parser.add_option("--input_name", action="append", default=[]) # names of multiple inputfiles
+    (options, _) = parser.parse_args()
+
+    
+    header = ""
+    header_temp = "" 
+    # open every file and concatenate the files
+    with(open(options.output, "w")) as output:
+	with(open(options.output2, "w")) as output2:
+            for i, (input_file, input_name) in enumerate(zip(options.input_file, options.input_name)):
+		# open a input file
+            	for j, line in enumerate(open(input_file, "r").readlines()): 
+                    line = line.strip()  
+		    split_tabs = line.split('  ')
+		    number_columns = len(split_tabs)
+		    # extract name of sample
+    		    if j == 0:
+                    	header_temp = "%s" %(line.replace(' ', '_'))
+			header += "%s\n"%(header_temp[1:-4])
+		    # extract the coordinates  	
+		    if number_columns == 3: 
+                    	output.write("%f,%f,%f\n"%(float(split_tabs[0]),float(split_tabs[1]),float(split_tabs[2])))
+	    output2.write("%s\n"%(header)) # writing header to output file     #name of sample
+
+main()