| Next changeset 1:6e7cf5ed7d62 (2014-05-20) |
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Commit message:
Uploaded |
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added:
converter.py |
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| diff -r 000000000000 -r aae5945b961e converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/converter.py Tue May 20 03:23:20 2014 -0400 |
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| @@ -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() |