Mercurial > repos > mb2013 > nepenthes_3dpca
comparison converter.py @ 0:aae5945b961e draft
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| author | mb2013 |
|---|---|
| date | Tue, 20 May 2014 03:23:20 -0400 |
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| children |
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| -1:000000000000 | 0:aae5945b961e |
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| 1 # python 2.7 | |
| 2 # MB | |
| 3 # Convertion multiple .dta files to one .csv file with coordinates | |
| 4 # and one .csv file with sample names. | |
| 5 | |
| 6 from optparse import OptionParser | |
| 7 from os.path import basename | |
| 8 | |
| 9 # Function for merging all files in .csv format | |
| 10 # and extracting the headers of the files. | |
| 11 def main(): | |
| 12 # extracting the users input | |
| 13 parser = OptionParser() | |
| 14 parser.add_option("--output") | |
| 15 parser.add_option("--output2") | |
| 16 parser.add_option("--input_file", action="append", default=[]) # multiple inputfiles | |
| 17 parser.add_option("--input_name", action="append", default=[]) # names of multiple inputfiles | |
| 18 (options, _) = parser.parse_args() | |
| 19 | |
| 20 | |
| 21 header = "" | |
| 22 header_temp = "" | |
| 23 # open every file and concatenate the files | |
| 24 with(open(options.output, "w")) as output: | |
| 25 with(open(options.output2, "w")) as output2: | |
| 26 for i, (input_file, input_name) in enumerate(zip(options.input_file, options.input_name)): | |
| 27 # open a input file | |
| 28 for j, line in enumerate(open(input_file, "r").readlines()): | |
| 29 line = line.strip() | |
| 30 split_tabs = line.split(' ') | |
| 31 number_columns = len(split_tabs) | |
| 32 # extract name of sample | |
| 33 if j == 0: | |
| 34 header_temp = "%s" %(line.replace(' ', '_')) | |
| 35 header += "%s\n"%(header_temp[1:-4]) | |
| 36 # extract the coordinates | |
| 37 if number_columns == 3: | |
| 38 output.write("%f,%f,%f\n"%(float(split_tabs[0]),float(split_tabs[1]),float(split_tabs[2]))) | |
| 39 output2.write("%s\n"%(header)) # writing header to output file #name of sample | |
| 40 | |
| 41 main() |