Source code for galaxy.datatypes.converters.tabular_csv

#!/usr/bin/env python
Uses the python csv library to convert to and from tabular

usage: %prog [--from-tabular] -i in_file -o out_file

import argparse
import csv

[docs]def main(): usage = "Usage: %prog [options]" parser = argparse.ArgumentParser(usage=usage) parser.add_argument("-f", "--from-tabular", action="store_true", default=False, dest="fromtabular") parser.add_argument("-i", "--input", type=str, dest="input") parser.add_argument("-o", "--output", type=str, dest="output") args = parser.parse_args() input_fname = args.input output_fname = args.output if args.fromtabular: convert_to_csv(input_fname, output_fname) else: convert_to_tsv(input_fname, output_fname)
[docs]def convert_to_tsv(input_fname, output_fname): with open(input_fname, newline="") as csvfile, open(output_fname, "w") as ofh: reader = csv.reader(csvfile) for line in reader: ofh.write("\t".join(line) + "\n")
[docs]def convert_to_csv(input_fname, output_fname): with open(input_fname) as tabfile, open(output_fname, "w", newline="") as ofh: writer = csv.writer(ofh, delimiter=",") for line in tabfile.readlines(): writer.writerow(line.strip().split("\t"))
if __name__ == "__main__": main()