Python multiple_file_alpha Examples

Example #1

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)
    if opts.show_metrics:
        print("Known metrics are: %s\n" \
              % (', '.join(list_known_metrics()),))
        print(
            "For more information, see http://qiime.org/scripts/alpha_diversity_metrics.html"
        )
        exit(0)
    almost_required_options = ['input_path', 'output_path', 'metrics']
    for option in almost_required_options:
        if getattr(opts, option) == None:
            option_parser.error('Required option --%s omitted.' % option)

    if os.path.isdir(opts.input_path):
        multiple_file_alpha(opts.input_path, opts.output_path, opts.metrics,
                            opts.tree_path)
    elif os.path.isfile(opts.input_path):
        try:
            f = open(opts.output_path, 'w')
            f.close()
        except IOError:
            if os.path.isdir(opts.output_path):
                option_parser.error(
                    "ioerror, couldn't create output file. The output path is a directory, which should be a single file"
                )
            else:
                option_parser.error("ioerror, couldn't create output file")
        single_file_alpha(opts.input_path, opts.metrics, opts.output_path,
                          opts.tree_path)

Example #2

File: alpha_diversity.py Project: andrea-campisano/qiime

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)
    if opts.show_metrics:
        print("Known metrics are: %s\n" \
              % (', '.join(list_known_metrics()),))
        print("For more information, see http://qiime.org/scripts/alpha_diversity_metrics.html")
        exit(0)
    almost_required_options = ['input_path','output_path','metrics']
    for option in almost_required_options:
        if getattr(opts,option) == None:
            option_parser.error('Required option --%s omitted.' % option)
    
    if os.path.isdir(opts.input_path):
      multiple_file_alpha(opts.input_path, opts.output_path, opts.metrics, 
        opts.tree_path)
    elif os.path.isfile(opts.input_path):
      try:
          f = open(opts.output_path, 'w')
          f.close()
      except IOError:
          print("ioerror, couldn't create output file")
          exit(1)
      single_file_alpha(opts.input_path, opts.metrics, 
          opts.output_path, opts.tree_path)
    else:
      print("io error, input path not valid. does it exist?")
      exit(1)

Example #3

File: alpha_diversity.py Project: YuJinhui/qiime

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)
    if opts.show_metrics:
        print("Known metrics are: %s\n"
              % (', '.join(list_known_metrics()),))
        print("For more information, see http://scikit-bio.org/docs/latest/ge"
              "nerated/skbio.diversity.alpha.html#module-skbio.diversity.alpha")
        exit(0)
    almost_required_options = ['input_path', 'output_path', 'metrics']
    for option in almost_required_options:
        if getattr(opts, option) is None:
            option_parser.error('Required option --%s omitted.' % option)

    if os.path.isdir(opts.input_path):
        multiple_file_alpha(opts.input_path, opts.output_path, opts.metrics,
                            opts.tree_path)
    elif os.path.isfile(opts.input_path):
        try:
            f = open(opts.output_path, 'w')
            f.close()
        except IOError:
            if os.path.isdir(opts.output_path):
                option_parser.error(
                    "ioerror, couldn't create output file. The output path is a directory, which should be a single file")
            else:
                option_parser.error("ioerror, couldn't create output file")
        single_file_alpha(opts.input_path, opts.metrics,
                          opts.output_path, opts.tree_path)

Example #4

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    if opts.show_metrics:
        print("Known metrics are: %s\n" \
              % (', '.join(list_known_metrics()),))
        exit(0)
    almost_required_options = ['input_path', 'output_path', 'metrics']
    for option in almost_required_options:
        if getattr(opts, option) == None:
            option_parser.error('Required option --%s omitted.' % option)

    if os.path.isdir(opts.input_path):
        multiple_file_alpha(opts.input_path, opts.output_path, opts.metrics,
                            opts.tree_path)
    elif os.path.isfile(opts.input_path):
        try:
            f = open(opts.output_path, 'w')
            f.close()
        except IOError:
            print("ioerror, couldn't create output file")
            exit(1)
        single_file_alpha(opts.input_path, opts.metrics, opts.output_path,
                          opts.tree_path)
    else:
        print("io error, input path not valid. does it exist?")
        exit(1)