csv_table2dict.py

#!/usr/bin/env python3
# encoding: utf-8

import glob
import os
import csv
import sys
from collections import defaultdict as ddict
import pprint as pp

if __name__ == '__main__':
    print('''
        Converting parameter tables from csv to params dict
''')
    input_file = sys.argv[1]
    output_file_name = sys.argv[1]

    # from ursgal_params import ursgal_params as urgsal_dict

    urgsal_dict = {}
    n = 0
    with open(input_file, 'r') as csvfile:
        reader = csv.DictReader(csvfile)
        for row in reader:
            if row['ursgal_params'] != '':
                ukey = row['ursgal_params']
            else:
                n += 1
                ukey = 'ukey{0}'.format(n)
            urgsal_dict[ ukey ] = {}
            description = ''
            urgsal_dict[ ukey ][ 'description' ] = row['ursgal_params_description'].strip()
            urgsal_dict[ ukey ][ 'default_value' ] = row['ursgal_default_params'].strip()
            available_in_unode = []
            translation = {}
            for engine in ['xtandem', 'omssa', 'msgfplus', 'myrimatch', 'msamanda']:
                for row_key, row_value in row.items():
                    if engine in row_key and row_value != '':
                        available_in_unode.append(engine)
                        translation['{0}_style_1'.format(engine)] = row_value.strip()

            urgsal_dict[ ukey ][ 'available_in_unode' ] = available_in_unode
            urgsal_dict[ ukey ][ 'utag' ] = ''
            urgsal_dict[ ukey ][ 'ukey_translation' ] = translation
            urgsal_dict[ ukey ][ 'uvalue_type' ] = ''
            urgsal_dict[ ukey ][ 'uvalue_translation' ] = ''

    csvfile.close()

    output_file = open(output_file_name, 'w')
    print('ursgal_params={', file=output_file)
    for param in sorted(urgsal_dict.keys()):
        print('''    '{0}':{1}'''.format(param, '{'), file=output_file )
        for k, v in sorted(urgsal_dict[param].items()):
            if k == 'description':
                print('''        '{0}':'''.format(k), "'''", v.strip(), "''',", file=output_file)
                continue
            if type(v) == str:
                print('''        '{0}':"{1}",'''.format(k,v), file=output_file)
            elif type(v) == dict:
                print('''        '{0}':{1}'''.format(k, '{'), file=output_file)
                for k2, v2 in sorted(urgsal_dict[param][k].items()):
                    print('''            '{0}':'{1}','''.format(k2,v2), file=output_file)
                print('        },', file=output_file)
            elif type(v) == list:
                print('''        '{0}':{1}'''.format(k, '['), file=output_file)
                for elem in sorted(v):
                    print('''            '{0}','''.format(elem), file=output_file)
                print('        ],', file=output_file)
            else:
                print('''        '{0}':'{1}','''.format(k,v), file=output_file)
        # pp.pprint(urgsal_dict, width=200, stream=output_file)
        print('    },', file=output_file)
    print('}', file=output_file)
    # pp.pprint(urgsal_dict)
    output_file.close()