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export_data.py
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Tue, Jul 8, 21:08

export_data.py
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#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
#export_data.py
import os, argparse
from json import load, dump
def Error(f=__file__, msg='', to_rm=[]):
print 'Error ['+ os.path.basename(f) +']: '+ msg
if len(to_rm) > 0:
for t in to_rm:
rmtree(t)
raise SystemExit(1)
class Export(object):
"""Export data"""
def __init__(self, json_fp=''):
"""Set the parameters"""
argument_parser = argparse.ArgumentParser()
argument_parser._action_groups.pop()
required_arguments = argument_parser.add_argument_group('required arguments')
optional_arguments = argument_parser.add_argument_group('optional arguments')
required_arguments.add_argument('--input',
help='Path to input file.',
nargs=1,
type=str)
required_arguments.add_argument('--input_format',
help='Input format.',
nargs=1,
type=str)
required_arguments.add_argument('--output',
help='Path to output file.',
nargs=1,
type=str)
optional_arguments.add_argument('--model',
help='Model',
nargs=1,
type=str)
optional_arguments.add_argument('--effect',
help='Effect',
nargs=1,
type=str)
optional_arguments.add_argument('--comparison',
help='Comparison',
nargs=1,
type=str)
self.params = argument_parser.parse_args().__dict__
def fc2txt(self):
"""Export changes"""
with open(self.params['input'][0], 'r') as f:
fc = load(f)
data = fc['data']
if len(fc['data']) == 1:
self.params['model'] = fc['data'].keys()
if len(fc['data'][self.params['model'][0]]) == 1:
self.params['effect'] = fc['data'][self.params['model'][0]].keys()
if len(fc['data'][self.params['model'][0]][self.params['effect'][0]]) == 1:
self.params['comparison'] = fc['data'][self.params['model'][0]][self.params['effect'][0]].keys()
data = fc['data'][self.params['model'][0]][self.params['effect'][0]][self.params['comparison'][0]]
header = data[0].keys()
row_names = fc['names']
with open(self.params['output'][0], 'w') as out:
out.write('%s\t%s\n' % ('|'.join([self.params['model'][0], self.params['effect'][0], self.params['comparison'][0]]), '\t'.join(header)))
i = 0
for l in data:
out.write('%s\t%s\n' % (row_names[i], '\t'.join([l[k] for k in header])))
i = i+1
export = Export()
if export.params['input_format'] is not None and export.params['input_format'][0] == 'change':
export.fc2txt()
exit()

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