#!/usr/bin/env python

# encoding: utf-8

"""

ped_parser

Command Line Interface for ped_parser

Created by Måns Magnusson on 2014-12-22.

Copyright (c) 2014 __MoonsoInc__. All rights reserved.

"""

from __future__ import print_function

import sys

import os

import click

from datetime import datetime

from codecs import open

from ped_parser import FamilyParser, init_log, logger, __version__

def print_version(ctx, param, value):

"""Callback function for printing version and exiting

Args:

ctx (object) : Current context

param (object) : Click parameter(s)

value (boolean) : Click parameter was supplied or not

Returns:

None:

"""

if not value or ctx.resilient_parsing:

return

click.echo('ped_parser version: ' + __version__)

ctx.exit()

### This is the main script ###

@click.command()

@click.argument('family_file',

nargs=1,

type=click.File('r'),

metavar='<family_file> or -'

)

@click.option('-t', '--family_type',

type=click.Choice(['ped', 'alt', 'cmms', 'mip']),

default='ped',

help='If the analysis use one of the known setups, please specify which one. Default is ped'

)

@click.option('-o', '--outfile',

type=click.File('a'),

help='Specify the path to a file where results should be stored.'

)

@click.option('--cmms_check',

is_flag=True,

help='If the id is in cmms format.'

)

@click.option('--to_json',

is_flag=True,

help='Print the ped file in json format.'

)

@click.option('--to_madeline',

is_flag=True,

help='Print the ped file in madeline format.'

)

@click.option('--to_ped',

is_flag=True,

help='Print the ped file in ped format with headers.'

)

@click.option('--to_dict',

is_flag=True,

help='Print the ped file in ped format with headers.'

)

@click.option('-v', '--verbose',

is_flag=True,

help='Increase output verbosity.'

)

@click.option('--version',

is_flag=True,

callback=print_version,

expose_value=False,

is_eager=True

)

@click.option('-l', '--logfile',

type=click.Path(exists=False),

help="Path to log file. If none logging is "\

"printed to stderr."

)

@click.option('--loglevel',

type=click.Choice(['DEBUG', 'INFO', 'WARNING', 'ERROR',

'CRITICAL']),

help="Set the level of log output."

)

def cli(family_file, family_type, outfile, to_json, to_madeline,

cmms_check, to_ped, to_dict, verbose, logfile, loglevel):

"""Tool for parsing ped files.\n

Default is to prints the family file to in ped format to output.

For more information, please see github.com/moonso/ped_parser.

"""

from pprint import pprint as pp

if not loglevel:

if verbose:

loglevel = 'INFO'

else:

loglevel = 'WARNING'

# Setup the logging environment

init_log(logger, logfile, loglevel)

my_parser = FamilyParser(family_info=family_file, family_type=family_type,

cmms_check=cmms_check)

start = datetime.now()

logger.info('Families found in file: {0}'.format(

','.join(list(my_parser.families.keys()))

)

)

if to_json:

if outfile:

outfile.write(my_parser.to_json())

else:

print(my_parser.to_json())

elif to_madeline:

for line in my_parser.to_madeline():

if outfile:

outfile.write(line + '\n')

else:

print(line)

elif to_ped:

for line in my_parser.to_ped():

if outfile:

outfile.write(line + '\n')

else:

print(line)

elif to_dict:

pp(my_parser.to_dict())

else:

# If no specific output is choosen, write a summary about the families to screen

for family in my_parser.families:

logger.info('Fam: {0}'.format(family))

if family_type in ['cmms', 'mip']:

logger.info('Expected Inheritance Models: {0}'.format(

my_parser.families[family].models_of_inheritance

)

)

logger.info('Individuals: ')

for individual in my_parser.families[family].individuals:

logger.info(my_parser.families[family].individuals[individual])

logger.info('Affected individuals: {0} \n'.format(

','.join(my_parser.families[family].affected_individuals)

)

)

if __name__ == '__main__':

cli()