# Path: alfpy/wmetric.py
# def count_seq_chars(seq, alphabet):
# def freq_seq_chars(counts):
# def freq_seqs_chars(seq_records, alphabet):
#     def __init__(self, seq_records, matrix):
#     def pairwise_distance(self, seqnum1, seqnum2):
# def main():
# class Distance:
# 
# Path: alfpy/utils/distmatrix.py
# def create(id_list, distance):
# def read_highcharts_matrix(id_list, data):
#     def __init__(self, id_list, data):
#     def normalize(self):
#     def __iter__(self):
#     def writer(self, handle, f, decimal_places):
#     def display(self, f="phylip", decimal_places=7):
#     def write_to_file(self, handle, f="phylip", decimal_places=7):
#     def highcharts(self):
#     def format(self, decimal_places=7):
#     def min(self):
#     def max(self):
#     def is_zero(self):
#     def __repr__(self):
# class Matrix():
# 
# Path: alfpy/utils/seqrecords.py
# class SeqRecords:
#     def __init__(self, id_list=None, seq_list=None):
#     def add(self, seqid, seq):
#     def fasta(self, wrap=70):
#     def length_list(self):
#     def __iter__(self):
#     def __len__(self):
#     def __repr__(self):
# def read_fasta(handle):
# def main():
# 
# Path: alfpy/utils/data/subsmat.py
# class SubsMat:
#     def __init__(self, name, data, alphabet_list):
# def get_alphabet_list(name):
# def get(name):
# def list_subsmats():
# def main():
# 
# Path: alfpy/version.py



import argparse
import sys
from alfpy import wmetric
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.utils.data import subsmat
from alfpy.version import __version__
#! /usr/bin/env python

# Copyright (c) 2016 Zielezinski A, combio.pl




def get_parser():
    parser = argparse.ArgumentParser(
        description='''Calculate distances between protein sequences based
        on W-metric (Wm).''', add_help=False, prog='calc_wmetric.py'
    )
    group = parser.add_argument_group('REQUIRED ARGUMENTS')
    group.add_argument('--fasta', '-f',
                       help='input FASTA sequence filename', required=True,
                       type=argparse.FileType('r'), metavar="FILE")

    l = subsmat.list_subsmats()
    group = parser.add_argument_group('OPTIONAL ARGUMENTS')
    group.add_argument('--matrix', '-m', choices=l,
                       help='choose from: {} [DEFAULT: %(default)s]'.format(
                           ", ".join(l)), metavar='',

# Path: alfpy/wmetric.py
# def count_seq_chars(seq, alphabet):
# def freq_seq_chars(counts):
# def freq_seqs_chars(seq_records, alphabet):
#     def __init__(self, seq_records, matrix):
#     def pairwise_distance(self, seqnum1, seqnum2):
# def main():
# class Distance:
# 
# Path: alfpy/utils/distmatrix.py
# def create(id_list, distance):
# def read_highcharts_matrix(id_list, data):
#     def __init__(self, id_list, data):
#     def normalize(self):
#     def __iter__(self):
#     def writer(self, handle, f, decimal_places):
#     def display(self, f="phylip", decimal_places=7):
#     def write_to_file(self, handle, f="phylip", decimal_places=7):
#     def highcharts(self):
#     def format(self, decimal_places=7):
#     def min(self):
#     def max(self):
#     def is_zero(self):
#     def __repr__(self):
# class Matrix():
# 
# Path: alfpy/utils/seqrecords.py
# class SeqRecords:
#     def __init__(self, id_list=None, seq_list=None):
#     def add(self, seqid, seq):
#     def fasta(self, wrap=70):
#     def length_list(self):
#     def __iter__(self):
#     def __len__(self):
#     def __repr__(self):
# def read_fasta(handle):
# def main():
# 
# Path: alfpy/utils/data/subsmat.py
# class SubsMat:
#     def __init__(self, name, data, alphabet_list):
# def get_alphabet_list(name):
# def get(name):
# def list_subsmats():
# def main():
# 
# Path: alfpy/version.py



# Path: bin/calc_wmetric.py
import argparse
import sys
from alfpy import wmetric
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.utils.data import subsmat
from alfpy.version import __version__

#! /usr/bin/env python

# Copyright (c) 2016 Zielezinski A, combio.pl




def get_parser():
    parser = argparse.ArgumentParser(
        description='''Calculate distances between protein sequences based
        on W-metric (Wm).''', add_help=False, prog='calc_wmetric.py'
    )
    group = parser.add_argument_group('REQUIRED ARGUMENTS')
    group.add_argument('--fasta', '-f',
                       help='input FASTA sequence filename', required=True,
                       type=argparse.FileType('r'), metavar="FILE")

    l = subsmat.list_subsmats()
    group = parser.add_argument_group('OPTIONAL ARGUMENTS')
    group.add_argument('--matrix', '-m', choices=l,
                       help='choose from: {} [DEFAULT: %(default)s]'.format(
                           ", ".join(l)), metavar='',

                       default="blosum62")