# -*- coding: utf-8 -*-
#
#  This file is part of Sequana software
#
#  Copyright (c) 2016 - Sequana Development Team
#
#  File author(s):
#      Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
#      Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>, 
#          <d.desvillechabrol@gmail.com>
#
#  Distributed under the terms of the 3-clause BSD license.
#  The full license is in the LICENSE file, distributed with this software.
#
#  website: https://github.com/sequana/sequana
#  documentation: http://sequana.readthedocs.io
#
##############################################################################
"""Utilities to manipulate FASTQ and Reads

"""
import os

from pysam import FastxFile


__all__ = ["FastA"]

# cannot inherit from FastxFile (no object in the API ?)
class FastA(object):
    """Class to handle FastA files


    """
    def __init__(self, filename, verbose=False):
        self._fasta = FastxFile(filename)
        self._N = len([x for x in FastxFile(filename)])

    def __iter__(self):
        return self

    def __next__(self): # python 3
        return self.next()

    def next(self): # python 2
        # reads 4 lines
        try:
            d = next(self._fasta)
            return d
        except KeyboardInterrupt:
            # This should allow developers to break a loop that takes too long
            # through the reads to run forever
            self._fasta.close()
            self._fasta = FastxFile(self._fasta.filename)
        except:
            self._fasta.close()
            self._fasta = FastxFile(self._fasta.filename)
            raise StopIteration
        return d

    def __len__(self):
        return self._N

    def _get_names(self):
        return [this.name for this in self]
    names = property(_get_names)

    def _get_sequences(self):
        return [this.sequence for this in self]
    sequences = property(_get_sequences)

    def _get_comment(self):
        return [this.comment for this in self]
    comment = property(_get_comment)

    def format_contigs_denovo(self, output_file, len_min=500):
        """Replace NODE with the project name and remove contigs with a length 
        lower than len_min.

        :param str output_file: output file name.
        :param int len_min: minimal length of contigs.

        Example:
        
            from sequana import FastA

            contigs = FastA("denovo_assembly.fasta")
            contigs.format_contigs_denovo("path/to/file.fasta", len_min=500)

        Results are stored in "path/to/file.fasta".
        """
        # catch basename of file without extension
        project = os.path.basename(output_file).split(".")[0]
        # check if directory exist
        output_dir = os.path.dirname(output_file)
        try:
            if not os.path.exists(output_dir):
                os.makedirs(output_dir)
        except FileNotFoundError:
            pass

        n = 1
        with open(output_file, "w") as fp:
            for contigs in self:
                if len(contigs.sequence) < len_min:
                    break
                name = ">{}_{} {}\n".format(project, n, contigs.name)
                sequence = "\n".join([contigs.sequence[i:min(i+80, 
                    len(contigs.sequence))] for i in range(0, 
                    len(contigs.sequence), 80)]) + "\n"
                fp.write(name + sequence)
                n += 1
