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

'''
Created by Brant Faircloth on 11 December 2010 11:28 PST (-0800).
Copyright (c) 2010 Brant C. Faircloth. All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

*   Redistributions of source code must retain the above copyright notice,
    this list of conditions and the following disclaimer.

*   Redistributions in binary form must reproduce the above copyright notice,
    this list of conditions and the following disclaimer in the documentation
    and/or other materials provided with the distribution.

*   Neither the name of the University of California nor the names of its
    contributors may be used to endorse or promote products derived from this
    software without specific prior written permission. THIS SOFTWARE IS
    PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS
    OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
    LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
    CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
    SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
    INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
    ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
    POSSIBILITY OF SUCH DAMAGE.

'''

import os
import tempfile
import multiprocessing

import pdb

def file_type(input):
    """given an input file, determine the type and return both type and record delimiter (> or @)"""
    name, extension = os.path.splitext(os.path.basename(input))
    fastas = set(['.fsa','.fasta','.fa'])
    fastqs = set(['.fastq','.fq'])
    gffs = set(['.gff'])
    if extension in fastas:
        ft = 'fasta'
        delim = '>'
    elif extension in fastqs:
        ft = 'fastq'
        delim = '@'
    # TODO:  sff ???
    #elif extension in gffs:
    #    ft = 'sff'
    #    delim = None
    else:
        raise IOError, "Input file not of correct extension"
    return ft, delim

def _get_file_chunks(input, delim, size):
    """given input, record delimiter, and chunk size, yield an iterator contains file seek (start)
    and file read (stop) positions.  Return final position as (6365605, None)."""
    f = open(input)
    while 1:
        start = f.tell()
        f.seek(size, 1)
        line = f.readline()
        if not line:
            break
        # if this isn't a fasta header line, read forward until
        # we get to one
        while not line.startswith(delim):
            line = f.readline()
        else:
            # now that we got to a fasta header, we're at the end.
            # back up the length of the fasta header.
            f.seek(-len(line), 1)
            # tuple up
            yield start, f.tell() - start, input
    # make sure we catch the (start, distance) for the end of the file, too
    yield start, None, input
    f.close()

def get_chunks(input, delim, split_type, mb=1, splits = None):
    """return a tuple of file seek (start, distance) positions covering chunks of a file"""
    if split_type == 'size':
        size = mb * (1024**2)
    if split_type == 'pieces':
        if not splits:
            splits = multiprocessing.cpu_count() - 1
        size = int(round((os.path.getsize(input)/float(splits)), 0))
    return _get_file_chunks(input, delim, size)

def _split_file(chunk):
    """function to split a file into appropriate pieces given (start, stop) file seek coords"""
    f = open(chunk[2])
    f.seek(chunk[0])
    if chunk[1]:
        d = f.read(chunk[1])
    else:
        d = f.read()
    td, tf = tempfile.mkstemp(suffix='.splt')
    os.close(td)
    otf = open(tf, 'w')
    otf.write(d)
    otf.close()
    f.close()
    return tf

def make_chunks(chunks, pool = None, mp = True):
    """return a list of tempfiles that are the chunked input file"""
    if mp and not pool:
        # create a multiprocessing pool
        procs = multiprocessing.cpu_count() - 1
        pool = multiprocessing.Pool(procs)
        chunks = pool.map(_split_file, chunks)
        # close up the pool if we no longer want to swim
        pool.close()
        pool.join()
    else:
        chunks = map(_split_file, chunks)
    return chunks

if __name__ == '__main__':
    input = '../test/galGal3.read1.fa'
    f_type, delim = file_type(input)
    chunk_offsets = get_chunks(input, delim, split_type='size', mb=24)
    chunks = make_chunks(chunk_offsets, mp=False)
    pdb.set_trace()