#!/usr/bin/env python 

"""Preprocess 454 sequencing data."""

__author__ = "Jens Reeder"
__copyright__ = "Copyright 2011, The QIIME Project" 
__credits__ = ["Jens Reeder", "Rob Knight"]#remember to add yourself if you make changes
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
__status__ = "Release"

from os.path import exists
from os import remove, rename, rmdir, makedirs
from random import sample

from qiime.util import get_tmp_filename

from qiime.util import parse_command_line_parameters, get_options_lookup,\
    make_option
from qiime.denoiser.utils import files_exist, store_mapping
from qiime.denoiser.preprocess import preprocess

options_lookup = get_options_lookup()
STANDARD_BACTERIAL_PRIMER = "CATGCTGCCTCCCGTAGGAGT"

#denoiser_preprocess.py
script_info={}
script_info['brief_description']="""Run phase of denoiser algorithm: prefix clustering"""
script_info['script_description']="""The script denoiser_preprocess.py runs the first clustering phase
which groups reads based on common prefixes."""

script_info['script_usage'] = [ \
    ( "",
      """Run program on flowgrams in 454Reads.sff. Remove reads which are not in split_lib_filtered_seqs.fasta. 
Remove primer CATGCTGCCTCCCGTAGGAGT from reads before running phase I""",
      """%prog -i 454Reads.sff.txt -f split_lib_filtered_seqs.fasta -p CATGCTGCCTCCCGTAGGAGT """ )
    ]

script_info['output_description']="""
prefix_dereplicated.sff.txt: human readable sff file containing the flowgram of the
                             cluster representative of each cluster.

prefix_dereplicated.fasta: Fasta file containing the cluster representative of each cluster.

prefix_mapping.txt: This file contains the actual clusters. The cluster centroid is given first,
                    the cluster members follw after the ':'.   
"""

script_info['required_options']=[\

    make_option('-i','--input_file',action='store', type='string',\
                          dest='sff_fp',help='path to flowgram file '+\
                          '[REQUIRED]')
    ]

script_info['optional_options']=[ \
    make_option('-f','--fasta_file',action='store', type='string',\
                    dest='fasta_fp',help='path to fasta input file '+\
                    '[default: %default]', default=None),

    make_option('-s','--squeeze',action='store_true', dest='squeeze',\
                    help='Use run-length encoding for prefix '+\
                    'filtering [default: %default]', default=False),

    make_option('-l','--log_file',action='store',\
                    type='string',dest='log_fp',help='path to log file '+\
                    '[default: %default]', default="preprocess.log"),
 
    make_option('-p','--primer',action='store',\
                    type='string',dest='primer',help='primer sequence '+\
                    'used for the amplification [default: %default]', \
                    default=STANDARD_BACTERIAL_PRIMER),

    make_option('-o','--output_dir',action='store',\
                    type='string',dest='output_dir',\
                    help='path to output directory '+\
                    '[default: %default]', default="/tmp/")
    ]

script_info['version'] = __version__

def main(commandline_args=None):
    parser, opts, args = parse_command_line_parameters(**script_info)
     
    if not opts.sff_fp:
        parser.error('Required option flowgram file path (-i) not specified')
    elif not files_exist(opts.sff_fp):
        parser.error('Flowgram file path does not exist:\n %s \n Pass a valid one via -i.'
                     % opts.sff_fp) 

    #make tmp and output dir
    tmp_dir = get_tmp_filename(tmp_dir = opts.output_dir+"/", suffix="/")
    try:
        makedirs(tmp_dir)
    except OSError:
        exit("Creating temporary directory failed")
    if(not exists(opts.output_dir)):
        try:
            makedirs(opts.output_dir)
        except OSError:
            exit("Creating output directory failed")
            
    #open logger
    log_fh=None
    if opts.verbose:
        #append to the log file of the master process
        log_fh = open(opts.output_dir+"/"+opts.log_fp, "a", 0)
        log_fh.write("SFF file: %s\n" % opts.sff_fp)
        log_fh.write("Fasta file: %s\n" % opts.fasta_fp)
        log_fh.write("Output dir: %s\n" % opts.output_dir)
        log_fh.write("Squeeze Seqs: %s\n" % opts.squeeze)
        log_fh.write("Primer sequence: %s\n" % opts.primer)

    (deprefixed_sff_fp, l, mapping, seqs) = \
        preprocess(opts.sff_fp, log_fh, fasta_fp=opts.fasta_fp,
                   out_fp=tmp_dir,
                   verbose=opts.verbose, squeeze=opts.squeeze,
                   primer=opts.primer)
        
    # explicitly close log file, as this file can be shared with the master
    # Closing it here assures that all preprocess writes happen before the
    # master writes    
    if log_fh:
        log_fh.close()

    #move files to output dir
    rename(tmp_dir+"/prefix_dereplicated.sff.txt",
           opts.output_dir+"/prefix_dereplicated.sff.txt")
    rename(tmp_dir+"/prefix_dereplicated.fasta",
           opts.output_dir+"/prefix_dereplicated.fasta")
    rename(tmp_dir+"/prefix_mapping.txt", opts.output_dir+"/prefix_mapping.txt")
    rmdir(tmp_dir)

if __name__ == "__main__":
    main()