#!/usr/bin/env python

import os
import sys
import argparse
import logging
############
#
#   filter fasta file
#
####
#   COPYRIGHT DISCALIMER:
#   This program is free software: you can redistribute it and/or modify
#   it under the terms of the GNU General Public License as published by
#   the Free Software Foundation, either version 3 of the License, or
#   (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
#
#
#   Author: <NAME>, <EMAIL>
#   Date:   April 2017
#



def main(args):
    
    logging.basicConfig(format='',level=logging.INFO)
    logger = logging.getLogger()

    logger.info("\n[BASTA STATUS] Reading BASTA taxonomy\n")
    hit_seqs = _get_seqs(args.basta,args.level,args.name)
    oh = open(args.output,"w")
    p = 0
    logger.info("\n[BASTA STATUS] Parsing fasta file\n")
    with open(args.fasta) as f:
        for (num,line) in enumerate(f):
            if not num%1000000:
                logger.info("\tLines parsed: %d" % num)
            if line[0]==">":
                if line.replace(">"," ").replace("."," ").split()[0] in hit_seqs:
                    p = 1
                else:
                    p = 0
            if not p:
                continue
            oh.write(line)
    oh.close()
    logger.info("\n[BASTA STATUS] Done.\n")



def _get_seqs(bf,l,n):
    levels = ["kingdom","phylum","class","order","family","genus","species"]
    seqs = {} 

    with open(bf,"r") as f:
        for line in f:
            ls = filter(None,line.split("\t"))
            if l:
                try:
                    if ls[1].split(";")[levels.index(l)] == n:
                        seqs[ls[0]]=1
                except IndexError:
                    pass
            else:
                if n in ls[1]:
                    seqs[ls[0]]=1
    return seqs








if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Filter sequences from given fasta file based on BASTA annotations")
    parser.add_argument("fasta", help="Fasta file to filter")
    parser.add_argument("output", help="Filtered output file")
    parser.add_argument("name", help="Name Taxonomy of sequence has to include (case sensitive)")
    parser.add_argument("basta", help="BASTA taxonomy file")
    parser.add_argument("-l","--level", help="If set name has to match taxonomic level", choices=["kingdom","phylum","order","class","family","genus","species"], default="")

    args = parser.parse_args()
    main(args)


#!/usr/bin/env python

import os
import sys
import argparse
import logging
############
#
#   filter fasta file
#
####
#   COPYRIGHT DISCALIMER:
#   This program is free software: you can redistribute it and/or modify
#   it under the terms of the GNU General Public License as published by
#   the Free Software Foundation, either version 3 of the License, or
#   (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
#
#
#   Author: <NAME>, <EMAIL>
#   Date:   April 2017
#



def main(args):
    
    logging.basicConfig(format='',level=logging.INFO)
    logger = logging.getLogger()

    logger.info("\n[BASTA STATUS] Reading BASTA taxonomy\n")
    hit_seqs = _get_seqs(args.basta,args.level,args.name)
    oh = open(args.output,"w")
    p = 0
    logger.info("\n[BASTA STATUS] Parsing fasta file\n")
    with open(args.fasta) as f:
        for (num,line) in enumerate(f):
            if not num%1000000:
                logger.info("\tLines parsed: %d" % num)
            if line[0]==">":
                if line.replace(">"," ").replace("."," ").split()[0] in hit_seqs:
                    p = 1
                else:
                    p = 0
            if not p:
                continue
            oh.write(line)
    oh.close()
    logger.info("\n[BASTA STATUS] Done.\n")



def _get_seqs(bf,l,n):
    levels = ["kingdom","phylum","class","order","family","genus","species"]
    seqs = {} 

    with open(bf,"r") as f:
        for line in f:
            ls = filter(None,line.split("\t"))
            if l:
                try:
                    if ls[1].split(";")[levels.index(l)] == n:
                        seqs[ls[0]]=1
                except IndexError:
                    pass
            else:
                if n in ls[1]:
                    seqs[ls[0]]=1
    return seqs








if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Filter sequences from given fasta file based on BASTA annotations")
    parser.add_argument("fasta", help="Fasta file to filter")
    parser.add_argument("output", help="Filtered output file")
    parser.add_argument("name", help="Name Taxonomy of sequence has to include (case sensitive)")
    parser.add_argument("basta", help="BASTA taxonomy file")
    parser.add_argument("-l","--level", help="If set name has to match taxonomic level", choices=["kingdom","phylum","order","class","family","genus","species"], default="")

    args = parser.parse_args()
    main(args)


#!/usr/bin/env python ############ # #   filter fasta file # #### #   COPYRIGHT DISCALIMER: #   This program is free software: you can redistribute it and/or modify #   it under the terms of the GNU General Public License as published by #   the Free Software Foundation, either version 3 of the License, or #   (at your option) any later version. # #   This program is distributed in the hope that it will be useful, #   but WITHOUT ANY WARRANTY; without even the implied warranty of #   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the #   GNU General Public License for more details. # #   You should have received a copy of the GNU General Public License #   along with this program.  If not, see <http://www.gnu.org/licenses/>. # # # #   Author: <NAME>, <EMAIL> #   Date:   April 2017 #