#!/usr/bin/env python

from __future__ import (absolute_import, division,
                        print_function, unicode_literals)
import sys
import os
import re
import argparse
import subprocess
import csv
import shutil
from Bio import SeqIO
from natsort import natsorted
import amptk.amptklib as lib


class MyFormatter(argparse.ArgumentDefaultsHelpFormatter):
    def __init__(self, prog):
        super(MyFormatter,self).__init__(prog, max_help_position=48)


class col(object):
    GRN = '\033[92m'
    END = '\033[0m'
    WARN = '\033[93m'


def restricted_float(x):
    x = float(x)
    if x < 0.0 or x > 1.0:
        raise argparse.ArgumentTypeError("%r not in range [0.0, 1.0]"%(x,))
    return x


def parseCustomDBs(db_path, DataBase):
    # DataBase is dict with predefined shortcuts, add others you find
    shortcuts = []
    alldb = []
    for f in os.listdir(db_path):
        if f.startswith('.'):
            continue
        if f.endswith('.udb'):
            alldb.append(f)
            if '_SINTAX' in f:
                continue
            if '_UTAX' in f:
                continue
            shortcuts.append(f)
    for x in shortcuts:
        bname = x.split('.udb')[0]
        if not bname in DataBase:  # this is a new one
            if '{}_SINTAX.udb'.format(bname) in alldb:
                sintax = os.path.join(db_path, '{}_SINTAX.udb'.format(bname))
            else:
                sintax = False
            if '{}_UTAX.udb'.format(bname) in alldb:
                utax = os.path.join(db_path, '{}_UTAX.udb'.format(bname))
            else:
                utax = False
            usearch = os.path.join(db_path, x)
            DataBase[bname] = (usearch, utax, sintax)
    return DataBase


def main(args):
    parser=argparse.ArgumentParser(prog='amptk-assign_taxonomy.py', usage="%(prog)s [options] -f <FASTA File>",
        description='''assign taxonomy to OTUs''',
        epilog="""Written by Jon Palmer (2015) nextgenusfs@gmail.com""",
        formatter_class=MyFormatter)
    parser.add_argument('-i', '--otu_table', dest="otu_table", help='Append Taxonomy to OTU table')
    parser.add_argument('-f','--fasta', required=True, help='FASTA input')
    parser.add_argument('-o','--out', help='Output file (FASTA)')
    parser.add_argument('-m','--mapping_file', help='Mapping file: QIIME format can have extra meta data columns')
    parser.add_argument('--method', default='hybrid',choices=['utax', 'usearch', 'sintax', 'hybrid', 'rdp', 'blast'], help='Taxonomy method')
    parser.add_argument('-d','--db', help='Pre-installed Databases: [ITS,ITS1,ITS2,16S,LSU,COI]')
    parser.add_argument('-t','--taxonomy', help='Incorporate taxonomy calculated elsewhere, 2 column file')
    parser.add_argument('--fasta_db', help='Alternative database of fasta sequences')
    parser.add_argument('--add2db', help='Custom FASTA database to add to DB on the fly')
    parser.add_argument('--utax_db', help='UTAX Reference Database')
    parser.add_argument('--utax', action='store_false', help='Run UTAX (requires usearch9)')
    parser.add_argument('--utax_cutoff', default=0.8, type=restricted_float, help='UTAX confidence value threshold.')
    parser.add_argument('--usearch_db', help='VSEARCH Reference Database')
    parser.add_argument('--sintax_db', help='VSEARCH SINTAX Reference Database')
    parser.add_argument('--usearch_cutoff', default=0.7, type=restricted_float, help='USEARCH percent ID threshold.')
    parser.add_argument('-r', '--rdp', dest='rdp', default='/Users/jon/scripts/rdp_classifier_2.10.1/dist/classifier.jar', help='Path to RDP Classifier')
    parser.add_argument('--rdp_db', dest='rdp_tax', default='fungalits_unite', choices=['16srrna', 'fungallsu', 'fungalits_warcup', 'fungalits_unite'], help='Training set for RDP Classifier')
    parser.add_argument('--rdp_cutoff', default=0.8, type=restricted_float, help='RDP confidence value threshold')
    parser.add_argument('--local_blast', help='Path to local Blast DB')
    parser.add_argument('-u','--usearch', dest="usearch", default='usearch9', help='USEARCH8 EXE')
    parser.add_argument('--tax_filter', help='Retain only OTUs with match in OTU table')
    parser.add_argument('--sintax_cutoff', default=0.8, type=restricted_float, help='SINTAX threshold.')
    parser.add_argument('--debug', action='store_true', help='Remove Intermediate Files')
    parser.add_argument('--cpus', type=int, help="Number of CPUs. Default: auto")
    args=parser.parse_args(args)

    parentdir = os.path.join(os.path.dirname(lib.__file__))

    if not args.out:
        #get base name of files
        if 'filtered' in args.fasta:
            base = args.fasta.split(".filtered")[0]
        elif 'otu' in args.fasta:
            base = args.fasta.split('.otu')[0]
        else:
            base = args.fasta.split('.fa')[0]
    else:
        base = args.out

    #remove logfile if exists
    log_name = base + '.amptk-taxonomy.log'
    if os.path.isfile(log_name):
        os.remove(log_name)

    lib.setupLogging(log_name)
    FNULL = open(os.devnull, 'w')
    cmd_args = " ".join(sys.argv)+'\n'
    lib.log.debug(cmd_args)
    print("-------------------------------------------------------")

    #initialize script, log system info and usearch version
    lib.SystemInfo()
    #Do a version check
    usearch = args.usearch
    lib.versionDependencyChecks(usearch, method='vsearch')

    #get number of cpus
    if args.cpus:
        cpus = args.cpus
    else:
        cpus = lib.getCPUS()

    #Setup DB locations and names, etc
    DBdir = os.path.join(parentdir, 'DB')
    DataBase = {'ITS1': (os.path.join(DBdir, 'ITS.udb'),
                         os.path.join(DBdir, 'ITS1_UTAX.udb'),
                         os.path.join(DBdir, 'ITS1_SINTAX.udb')),
                'ITS2': (os.path.join(DBdir, 'ITS.udb'),
                         os.path.join(DBdir, 'ITS2_UTAX.udb'),
                         os.path.join(DBdir, 'ITS2_SINTAX.udb')),
                'ITS': (os.path.join(DBdir, 'ITS.udb'),
                        os.path.join(DBdir, 'ITS_UTAX.udb'),
                        os.path.join(DBdir, 'ITS_SINTAX.udb')),
                '16S': (os.path.join(DBdir, '16S.udb'),
                        os.path.join(DBdir, '16S.udb'),
                        os.path.join(DBdir, '16S_SINTAX.udb')),
                'LSU': (os.path.join(DBdir, 'LSU.udb'),
                        os.path.join(DBdir, 'LSU_UTAX.udb'),
                        os.path.join(DBdir, 'LSU_SINTAX.udb')),
                'COI': (os.path.join(DBdir, 'COI.udb'),
                        os.path.join(DBdir, 'COI_UTAX.udb'),
                        os.path.join(DBdir, 'COI_SINTAX.udb'))
                }

    # get custom database shorcuts
    DataBase = parseCustomDBs(DBdir, DataBase)

    #get DB names up front
    if args.db in DataBase:
        utax_db = DataBase.get(args.db)[1]
        usearch_db = DataBase.get(args.db)[0]
        sintax_db = DataBase.get(args.db)[2]
        if not utax_db:
            utax_db = args.utax_db
        if not usearch_db:
            usearch_db = args.usearch_db
    else:
        utax_db = args.utax_db
        usearch_db = args.usearch_db
        if args.sintax_db:
            sintax_db = args.sintax_db
        else:
            if args.fasta_db:
                sintax_db = args.fasta_db
            else:
                sintax_db = args.usearch_db

    if args.method in ['hybrid', 'usearch', 'utax']:
        if not utax_db and not usearch_db and not args.fasta_db:
            lib.log.error("You have not selected a database, need either --db, --utax_db, --usearch_db, or --fasta_db")
            sys.exit(1)
        else: #check that the DB exists
            if args.method == 'usearch' and usearch_db:
                if not lib.checkfile(usearch_db):
                    lib.log.error('USEARCH DB not found: {:}'.format(usearch_db))
                    lib.log.error('Use `amptk install` to install pre-formatted databases or `amptk database` to create custom DB')
                    sys.exit(1)
            if args.method == 'sintax' and sintax_db:
                if not lib.checkfile(sintax_db):
                    lib.log.error('SINTAX DB not found: {:}'.format(sintax_db))
                    lib.log.error('Use `amptk install` to install pre-formatted databases or `amptk database` to create custom DB')
                    sys.exit(1)
            if args.method == 'utax' and utax_db:
                if not lib.checkfile(utax_db):
                    lib.log.error('UTAX DB not found: {:}'.format(utax_db))
                    lib.log.error('Use `amptk install` to install pre-formatted databases or `amptk database` to create custom DB')
                    sys.exit(1)


    custom_db = None
    if args.add2db: #means user wants to add sequences to the usearch database on the so will need to rebuild database
        custom_db = base + '.custom_database.fa'
        if lib.checkfile(custom_db):
            lib.SafeRemove(custom_db)
        if args.db: #this means that the fasta files need to be extracted
            lib.log.info("Adding {:} to the {:} database".format(os.path.basename(args.add2db), os.path.basename(usearch_db)))
            cmd = ['vsearch', '--udb2fasta', usearch_db, '--output', custom_db]
            lib.runSubprocess(cmd, lib.log)
            with open(custom_db, 'a') as outfile:
                with open(args.add2db, 'r') as infile:
                    shutil.copyfileobj(infile, outfile)
        elif args.fasta_db:
            lib.log.info("Adding {:} to the {:} database".format(os.path.basename(args.add2db), os.path.basename(args.fasta_db)))
            with open(custom_db, 'w') as outfile:
                with open(args.fasta_db, 'r') as infile:
                    shutil.copyfileobj(infile, outfile)
                with open(args.add2db, 'r') as infile:
                    shutil.copyfileobj(infile, outfile)

    #Count records
    lib.log.info("Loading FASTA Records")
    total = lib.countfasta(args.fasta)
    lib.log.info('{0:,}'.format(total) + ' OTUs')

    #declare output files/variables here
    blast_out = base + '.blast.txt'
    rdp_out = base + '.rdp.txt'
    utax_out = base + '.utax.txt'
    usearch_out = base + '.usearch.txt'
    sintax_out = base + '.sintax.txt'
    otuDict = {}

    if not args.taxonomy:
        #start with less common uses, i.e. Blast, rdp
        if args.method == 'blast':
            #check if command line blast installed
            if not lib.which('blastn'):
                lib.log.error("BLASTN not found in your PATH, exiting.")
                sys.exit(1)

            #now run blast remotely using NCBI nt database
            outformat = "6 qseqid sseqid pident stitle"
            if args.local_blast:
                #get number of cpus
                lib.log.info("Running local BLAST using db: %s" % args.local_blast)
                cmd = ['blastn', '-num_threads', str(cpus), '-query', args.fasta, '-db', os.path.abspath(args.local_blast), '-max_target_seqs', '1', '-outfmt', outformat, '-out', blast_out]
                lib.runSubprocess(cmd, lib.log)
            else:
                lib.log.info("Running BLASTN using NCBI remote nt database, this may take awhile")
                cmd = ['blastn', '-query', args.fasta, '-db', 'nt', '-remote', '-max_target_seqs', '1', '-outfmt', outformat, '-out', blast_out]
                lib.runSubprocess(cmd, lib.log)

            #load results and reformat
            new = []
            f = csv.reader(open(blast_out), delimiter=str('\t'))
            for col in f:
                query = col[0]
                gbID = col[1].split("|")[3]
                pident = col[2]
                name = col[3]
                tax = gbID + ";" + name + " (" + pident + ")"
                line = [query,tax]
                new.append(line)
            otuDict = dict(new)
        elif args.method == 'rdp':
            #check that classifier is installed
            try:
                rdp_test = subprocess.Popen(['java', '-Xmx2000m', '-jar', args.rdp, 'classify'], stdout=subprocess.PIPE).communicate()[0].rstrip()
            except OSError:
                lib.log.error("%s not found in your PATH, exiting." % args.rdp)
                sys.exit(1)

            #RDP database
            lib.log.info("Using RDP classifier %s training set" % args.rdp_tax)

            #run RDP
            cmd = ['java', '-Xmx2000m', '-jar', args.rdp, 'classify', '-g', args.rdp_tax, '-o', rdp_out, '-f', 'fixrank', args.fasta]
            lib.runSubprocess(cmd, lib.log)

            #load in results and put into dictionary
            new = []
            removal = ["unidentified", "Incertae", "uncultured", "incertae"]
            remove_exp = [re.compile(x) for x in removal]
            f = csv.reader(open(rdp_out), delimiter=str('\t'))
            for col in f:
                if float(col[19]) > args.rdp_cutoff:
                    tax = "RDP;k:"+col[2]+",p:"+col[5]+",c:"+col[8]+",o:"+col[11]+",f:"+col[14]+",g:"+col[17]
                elif float(col[16]) > args.rdp_cutoff:
                    tax = "RDP;k:"+col[2]+",p:"+col[5]+",c:"+col[8]+",o:"+col[11]+",f:"+col[14]
                elif float(col[13]) > args.rdp_cutoff:
                    tax = "RDP;k:"+col[2]+",p:"+col[5]+",c:"+col[8]+",o:"+col[11]
                elif float(col[10]) > args.rdp_cutoff:
                    tax = "RDP;k:"+col[2]+",p:"+col[5]+",c:"+col[8]
                elif float(col[7]) > args.rdp_cutoff:
                    tax = "RDP;k:"+col[2]+",p:"+col[5]
                elif float(col[4]) > args.rdp_cutoff:
                    tax = "RDP;k:"+col[2]
                else:
                    tax = "RDP;k:unclassified"
                tax_split = tax.split(",")
                tax = [s for s in tax_split if not any(re.search(s) for re in remove_exp)]
                tax = ",".join(tax)
                line = [col[0],tax]
                new.append(line)
            otuDict = dict(new)
        else:
            #check status of USEARCH DB and run
            if args.method in ['hybrid', 'usearch']:
                if args.fasta_db:
                    #now run through usearch global
                    lib.log.info("Global alignment OTUs with usearch_global (VSEARCH) against {:}".format(os.path.basename(args.fasta_db)))
                    cmd = ['vsearch', '--usearch_global', args.fasta, '--db', os.path.abspath(args.fasta_db),
                           '--userout', usearch_out, '--id', str(args.usearch_cutoff), '--strand', 'both',
                           '--output_no_hits', '--maxaccepts', '500', '--top_hits_only', '--userfields',
                           'query+target+id', '--notrunclabels', '--threads', str(cpus)]
                    lib.runSubprocess(cmd, lib.log)
                elif custom_db:
                    #now run through usearch global
                    lib.log.info("Global alignment OTUs with usearch_global (VSEARCH) against custom DB")
                    cmd = ['vsearch', '--usearch_global', args.fasta, '--db', os.path.abspath(custom_db),
                           '--userout', usearch_out, '--id', str(args.usearch_cutoff), '--strand', 'both',
                           '--output_no_hits', '--maxaccepts', '500', '--top_hits_only', '--userfields',
                           'query+target+id', '--notrunclabels', '--threads', str(cpus)]
                    lib.runSubprocess(cmd, lib.log)
                else:
                    if usearch_db:
                        lib.log.info("Global alignment OTUs with usearch_global (VSEARCH) against {:}".format(os.path.basename(usearch_db)))
                        cmd = ['vsearch', '--usearch_global', args.fasta, '--db', os.path.abspath(usearch_db),
                               '--userout', usearch_out, '--id', str(args.usearch_cutoff), '--strand', 'both',
                               '--output_no_hits', '--maxaccepts', '500', '--top_hits_only', '--userfields',
                               'query+target+id', '--notrunclabels', '--threads', str(cpus)]
                        lib.runSubprocess(cmd, lib.log)

            if not args.utax and args.method in ['hybrid', 'utax']:
                if utax_db:
                    #now run through UTAX
                    utax_out = base + '.utax.txt'
                    lib.log.info("Classifying OTUs with UTAX (USEARCH)")
                    cutoff = str(args.utax_cutoff)
                    cmd = [usearch, '-utax', args.fasta, '-db', utax_db, '-utaxout', utax_out, '-utax_cutoff', cutoff,
                           '-strand', 'plus', '-notrunclabels', '-threads', str(cpus)]
                    lib.runSubprocess(cmd, lib.log)
                else:
                    lib.log.error("UTAX DB %s not found, skipping" % utax_db)

            if args.method in ['hybrid', 'sintax']:
                if args.fasta_db: #if you pass fasta file here, over ride any auto detection
                    sintax_db = args.fasta_db
                #now run sintax
                lib.log.info("Classifying OTUs with SINTAX (VSEARCH)")
                cmd = ['vsearch', '--sintax', args.fasta, '--db', os.path.abspath(sintax_db), '--tabbedout', sintax_out,
                       '-sintax_cutoff', str(args.sintax_cutoff), '--threads', str(cpus)]
                #cmd = [usearch, '-sintax', args.fasta, '-db', os.path.abspath(sintax_db), '-tabbedout', sintax_out,
                #       '-sintax_cutoff', str(args.sintax_cutoff), '-strand', 'both', '-threads', str(cpus)]
                lib.runSubprocess(cmd, lib.log)

            #now process results, load into dictionary - slightly different depending on which classification was run.
            if args.method == 'hybrid':
                #run upgraded method, first load dictionaries with resuls
                if lib.checkfile(utax_out):
                    utaxDict = lib.classifier2dict(utax_out, args.utax_cutoff)
                    lib.log.debug('UTAX results parsed, resulting in {:,} taxonomy predictions'.format(len(utaxDict)))
                else:
                    if not args.utax:
                        lib.log.info('UTAX results empty')
                    utaxDict = {}
                if lib.checkfile(sintax_out):
                    sintaxDict = lib.classifier2dict(sintax_out, args.sintax_cutoff)
                    lib.log.debug('SINTAX results parsed, resulting in {:,} taxonomy predictions'.format(len(sintaxDict)))
                else:
                    lib.log.info('SINTAX results empty')
                    sintaxDict = {}
                usearchDict = lib.usearchglobal2dict(usearch_out)
                lib.log.debug('Global alignment results parsed, resulting in {:,} taxonomy predictions'.format(len(usearchDict)))
                otuList = natsorted(list(usearchDict.keys()))
                #first compare classifier results, getting better of the two
                bestClassify = lib.bestclassifier(utaxDict, sintaxDict, otuList)
                #now get best taxonomy by comparing to global alignment results
                otuDict = lib.bestTaxonomy(usearchDict, bestClassify)
                lib.log.debug('Combined OTU taxonomy dictionary contains {:,} taxonomy predictions'.format(len(otuDict)))
                if len(otuDict) < 1:
                    lib.log.info('Parsing taxonomy failed -- see logfile')
                    sys.exit(1)

            elif args.method == 'utax' and lib.checkfile(utax_out):
                #load results into dictionary for appending to OTU table
                lib.log.debug("Loading UTAX results into dictionary")
                with open(utax_out, 'r') as infile:
                    reader = csv.reader(infile, delimiter=str("\t"))
                    otuDict = {rows[0]:'UTAX;'+rows[2] for rows in reader}

            elif args.method == 'usearch' and lib.checkfile(usearch_out):
                #load results into dictionary for appending to OTU table
                lib.log.debug("Loading Global Alignment results into dictionary")
                otuDict = {}
                usearchDict = lib.usearchglobal2dict(usearch_out)
                for k,v in natsorted(list(usearchDict.items())):
                    pident = float(v[0]) * 100
                    pident = "{0:.1f}".format(pident)
                    ID = v[1]
                    tax = ','.join(v[-1])
                    LCA = v[2]
                    if LCA == '':
                        fulltax = 'GS|'+pident+'|'+ID+';'+tax
                    else:
                        fulltax = 'GSL|'+pident+'|'+ID+';'+tax
                    otuDict[k] = fulltax

            elif args.method == 'sintax' and lib.checkfile(sintax_out):
                #load results into dictionary for appending to OTU table
                lib.log.debug("Loading SINTAX results into dictionary")
                with open(sintax_out, 'r') as infile:
                    reader = csv.reader(infile, delimiter=(str("\t")))
                    otuDict = {rows[0]:'SINTAX;'+rows[3] for rows in reader}
    else:
        #you have supplied a two column taxonomy file, parse and build otuDict
        lib.log.debug("Loading custom Taxonomy into dictionary")
        with open(args.taxonomy, 'r') as infile:
            reader = csv.reader(infile, delimiter=str("\t"))
            otuDict = {rows[0]:rows[1] for rows in reader}

    #now format results
    if args.otu_table:
        #check if otu_table variable is empty, then load in otu table
        lib.log.info("Appending taxonomy to OTU table and OTUs")
        taxTable = base + '.otu_table.taxonomy.txt'
        tmpTable = base + '.otu_table.tmp'

        #append to OTU table
        counts = 0
        with open(taxTable, 'w') as outTable:
            with open(args.otu_table, 'r') as inTable:
                #guess the delimiter format
                firstline = inTable.readline()
                dialect = lib.guess_csv_dialect(firstline)
                inTable.seek(0)
                #parse OTU table
                reader = csv.reader(inTable, dialect)
                for line in reader:
                    if line[0].startswith(("#OTU", "OTUId")):
                        line.append('Taxonomy')
                    else:
                        tax = otuDict.get(line[0]) or "No Hit"
                        line.append(tax)
                    if args.tax_filter and not args.method == 'blast':
                        if line[0].startswith(("#OTU", "OTUId")):
                            join_line = ('\t'.join(str(x) for x in line))
                        else:
                            if args.tax_filter in line[-1]:
                                join_line = ('\t'.join(str(x) for x in line))
                                counts += 1
                            else:
                                continue
                    else:
                        join_line = ('\t'.join(str(x) for x in line))
                        counts += 1
                    outTable.write("%s\n" % join_line)

        if args.tax_filter:
            if args.method == 'blast':
                lib.log.info("Blast is incompatible with --tax_filter, use a different method")
                tmpTable = args.otu_table
            else:
                nonfungal = total - counts
                lib.log.info("Found %i OTUs not matching %s, writing %i %s hits to taxonomy OTU table" % (nonfungal, args.tax_filter, counts, args.tax_filter))
                #need to create a filtered table without taxonomy for BIOM output
                with open(tmpTable, 'w') as output:
                    with open(taxTable, 'r') as input:
                        firstline = input.readline()
                        dialect = lib.guess_csv_dialect(firstline)
                        input.seek(0)
                        #parse OTU table
                        reader = csv.reader(input, dialect)
                        for line in reader:
                            del line[-1]
                            join_line = '\t'.join(str(x) for x in line)
                            output.write("%s\n" % join_line)
        else:
            tmpTable = args.otu_table

    #append to OTUs
    otuTax = base + '.otus.taxonomy.fa'
    with open(otuTax, 'w') as output:
        with open(args.fasta, 'r') as input:
            SeqRecords = SeqIO.parse(input, 'fasta')
            for rec in SeqRecords:
                tax = otuDict.get(rec.id) or "No hit"
                rec.description = tax
                SeqIO.write(rec, output, 'fasta')

    if not args.taxonomy:
        #output final taxonomy in two-column format, followed by the hits for usearch/sintax/utax if hybrid is used.
        taxFinal = base + '.taxonomy.txt'
        with open(taxFinal, 'w') as finaltax:
            if args.method == 'hybrid':
                finaltax.write('#OTUID\ttaxonomy\tUSEARCH\tSINTAX\tUTAX\n')
                for k,v in natsorted(list(otuDict.items())):
                    if k in usearchDict:
                        usearchResult = usearchDict.get(k)
                        usearchResult = ','.join(usearchResult[-1])
                    else:
                        usearchResult = 'No hit'
                    if k in sintaxDict:
                        sintaxResult = sintaxDict.get(k)
                        sintaxResult = ','.join(sintaxResult[-1])
                    else:
                        sintaxResult = 'No hit'
                    if k in utaxDict:
                        utaxResult = utaxDict.get(k)
                        utaxResult = ','.join(utaxResult[-1])
                    else:
                        utaxResult = 'No hit'
                    finaltax.write('{:}\t{:}\t{:}\t{:}\t{:}\n'.format(k, v, usearchResult, sintaxResult, utaxResult))
            else:
                finaltax.write('#OTUID\ttaxonomy\n')
                for k,v in natsorted(list(otuDict.items())):
                    finaltax.write('%s\t%s\n' % (k,v))
    else:
        taxFinal = args.taxonomy
    #convert taxonomy to qiime format for biom
    qiimeTax = None
    if not args.method == 'blast':
        qiimeTax = base + '.qiime.taxonomy.txt'
        lib.utax2qiime(taxFinal, qiimeTax)
    else:
        lib.log.error("Blast taxonomy is not compatible with BIOM output, use a different method")

    #create OTU phylogeny for downstream processes
    lib.log.info("Generating phylogenetic tree (MAFFT/FastTree)")
    tree_out = base + '.tree.phy'
    align_out = base + '.mafft.fasta'
    cmd = ['mafft', args.fasta]
    lib.runSubprocess2(cmd, lib.log, align_out)
    cmd = ['fasttree', '-nt', align_out]
    lib.runSubprocess2(cmd, lib.log, tree_out)
    #cmd = [usearch, '-cluster_agg', args.fasta, '-treeout', tree_out]
    #lib.runSubprocess(cmd, lib.log)

    #print some summary file locations
    lib.log.info("Taxonomy finished: %s" % taxFinal)
    if args.otu_table and not args.method == 'blast':
        lib.log.info("Classic OTU table with taxonomy: %s" % taxTable)
        #output final OTU table in Biom v1.0 (i.e. json format if biom installed)
        outBiom = base + '.biom'
        if lib.which('biom'):
            lib.removefile(outBiom)
            cmd = ['biom', 'convert', '-i', tmpTable, '-o', outBiom+'.tmp', '--table-type', "OTU table", '--to-json']
            lib.runSubprocess(cmd, lib.log)
            if args.mapping_file:
                mapSamples = []
                repeatSamples = []
                with open(args.mapping_file, 'r') as mapin:
                    for line in mapin:
                        line = line.rstrip()
                        if line.startswith('#'):
                            continue
                        sampleID = line.split('\t')[0]
                        if not sampleID in mapSamples:
                            mapSamples.append(sampleID)
                        else:
                            repeatSamples.append(sampleID)
                otuSamples = []
                with open(tmpTable, 'r') as otuin:
                    for line in otuin:
                        line = line.rstrip()
                        if line.startswith('#'):
                            otuSamples = line.split('\t')[1:]
                missingMap = []
                for otu in otuSamples:
                    if not otu in mapSamples:
                        missingMap.append(otu)
                if len(missingMap) > 0:
                    lib.log.error("%s are missing from mapping file (metadata), skipping biom file creation" % ', '.join(missingMap))
                elif len(repeatSamples) > 0:
                    lib.log.error('%s duplicate sample IDs in mapping file, skipping biom file creation' % ', '.join(repeatSamples))
                else:
                    if qiimeTax:
                        cmd = ['biom', 'add-metadata', '-i', outBiom+'.tmp', '-o', outBiom, '--observation-metadata-fp', qiimeTax, '-m', args.mapping_file, '--sc-separated', 'taxonomy', '--output-as-json']
                    else:
                        cmd = ['biom', 'add-metadata', '-i', outBiom+'.tmp', '-o', outBiom, '-m', args.mapping_file, '--output-as-json']
                    lib.runSubprocess(cmd, lib.log)
            else:
                cmd = ['biom', 'add-metadata', '-i', outBiom+'.tmp', '-o', outBiom, '--observation-metadata-fp', qiimeTax, '--sc-separated',  'taxonomy', '--output-as-json']
                lib.runSubprocess(cmd, lib.log)
            lib.removefile(outBiom+'.tmp')
            lib.log.info("BIOM OTU table created: %s" % outBiom)
        else:
            lib.log.info("biom program not installed, install via `pip install biom-format` or `conda install biom-format`")
    lib.log.info("OTUs with taxonomy: %s" % otuTax)
    lib.log.info("OTU phylogeny: %s" % tree_out)

    #clean up intermediate files
    if not args.debug:
        for i in [utax_out, usearch_out, sintax_out, align_out, qiimeTax, base+'.otu_table.tmp']:
            if i:
                lib.removefile(i)
    print("-------------------------------------------------------")


if __name__ == "__main__":
    main(args)
