Bug fixes for database creation

MANIFEST.in

 include LICENSE
 include README.md
-include MANIFEST.in
-include src/expam/c/*.pyx
\ No newline at end of file
+include MANIFEST.in
\ No newline at end of file

src/expam/__init__.py

-import gzip
-
-
-COMPRESSION_EXTNS = ['.tar.gz', '.tar', '.gz']
-DEFAULT_MODE = "rb"
-DEFAULT_OPENER = open
-COMP_PARSE = {
-    ".tar.gz": {"mode": "rb", "opener": gzip.open},
-    ".gz": {"mode": "rb", "opener": gzip.open}
-}
-
-from .main import ExpamOptions, clear_logs, CommandGroup, PlotLogs

src/expam/cli/build.py

 import os
-from expam.main import CommandGroup, ExpamOptions, clear_logs
+from expam.cli.main import CommandGroup, ExpamOptions, clear_logs
 from expam.database import FileLocationConfig
 from expam.database.config import JSONConfig, create_database, make_database_config, validate_database_file_configuration
 from expam.logger import Timer

src/expam/cli/classify.py

@@ -3,7 +3,7 @@ from expam.classify import ResultsPathConfig
 from expam.classify.classify import ClassificationResults, name_to_id, run_classifier
 from expam.classify.config import make_results_config, validate_results_configuration
 from expam.classify.taxonomy import TaxonomyNCBI
-from expam.main import CommandGroup, ExpamOptions, clear_logs
+from expam.cli.main import CommandGroup, ExpamOptions, clear_logs
 from expam.database import FileLocationConfig
 from expam.database.config import JSONConfig, make_database_config, validate_database_file_configuration
 from expam.utils import die, is_hex, make_path_absolute

src/expam/cli/main.py

+from argparse import ArgumentParser, Namespace, RawTextHelpFormatter
+from collections import namedtuple
+import datetime
+import os
+import shutil
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+from expam.utils import die, ls, make_path_absolute
+
+
+ExpamOptions = namedtuple(
+    'ExpamOptions',
+    [
+        # Runtime arguments
+        'command', 'db_name', 'k', 'n', 's', 'phylogeny', 'alpha',
+        # Directory arguments
+        'directory', 'out_url', 'truth_dir',
+        # Parameter arguments
+        'length', 'pile', 'error_rate', 'first_n', 'paired_end',
+        # Summary arguments
+        'plot', 'cutoff', 'cpm', 'taxonomy',
+        # Plot arguments
+        'groups', 'phyla', 'keep_zeros', 'ignore_names', 'colour_list', 'rank', 'log_scores', 'itol_mode',
+        # Tree arguments
+        'use_sourmash', 'use_rapidnj', 'use_quicktree'
+    ]
+)
+
+def retrieve_arguments() -> ExpamOptions:
+    parser = ArgumentParser(description="  expam CLI\n--------------\n", formatter_class=RawTextHelpFormatter)
+    
+    parser.add_argument("command", default=None,
+                        help='\nCommand to execute. Valid commands include:\n'
+                             '-------------------------------------------\n'
+                             'create:-\tInitialise database.\n'
+                             'build:-\t\tStart building database.\n'
+                             'print:-\t\tPrint current database parameters.\n'
+                             'run:-\t\tRun reads against database.\n'
+                             'add:-\t\tAdd sequence to the database.\n'
+                             'remove:-\tRemove sequence from database (only impacts future db builds).\n'
+                             'set:-\t\tSet database build parameters.\n'
+                             'to_taxonomy:-\t\tConvert results to taxonomic setting.\n'
+                             'phylotree:-\t\tDraw results on phylotree.\n'
+                             'draw_tree:-\t\tDraw the reference tree.\n'
+                             'download_taxonomy:-\t\tDownload taxonomic information for reference seqeunces.\n'
+                             'cutoff:-\t\tApply cutoff to some set of already processed classifications. THIS WILL OVERWRITE OLD RESULTS!\n'
+                             'mashtree:-\tCreate mashtree from current sequences and add to database.\n'
+                             'quickrun:-\tInitialise, set parameters and start building db (assumes\n'
+                             '\t\t\tsequences all lie in the same folder).\n'
+                             'make_reads:-\tUniformly sample reads of length l from some input sequence.\n'
+                             '\t\tThis is for testing purposes only, and is not a replacement\n'
+                             '\t\tfor actual read generating software.\n',
+                        metavar="[command]")
+    parser.add_argument("-db", "--db_name", dest="db_name",
+                        help="Name of database.",
+                        metavar="[database name]")
+    parser.add_argument("-k", "--kmer", dest="k",
+                        help="Length of mer used for analysis.",
+                        metavar="[k value (int)]")
+    parser.add_argument("-n", "--n-processes", dest="n",
+                        help="Number of CPUs to use for processing.",
+                        metavar="[n (int)]")
+    parser.add_argument("-s", "--sketch", dest="s",
+                        help="Sketch size for mash.",
+                        metavar="[sketch size (int)]")
+    parser.add_argument("-p", "--phylogeny", dest="phylogeny",
+                        help="URL of Newick file containing phylogeny.",
+                        metavar="[phylogeny URL]")
+    parser.add_argument("-d", "--directory", dest="directory", action="append",
+                        help="File URL, context depending on command supplied.",
+                        metavar="[directory]")
+    parser.add_argument("-l", "--length", dest="length",
+                        help="Length of simulated reads.",
+                        metavar="[read length]")
+    parser.add_argument("-o", "--out", dest="out_url",
+                        help="Where to save classification results.",
+                        metavar="[out URL]")
+    parser.add_argument("-y", "--pile", dest="pile",
+                        help="Number of genomes to pile at a time (or inf).",
+                        metavar="[pile size]")
+    parser.add_argument("-e", "--error-rate", dest="error_rate",
+                        help="Generate error in reads (error ~ reads with errors / reads).",
+                        metavar="[error rate]")
+    parser.add_argument("-t", "--truth", dest="truth_dir",
+                        help="Location of truth dataset.")
+    parser.add_argument("--plot", dest="plot", default=False, action="store_true",
+                        help="Plot timing data of database build.")
+    parser.add_argument("--first", dest="first_n", default=None,
+                        help="Add first n genomes in folder.")
+    parser.add_argument("--cutoff", dest="cutoff", default=0,
+                        help="Ignore organisms with less than `cutoff` reads in results.")
+    parser.add_argument("--cpm", dest="cpm", default=100,
+                        help="Counts/million cutoff for read-count to be non-negligible.")
+    parser.add_argument("--taxonomy", dest="taxonomy", default=False, action="store_true",
+                        help="Convert phylogenetic results to taxonomic results.")
+    parser.add_argument("--phyla", dest="phyla", default=False, action="store_true",
+                        help="Colour phylotree results by phyla.")
+    parser.add_argument("--rank", dest="rank", default=None,
+                        help="Rank at which to sort results.")
+    parser.add_argument("--keep-zeros", dest="keep_zeros", default=False, action="store_true",
+                        help="Keep nodes of output where no reads have been assigned.")
+    parser.add_argument("--ignore-names", dest="ignore_names", default=False, action="store_true")
+    parser.add_argument("--group", dest="groups", action="append", nargs="+",
+                        help="Space-separated list of sample files to be treated as a single group in phylotree.")
+    parser.add_argument("--colour-list", dest="colour_list", nargs="+",
+                        help="List of colours to use when plotting groups in phylotree.")
+    parser.add_argument("--sourmash", dest="use_sourmash", default=False, action="store_true",
+                        help="Use sourmash for distance estimation.")
+    parser.add_argument("--rapidnj", dest="use_rapidnj", default=True, action="store_true",
+                        help="Use RapidNJ for Neighbour-Joining algorithm.")
+    parser.add_argument("--quicktree", dest="use_quicktree", default=False, action="store_true",
+                        help="Use QuickTree for Neighbour-Joining algorithm.")
+    parser.add_argument("--paired", dest="paired_end", default=False, action="store_true",
+                        help="Treat reads as paired-end.")
+    parser.add_argument("--alpha", dest="alpha", default=0.1,
+                        help="Percentage requirement for classification subtrees (see Tutorials 1 & 2).")
+    parser.add_argument("--log-scores", dest="log_scores", default=False, action="store_true",
+                        help="Log transformation to opacity scores on phylotree (think uneven distributions).")
+    parser.add_argument("--itol", dest="itol_mode", default=False, action="store_true",
+                        help="Output plotting data in ITOL format.")
+
+    # Parse arguments.
+    args: Namespace = parser.parse_args()
+
+    if args.db_name is None:
+        args.db_name = db_name_from_environment()
+    else:
+        args.db_name = make_path_absolute(args.db_name, os.getcwd())
+
+    return ExpamOptions(**{field: getattr(args, field) for field in ExpamOptions._fields})
+
+
+def db_name_from_environment():
+    try:
+        return os.environ["EXPAM_DB_DIR"]
+    except KeyError:
+        return None
+
+
+def clear_logs(log_path) -> None:
+    print("Clearing old log files...")
+
+    try:
+        shutil.rmtree(log_path)
+    except FileNotFoundError:
+        pass
+
+    try:
+        os.mkdir(log_path)
+    except OSError:
+        die("Can't make log path %s!" % log_path)
+
+
+class CommandGroup:
+    commands: set[str] = {}
+
+    @classmethod
+    def take_args(cls, args: ExpamOptions) -> dict:
+        return {}
+
+    def run(self, command) -> None:
+        try:
+            getattr(self, command)()
+        except AttributeError:
+            raise AttributeError("Command %s not found!" % command)
+
+    @staticmethod
+    def parse_ints(*params):
+        for param in params:
+            INVALID_PARAM_MSG = ("Invalid parameter (%s), must be integer!" % str(param))
+
+            if param is not None:
+
+                try:
+                    # Convert to float.
+                    param = float(param)
+
+                except ValueError:
+                    die(INVALID_PARAM_MSG)
+
+                # Convert to int and see if the value changes.
+                new_param = int(param)
+                if new_param != param:
+                    die(INVALID_PARAM_MSG)
+
+                param = new_param
+
+            yield param
+
+    @staticmethod
+    def parse_floats(*params):
+        for param in params:
+            INVALID_PARAM_MSG = ("Invalid parameter (%s), must be integer!" % str(param))
+
+            if param is not None:
+                try:
+                    param = float(param)
+
+                except ValueError:
+                    die(INVALID_PARAM_MSG)
+
+            yield param
+
+    @staticmethod
+    def get_user_confirmation(msg):
+        if "y/n" not in msg:
+            msg += " (y/n)"
+
+        while True:
+            ans = input(msg)
+            ans = ans.lower().strip()
+
+            if ans == "y":
+                return True
+            elif ans == "n":
+                return False
+            else:
+                die("Invalid response, please provide y/n.")
+
+    @staticmethod
+    def get_time(data) -> datetime.datetime:
+        date_data, time_data, am_pm = data.split(" ")[:3]
+
+        mon, day, year = (int(v) for v in date_data.split("/"))
+        hr, min, sec = (int(v) for v in time_data.split(":"))
+
+        if "PM" in am_pm and hr < 12:
+            hr += 12
+        elif "AM" in am_pm and hr == 12:
+            hr = 0
+
+        return datetime.datetime(year, mon, day, hr, min, sec)
+
+    def get_t0(self, logs_dir: str):
+        def _first(itr):
+            try:
+                return itr[0]
+            except IndexError:
+                raise ValueError("Can't find main log file!")
+
+        # Get effective t0 from main log.
+        main_log_dir = _first([
+            os.path.join(logs_dir, log_name)
+            for log_name in ls(logs_dir, ext=".log")
+            if "_main" in log_name
+        ])
+
+        with open(main_log_dir, "r") as f:
+            log_data = f.readline()  # Get time of first log point.
+
+        return main_log_dir, self.get_time(log_data)
+
+
+class PlotLogs:
+    def __init__(self, logs_dir: str, t0: datetime.datetime) -> None:
+        self.logs_dir = logs_dir
+        self.t0 = t0
+
+    def plot(self):
+        job_type_map = {  # For labels.
+            "request_extension": "remap",
+            "disjoint": "disjoint",
+            "collapse_pile": "fill",
+            "import_sequence": "kmers",
+            "send_kmers": "send",
+        }
+        job_colours = {  # For plotting.
+            "request_extension": "red",
+            "disjoint": "blue",
+            "collapse_pile": "green",
+            "import_sequence": "orange",
+            "send_kmers": "black",
+        }
+
+        process_type_jobs = {
+            "_extract": [
+                "import_sequence",
+                "send_kmers",
+            ],
+            "_union": [
+                "request_extension",
+                "disjoint",
+                "collapse_pile"
+            ],
+        }
+
+        fig, ax = plt.subplots(figsize=(20, 15))
+        ax.grid()
+
+        log_urls = [
+            os.path.join(self.logs_dir, log_name)
+            for log_name in ls(self.logs_dir, ext=".log")
+            if "_main.log" not in log_name
+        ]
+
+        # Plot data one child process at a time.
+        for log_url in log_urls:
+            process_type = "_extract" if "_extract.log" in log_url else "_union"
+
+            # Data for plotting.
+            data = {job_name: ([], []) for job_name in process_type_jobs[process_type]}
+
+            with open(log_url, "r") as f:
+                log_data = f.readlines()
+
+            # Read data line by line and append data.
+            for i, line in enumerate(log_data):
+                for job_name in process_type_jobs[process_type]:
+
+                    if job_name in line:
+                        data[job_name][0].append(self._get_time(line) / 3600)
+                        data[job_name][1].append(self._get_data(line) / 60)
+
+            # Plot data on same graph.
+            for job_name in process_type_jobs[process_type]:
+                x, y = np.array(data[job_name][0]), np.array(data[job_name][1])
+                ax.plot(
+                    x,
+                    y,
+                    label=job_type_map[job_name],
+                    marker="x",
+                    color=job_colours[job_name],
+                )
+
+                # Don't allow duplicate labels.
+                job_type_map[job_name] = ""
+
+        ax.set(
+            xlabel="Time since start [hrs]",
+            ylabel="Time taken for task [mins]",
+            title="Time taken to do tasks"
+        )
+
+        ax.legend(loc='best')
+        fig.savefig(os.path.join(self.logs_dir, "timing.png"))
+
+    def _get_time(self, string):
+        date, current_time, am_pm = string.split(" ")[:3]
+        mon, day, yr = (int(v) for v in date.split("/"))
+        hr, mn, sec = (int(v) for v in current_time.split(":"))
+
+        if "PM" in am_pm and hr < 12:
+            hr += 12
+        elif "AM" in am_pm and hr == 12:
+            hr = 0
+
+        time_point = datetime.datetime(yr, mon, day, hr, mn, sec)
+
+        return (time_point - self.t0).total_seconds()
+
+    @staticmethod
+    def _get_data(string):
+        return float(
+            (string.split(" took ")[1])[:-3]
+        )

src/expam/cli/tree.py

@@ -7,7 +7,7 @@ from expam.classify import ResultsPathConfig
 from expam.classify.classify import ClassificationResults, name_to_id
 from expam.classify.config import make_results_config, validate_results_configuration
 from expam.classify.taxonomy import TaxonomyNCBI
-from expam.main import CommandGroup, ExpamOptions
+from expam.cli.main import CommandGroup, ExpamOptions
 from expam.database import FileLocationConfig
 from expam.database.config import JSONConfig, make_database_config, validate_database_file_configuration
 from expam.tree import PHYLA_COLOURS

src/expam/cli/utils.py

@@ -2,7 +2,7 @@ import os
 import matplotlib.pyplot as plt
 from expam.classify import ResultsPathConfig
 from expam.classify.config import make_results_config, validate_classification_results, validate_results_configuration
-from expam.main import CommandGroup, ExpamOptions
+from expam.cli.main import CommandGroup, ExpamOptions
 from expam.database import FileLocationConfig
 from expam.database.config import JSONConfig, make_database_config, validate_database_file_configuration
 from expam.sequences import format_name

src/expam/database/__init__.py

@@ -30,7 +30,7 @@ DATABASE_FILE_RELATIVE_PATH = os.path.join(DATABASE_RELATIVE_PATH, "expam_db.h5"
 FileLocationConfig = namedtuple(
     'FileLocationConfig',
     [
-        'database', 'phylogeny', 'logs', 'conf',
+        'base', 'database', 'phylogeny', 'logs', 'conf',
         'accession_id', 'taxid_lineage', 'taxon_rank',
         'lca_matrix',
         'database_file'

src/expam/database/build.py

@@ -5,13 +5,12 @@ import os
 import subprocess
 
 import numpy as np
-from expam import COMP_PARSE
 from expam.database import CHUNK_SIZE, TIMEOUT, UNION_RATIO, FileLocationConfig, expam_dtypes
 from expam.database.config import load_database_config
 from expam.process.genome import ExtractWorker
 from expam.process.manager import ControlCenter, ExpamProcesses
 from expam.process.piler import UnionWorker
-from expam.sequences import check_suffix
+from expam.sequences import COMP_PARSE, check_suffix
 from expam.tree.tree import Index, propose_lca
 from expam.utils import ls
 

src/expam/database/config.py

@@ -216,6 +216,7 @@ class ExpamDatabaseExistsError(Exception):
 
 def make_database_config(db_path: str) -> FileLocationConfig:
     database_file_locations = {
+        'base': db_path,
         'database': os.path.join(db_path, DATABASE_RELATIVE_PATH),
         'phylogeny': os.path.join(db_path, PHYLOGENY_RELATIVE_PATH),
         'logs': os.path.join(db_path, LOG_RELATIVE_PATH),
@@ -239,7 +240,7 @@ def load_database_config(db_path: str) -> FileLocationConfig:
 
 
 def create_database(config: FileLocationConfig) -> None:
-    for field_to_check in ('database', 'phylogeny', 'logs'):
+    for field_to_check in ('base', 'database', 'phylogeny', 'logs'):
         path: str = getattr(config, field_to_check)
 
         if not os.path.exists(path):
@@ -247,9 +248,13 @@ def create_database(config: FileLocationConfig) -> None:
         else:
             raise ExpamDatabaseExistsError("Database %s already exists!" % config.database)
 
+    # Create new configuration file.
+    conf: JSONConfig = JSONConfig()
+    conf.save(url=config.conf)
+
 
 def validate_database_file_configuration(proposed_config: FileLocationConfig) -> bool:
-    for field_to_check in ('database', 'phylogeny', 'conf'):
+    for field_to_check in ('base', 'database', 'phylogeny', 'conf'):
         if not os.path.exists(getattr(proposed_config, field_to_check)):
             return False
     else:

src/expam/main.py

-from argparse import ArgumentParser, Namespace, RawTextHelpFormatter
-from collections import namedtuple
-import datetime
 import multiprocessing
-import os
 import platform
-import shutil
 
-import matplotlib.pyplot as plt
-import numpy as np
 from expam.cli.build import BuildCommand
 from expam.cli.classify import ClassifyCommand
+from expam.cli.main import CommandGroup, ExpamOptions, retrieve_arguments
 from expam.cli.tree import TreeCommand
-
-from expam.utils import die, ls, make_path_absolute
-
-
-ExpamOptions = namedtuple(
-    'ExpamOptions',
-    [
-        # Runtime arguments
-        'command', 'db_name', 'k', 'n', 's', 'phylogeny', 'alpha',
-        # Directory arguments
-        'directory', 'out_url', 'truth_dir',
-        # Parameter arguments
-        'length', 'pile', 'error_rate', 'first_n', 'sketch', 'paired_end',
-        # Summary arguments
-        'plot', 'cutoff', 'cpm', 'taxonomy',
-        # Plot arguments
-        'groups', 'phyla', 'keep_zeros', 'ignore_names', 'colour_list', 'rank', 'log_scores', 'itol_mode',
-        # Tree arguments
-        'use_sourmash', 'use_rapidnj', 'use_quicktree'
-    ]
-)
-
-def retrieve_arguments() -> ExpamOptions:
-    parser = ArgumentParser(description="  expam CLI\n--------------\n", formatter_class=RawTextHelpFormatter)
-    
-    parser.add_argument("command", default=None,
-                        help='\nCommand to execute. Valid commands include:\n'
-                             '-------------------------------------------\n'
-                             'create:-\tInitialise database.\n'
-                             'build:-\t\tStart building database.\n'
-                             'print:-\t\tPrint current database parameters.\n'
-                             'run:-\t\tRun reads against database.\n'
-                             'add:-\t\tAdd sequence to the database.\n'
-                             'remove:-\tRemove sequence from database (only impacts future db builds).\n'
-                             'set:-\t\tSet database build parameters.\n'
-                             'to_taxonomy:-\t\tConvert results to taxonomic setting.\n'
-                             'phylotree:-\t\tDraw results on phylotree.\n'
-                             'draw_tree:-\t\tDraw the reference tree.\n'
-                             'download_taxonomy:-\t\tDownload taxonomic information for reference seqeunces.\n'
-                             'cutoff:-\t\tApply cutoff to some set of already processed classifications. THIS WILL OVERWRITE OLD RESULTS!\n'
-                             'mashtree:-\tCreate mashtree from current sequences and add to database.\n'
-                             'quickrun:-\tInitialise, set parameters and start building db (assumes\n'
-                             '\t\t\tsequences all lie in the same folder).\n'
-                             'make_reads:-\tUniformly sample reads of length l from some input sequence.\n'
-                             '\t\tThis is for testing purposes only, and is not a replacement\n'
-                             '\t\tfor actual read generating software.\n',
-                        metavar="[command]")
-    parser.add_argument("-db", "--db_name", dest="db_name",
-                        help="Name of database.",
-                        metavar="[database name]")
-    parser.add_argument("-k", "--kmer", dest="k",
-                        help="Length of mer used for analysis.",
-                        metavar="[k value (int)]")
-    parser.add_argument("-n", "--n-processes", dest="n",
-                        help="Number of CPUs to use for processing.",
-                        metavar="[n (int)]")
-    parser.add_argument("-s", "--sketch", dest="sketch",
-                        help="Sketch size for mash.",
-                        metavar="[sketch size (int)]")
-    parser.add_argument("-p", "--phylogeny", dest="phylogeny",
-                        help="URL of Newick file containing phylogeny.",
-                        metavar="[phylogeny URL]")
-    parser.add_argument("-d", "--directory", dest="directory", action="append",
-                        help="File URL, context depending on command supplied.",
-                        metavar="[directory]")
-    parser.add_argument("-l", "--length", dest="length",
-                        help="Length of simulated reads.",
-                        metavar="[read length]")
-    parser.add_argument("-o", "--out", dest="out_url",
-                        help="Where to save classification results.",
-                        metavar="[out URL]")
-    parser.add_argument("-y", "--pile", dest="pile",
-                        help="Number of genomes to pile at a time (or inf).",
-                        metavar="[pile size]")
-    parser.add_argument("-e", "--error-rate", dest="error_rate",
-                        help="Generate error in reads (error ~ reads with errors / reads).",
-                        metavar="[error rate]")
-    parser.add_argument("-t", "--truth", dest="truth_dir",
-                        help="Location of truth dataset.")
-    parser.add_argument("--plot", dest="plot", default=False, action="store_true",
-                        help="Plot timing data of database build.")
-    parser.add_argument("--first", dest="first_n", default=None,
-                        help="Add first n genomes in folder.")
-    parser.add_argument("--cutoff", dest="cutoff", default=0,
-                        help="Ignore organisms with less than `cutoff` reads in results.")
-    parser.add_argument("--cpm", dest="cpm", default=100,
-                        help="Counts/million cutoff for read-count to be non-negligible.")
-    parser.add_argument("--taxonomy", dest="taxonomy", default=False, action="store_true",
-                        help="Convert phylogenetic results to taxonomic results.")
-    parser.add_argument("--phyla", dest="phyla", default=False, action="store_true",
-                        help="Colour phylotree results by phyla.")
-    parser.add_argument("--rank", dest="rank", default=None,
-                        help="Rank at which to sort results.")
-    parser.add_argument("--keep-zeros", dest="keep_zeros", default=False, action="store_true",
-                        help="Keep nodes of output where no reads have been assigned.")
-    parser.add_argument("--ignore-names", dest="ignore_node_names", default=False, action="store_true")
-    parser.add_argument("--group", dest="groups", action="append", nargs="+",
-                        help="Space-separated list of sample files to be treated as a single group in phylotree.")
-    parser.add_argument("--colour-list", dest="colour_list", nargs="+",
-                        help="List of colours to use when plotting groups in phylotree.")
-    parser.add_argument("--circle-scale", dest="circle_scale", default=1.0,
-                        help="Scale of circles that represent splits in phylotree.")
-    parser.add_argument("--sourmash", dest="use_sourmash", default=False, action="store_true",
-                        help="Use sourmash for distance estimation.")
-    parser.add_argument("--rapidnj", dest="use_rapidnj", default=True, action="store_true",
-                        help="Use RapidNJ for Neighbour-Joining algorithm.")
-    parser.add_argument("--quicktree", dest="use_quicktree", default=False, action="store_true",
-                        help="Use QuickTree for Neighbour-Joining algorithm.")
-    parser.add_argument("--paired", dest="paired_end", default=False, action="store_true",
-                        help="Treat reads as paired-end.")
-    parser.add_argument("--alpha", dest="alpha", default=0.1,