init

MANIFEST.in

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+include README.md
+include LICENSE
+
+global-exclude *.DS_Store

setup.cfg

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+[metadata]
+name = melon
+version = attr: melon.__version__
+classifiers = 
+	Programming Language :: Python :: 3
+
+license = MIT
+description = MELON: Metagenomic Taxonomy Profiling and Genome Copies Estimation using Nanopore Long Reads
+long_description = file: README.md
+long_description_content_type = text/markdown
+keywords = 
+    taxonomy
+    taxonomy profiling
+
+[options]
+zip_safe = False
+python_requires = >=3.7
+package_dir =
+    = src
+packages = find:
+
+[options.entry_points]
+    console_scripts = 
+        melon = melon.cli:cli
+
+[options.packages.find]
+    where = src

setup.py

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+from setuptools import setup
+setup()

src/melon/__init__.py

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+__version__ = '0.0.1'
+
+from .melon import GenomeProfiler

src/melon/cli.py

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+import sys
+import os
+import glob
+
+from argparse import ArgumentParser, SUPPRESS
+from . import __version__
+from .utils import logger
+from .melon import GenomeProfiler
+
+
+def cli(argv=sys.argv):
+    '''
+    Entry point for command line interface.
+    '''
+    parser = ArgumentParser(description='Melon: \
+        long-read targeting taxonomic profiling and genome copies estimation \
+        phylogenetic marker genes.', add_help=False)
+    required = parser.add_argument_group('required arguments')
+    optional = parser.add_argument_group('optional arguments')
+    additional = parser.add_argument_group('additional arguments')
+
+    parser.add_argument(
+        'FILE',
+        nargs='+',
+        help='Input fasta <*.fa|*.fasta> or fastq <*.fq|*.fastq> file, gzip optional <*.gz>.')
+
+    required.add_argument(
+        '-d',
+        '--db',
+        metavar='DIR',
+        required=True,
+        help='Unzipped database folder, should contains <prot.fa>, <nucl.*.fa> and <metadata.tsv>.')
+
+    required.add_argument(
+        '-o',
+        '--output',
+        metavar='DIR',
+        required=True,
+        help='Output folder.')
+
+    optional.add_argument(
+        '-t',
+        '--threads',
+        metavar='INT',
+        type=int,
+        default=32,
+        help='Number of CPU threads. [32]')
+
+    optional.add_argument(
+        '-k',
+        '--db_kraken',
+        metavar='DIR',
+        help='Unzipped kraken2 database for pre-filtering of non-prokaryotic reads. Skip if not given.')
+
+    optional.add_argument(
+        '--skip-profile',
+        action='store_true',
+        help='Skip profiling, output only estimated total genome copies.')
+
+    optional.add_argument(
+        '--skip-clean',
+        action='store_true',
+        help='Skip cleaning, keep all temporary <*.tmp> files.')
+
+    additional.add_argument(
+        '-m',
+        metavar='INT',
+        type=int,
+        default=25,
+        help='Max. number of target sequences to report (--max-target-seqs/-k in diamond). [25]')
+
+    additional.add_argument(
+        '-e',
+        metavar='FLOAT',
+        type=float,
+        default=1e-15,
+        help='Max. expected value to report alignments (--evalue/-e in diamond). [1e-15]')
+
+    additional.add_argument(
+        '-i',
+        metavar='FLOAT',
+        type=float,
+        default=0,
+        help='Min. identity in percentage to report alignments (--id in diamond). [0]')
+
+    additional.add_argument(
+        '-s',
+        metavar='FLOAT',
+        type=float,
+        default=75,
+        help='Min. subject cover to report alignments (--subject-cover in diamond). [75]')
+
+    additional.add_argument(
+        '-n',
+        metavar='INT',
+        type=int,
+        default=2147483647,
+        help='Max. number of secondary alignments to report (-N in minimap2). [2147483647]')
+
+    additional.add_argument(
+        '-p',
+        metavar='FLOAT',
+        type=float,
+        default=0.9,
+        help='Min. secondary-to-primary score ratio to report secondary alignments (-p in minimap2). [0.9]')
+
+    parser.add_argument('-v', '--version', action='version', version=__version__, help=SUPPRESS)
+    parser.add_argument('-h', '--help', action='help', help=SUPPRESS)
+
+    if len(argv)==1:
+        print("             __        \n  __ _  ___ / /__  ___ \n /  ' \\/ -_) / _ \\/ _ \\\n/_/_/_/\\__/_/\\___/_//_/ ver. {}\n".format(__version__))
+
+    opt = parser.parse_args(argv[1:])
+    run(opt)
+
+
+def run(opt):
+    '''
+    Sanity check of options.
+    '''
+    ## check for output folder
+    if not os.path.isdir(opt.output):
+        os.makedirs(opt.output, exist_ok=True)
+    else:
+        logger.warning('Folder <{}> exists. Files will be overwritten.'.format(opt.output))
+
+    ## check for input files
+    for file in opt.FILE:
+        if not os.path.isfile(file):
+            logger.critical('File <{}> does not exist.'.format(file))
+            sys.exit(2)
+
+    ## check for database
+    if not os.path.isdir(opt.db):
+        logger.critical('Database folder <{}> does not exist.'.format(opt.db))
+        sys.exit(2)
+    else:
+        files = [os.path.basename(x) for x in glob.glob(os.path.join(opt.db, '*'))]
+        if 'metadata.tsv' not in files or len([x for x in files if 'prot' in x]) != 1 or len([x for x in files if 'nucl' in x]) != 16:
+            logger.critical('Database <{}> is not complete.'.format(opt.db))
+            sys.exit(2)
+
+    ## check for kraken2 database
+    if opt.db_kraken is not None:
+        if not os.path.isdir(opt.db_kraken):
+            logger.critical('Kraken2 database folder <{}> does not exist.'.format(opt.db_kraken))
+            sys.exit(2)
+        else:
+            files = [os.path.basename(x) for x in glob.glob(os.path.join(opt.db_kraken, '*'))]
+            if 'ktaxonomy.tsv' not in files or len([x for x in files if 'database' in x]) != 7:
+                logger.critical('Kraken2 database <{}> is not complete.'.format(opt.db_kraken))
+                sys.exit(2)
+
+    ## run
+    for i, file in enumerate(opt.FILE):
+        if len(opt.FILE) > 1:
+            logger.info('Processing file <{}> ({}/{}) ...'.format(file, i+1, len(opt.FILE)))
+
+        GenomeProfiler(file, opt.output, opt.threads).run(
+            db=opt.db,
+            db_kraken=opt.db_kraken,
+            skip_profile=opt.skip_profile,
+            skip_clean=opt.skip_clean,
+            max_target_seqs=opt.m, evalue=opt.e, identity=opt.i, subject_cover=opt.s,
+            secondary_num=opt.n, secondary_ratio=opt.p)
+
+        if i == len(opt.FILE) - 1:
+            logger.info('Done.')
+        else:
+            logger.info('Done.\n')
+
+
+if __name__ == '__main__':
+    cli(sys.argv)