Implement click

Remove argparse. This addresses issue #1 suggesting a refactor from argparse
to click. The different workflows
are now called via a flat (-w), and
the FASTA arguments are now at the end of the command
line call, allowing for
patterns like emmtyper *.fasta
to be used.
This also simplified the code by
removing duplication in the
run_ispcr and run_blast
modules from the utilities submodules.

emmtyper/bin/run_emmtyper.py

@@ -2,113 +2,200 @@
 For running emmtyper
 """
 
-import argparse
+import logging
 import pathlib
 import os
 
-from emmtyper.__init__ import __version__ as version
-from emmtyper.__init__ import __name__ as name
-from emmtyper.__init__ import __description__ as description
-from emmtyper.__init__ import __epilog__ as epilog
-
+import click
 
-from emmtyper.utilities import run_blast
-from emmtyper.utilities import run_ispcr
+from emmtyper.__init__ import __version__ as version
+from emmtyper.utilities import run_ispcr, run_blast
+from emmtyper.objects.clusterer import Clusterer
 
 DEFAULT_DB = pathlib.Path(__file__).parent.parent / "db" / "emm.fna"
-
-class CustomFormatter(
-    argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescriptionHelpFormatter
+DEFAULT_PRIMERS = pathlib.Path(__file__).parent.parent / "data" / "isPcrPrim.tsv"
+
+logger = logging.getLogger(__name__)
+
+
+@click.command()
+@click.version_option(
+    version=version, prog_name="emmtyper", message=("%(prog)s v%(version)s")
+)
+@click.argument("fasta", nargs=-1)
+@click.option(
+    "-w",
+    "--workflow",
+    default="blast",
+    help="Choose workflow",
+    type=click.Choice(["blast", "pcr"]),
+    show_default=True,
+)
+@click.option(
+    "-d",
+    "--blast_db",
+    default=os.environ.get("EMM_DB", DEFAULT_DB),
+    help="Path to EMM BLAST DB",
+    show_default=True,
+)
+@click.option(
+    "-k",
+    "--keep",
+    is_flag=True,
+    help="Keep BLAST and isPcr output files.",
+    show_default=True,
+)
+@click.option(
+    "-d",
+    "--cluster-distance",
+    default=500,
+    help="Distance between cluster of matches to consider as different clusters.",
+    show_default=True,
+)
+@click.option(
+    "-o",
+    "--output",
+    default="stdout",
+    help="Output stream. Path to file for output to a file.",
+    show_default=True,
+)
+@click.option(
+    "-f",
+    "--output-format",
+    default="short",
+    help="Output format.",
+    type=click.Choice(["short", "verbose", "visual"]),
+)
+@click.option(
+    "--dust",
+    default="no",
+    help="[BLAST] Filter query sequence with DUST.",
+    type=click.Choice(["yes", "no", "level window linker"]),
+    show_default=True,
+)
+@click.option(
+    "--percent-identity",
+    default=95,
+    help="[BLAST] Minimal percent identity of sequence.",
+    show_default=True,
+)
+@click.option(
+    "--culling-limit",
+    default=5,
+    help="[BLAST] Total hits to return in a position.",
+    show_default=True,
+)
+@click.option(
+    "--mismatch",
+    default=4,
+    help="[BLAST] Threshold for number of mismatch to allow in BLAST hit.",
+    show_default=True,
+)
+@click.option(
+    "--align-diff",
+    default=5,
+    help="[BLAST] Threshold for difference between alignment length and subject length in BLAST hit.",
+    show_default=True,
+)
+@click.option(
+    "--gap",
+    default=2,
+    help="[BLAST] Threshold gap to allow in BLAST hit.",
+    show_default=True,
+)
+@click.option(
+    "--blast-path",
+    help="[BLAST] Specify full path to blastn executable.",
+    show_default=True,
+)
+@click.option(
+    "--primer-db",
+    default=os.environ.get("EMM_PCR", DEFAULT_PRIMERS),
+    help="[isPcr] PCR primer. Text file with 3 columns: Name, Forward Primer, Reverse Primer.",
+    show_default=True,
+)
+@click.option(
+    "--min-perfect",
+    default=15,
+    help="[isPcr] Minimum size of perfect match at 3' primer end.",
+    show_default=True,
+)
+@click.option(
+    "--min-good",
+    default=15,
+    help="[isPcr] Minimum size where there must be 2 matches for each mismatch.",
+    show_default=True,
+)
+@click.option(
+    "--max-size",
+    default=2000,
+    help="[isPcr] Maximum size of PCR product.",
+    show_default=True,
+)
+@click.option(
+    "--ispcr-path",
+    help="[isPcr] Specify full path to isPcr executable.",
+    show_default=True,
+)
+def main(
+    fasta,
+    workflow,
+    blast_db,
+    keep,
+    cluster_distance,
+    output,
+    output_format,
+    dust,
+    percent_identity,
+    culling_limit,
+    mismatch,
+    align_diff,
+    gap,
+    blast_path,
+    primer_db,
+    min_perfect,
+    min_good,
+    max_size,
+    ispcr_path,
 ):
     """
-    Better formatting of argparse description and epilog, and include defaults.
-    """
-
-    pass
-
-
-def build_parser():
-    '''
-    Parse command line arguments and options
-    '''
-    parser = argparse.ArgumentParser(
-        prog=name,
-        description="{} - Version {}".format(description, version),
-        epilog=epilog,
-        formatter_class=CustomFormatter,
-    )
-
-    subparsers = parser.add_subparsers(title="Approaches to choose from", metavar="")
-
-    parser.add_argument(
-        "--query", required=True, type=str, nargs="+", help="Genome(s) to PCR against."
-    )
-    parser.add_argument(
-        "--db",
-        required=True,
-        type=str,
-        help="The database to BLAST PCR product against.",
-        default=os.environ.get("EMM_DB", DEFAULT_DB),
-    )
+    Welcome to emmtyper.
 
-    parser.add_argument(
-        "-v",
-        "--version",
-        action="version",
-        version="%(prog)s {version}".format(version=version),
-    )
+    Usage:
 
-    parser.add_argument(
-        "-save",
-        "--save_intermediary",
-        default=False,
-        action="store_true",
-        help="Do not remove temporary isPcr and BLAST outputs.",
-    )
-
-    # Clusterer Options
-
-    parser.add_argument(
-        "-clust_distance",
-        default=500,
-        type=int,
-        help="Distance in bp between clusters.",
-    )
-    parser.add_argument(
-        "-output_type",
-        nargs="?",
-        type=str,
-        default="short",
-        choices=["short", "verbose", "visual"],
-        help="Choose output type.",
-    )
-    parser.add_argument(
-        "-output_file", default="stdout", type=str, help="File to stream final output."
-    )
-
-    # BLAST subparser
-    parser_blast = subparsers.add_parser("blast", help="BLAST genomes against DB.")
-    parser_blast = runBLAST.buildSubparser(parser_blast)
-    parser_blast.set_defaults(func=runBLAST.main)
-
-    # PCR + BLAST subparser
-
-    parser_pcr = subparsers.add_parser(
-        "pcr", help="Generate in silico PCR products, then BLAST against DB."
-    )
-    parser_pcr = runIsPCR.buildSubparser(parser_pcr)
-    parser_pcr.set_defaults(func=runIsPCR.main)
-
-    return parser
-
-
-def main():
-    '''
-    Main function to parse command line arguments and options
-    '''
-    parser = build_parser()
-    args = parser.parse_args()
-    args.func(args)
+    emmtyper *.fasta
+    """
+    logger.info("Start running emmtyper on {} queries.".format(len(fasta)))
+    for i, query in enumerate(fasta):
+        if workflow == "pcr":
+            query = run_ispcr.get_amplicons(
+                query, str(primer_db), min_perfect, min_good, max_size, ispcr_path
+            )
+
+        blast_matches = run_blast.get_matches(
+            query,
+            str(blast_db),
+            dust,
+            percent_identity,
+            culling_limit,
+            mismatch,
+            align_diff,
+            gap,
+            blast_path,
+        )
+
+        clusterer = Clusterer(
+            blastOutputFile=blast_matches,
+            distance=cluster_distance,
+            output_stream=output,
+            output_type=output_format,
+        )
+        clusterer()
+
+        if not keep:
+            os.remove(blast_matches)
+
+    logger.info("Finished emmtyper.")
 
 
 if __name__ == "__main__":