fix #299 extra parameter options

bin/input_commands.py

@@ -149,6 +149,18 @@ def get_input():
         help="Skips running mash to find the closest match for each contig in INPHARED.",
         action="store_true",
     )
+    parser.add_argument(
+        "--minced_args",
+        help="extra commands to pass to MINced (please omit the leading hyphen for the first argument). You will need to use quotation marks e.g. --minced_args \"minNR 2 -minRL 21\"",
+        default="",
+        type=str
+    )
+    parser.add_argument(
+        "--mash_distance",
+        help="mash distance for the search against INPHARED. Defaults to 0.2.",
+        default=0.2,
+        type=float
+    )
     parser.add_argument(
         "-V",
         "--version",

bin/pharokka.py

@@ -321,7 +321,7 @@ def main():
             logger.info("Starting tRNA-scanSE.")
             run_trna_scan(input_fasta, args.threads, out_dir, logdir)
         # run minced and aragorn
-        run_minced(input_fasta, out_dir, prefix, logdir)
+        run_minced(input_fasta, out_dir, prefix, args.minced_args, logdir)
         run_aragorn(input_fasta, out_dir, prefix, logdir)
 
     # running mmseqs2 on the 3 databases
@@ -460,7 +460,7 @@ def main():
         logger.info("Finding the closest match for each contig in INPHARED using mash.")
         # in process.py
         run_mash_sketch(input_fasta, out_dir, logdir)
-        run_mash_dist(out_dir, db_dir, logdir)
+        run_mash_dist(out_dir, db_dir, args.mash_distance, logdir)
         # part of the class
         pharok.inphared_top_hits()
     else:

bin/processes.py

@@ -776,12 +776,13 @@ def convert_gff_to_gbk(filepath_in, input_dir, out_dir, prefix, prot_seq_df):
             SeqIO.write(record, gbk_handler, "genbank")
 
 
-def run_minced(filepath_in, out_dir, prefix, logdir):
+def run_minced(filepath_in, out_dir, prefix, minced_args, logdir):
     """
     Runs MinCED
     :param filepath_in: input fasta file
     :param out_dir: output directory
     :param logger: logger
+    :param minced_args: str with extra arguments to pass to MINced
     :params prefix: prefix
     :return:
     """
@@ -791,11 +792,14 @@ def run_minced(filepath_in, out_dir, prefix, logdir):
     output_spacers = os.path.join(out_dir, prefix + "_minced_spacers.txt")
     output_gff = os.path.join(out_dir, prefix + "_minced.gff")
 
+    if minced_args != "":
+        minced_args = f"-{minced_args}"
+
     minced_fast = ExternalTool(
         tool="minced",
         input=f"",
-        output=f"{output_spacers} {output_gff}",
-        params=f" {filepath_in}",  # need strange order for minced params go first
+        output=f" {output_spacers} {output_gff}",
+        params=f" {minced_args} {filepath_in}",  # need strange order for minced params go first
         logdir=logdir,
         outfile="",
     )
@@ -910,11 +914,12 @@ def run_mash_sketch(filepath_in, out_dir, logdir):
         logger.error("Error with mash sketch\n")
 
 
-def run_mash_dist(out_dir, db_dir, logdir):
+def run_mash_dist(out_dir, db_dir, mash_distance, logdir):
     """
     Runs mash
     :param filepath_in: input filepath
     :param out_dir: output directory
+    :param mash_distance: mash distance - float
     :param logger logger
     :return:
     """
@@ -927,7 +932,7 @@ def run_mash_dist(out_dir, db_dir, logdir):
         tool="mash",
         input="",
         output="",
-        params=f" dist  {mash_sketch} {phrog_sketch} -d 0.2 -i ",
+        params=f" dist  {mash_sketch} {phrog_sketch} -d {mash_distance} -i ",
         logdir=logdir,
         outfile=mash_tsv,
     )

tests/test_overall.py

@@ -85,13 +85,24 @@ def test_overall(tmp_dir):
     cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f"
     exec_command(cmd)
 
+def test_overall_mash_distance(tmp_dir):
+    """test pharokka overall with stricter mash distance"""
+    input_fasta: Path = f"{standard_data}/SAOMS1.fasta"
+    cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f --mash_distance 0.05"
+    exec_command(cmd)
 
 def test_overall_crispr(tmp_dir):
     """test pharokka overall crispr"""
     input_fasta: Path = f"{CRISPR_data}/Biggiephage_A_fullcontig_CasΦ1.fasta"
     cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f"
     exec_command(cmd)
 
+def test_overall_crispr_minced_args(tmp_dir):
+    """test pharokka crispr with minced args"""
+    input_fasta: Path = f"{CRISPR_data}/Biggiephage_A_fullcontig_CasΦ1.fasta"
+    cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f -g prodigal --minced_args \"minNR 2 -minRL 21\" "
+    exec_command(cmd)
+
 
 def test_overall_vfdb(tmp_dir):
     """test pharokka overall on a phage with vfdb hits. Also include --skip_extra_annotations"""
@@ -137,14 +148,12 @@ def test_meta_prodigal_gv(tmp_dir):
     cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f -m -g prodigal-gv"
     exec_command(cmd)
 
-
 def test_meta_dnaapler_all_bug(tmp_dir):
     """test pharokka meta dnaapler bug and split"""
     input_fasta: Path = f"{meta_data}/combined_meta.fasta"
     cmd = f"pharokka.py -i {input_fasta} -d {database_dir} -o {tmp_dir} -t {threads} -f -m -s --dnaapler --meta_hmm"
     exec_command(cmd)
 
-
 def test_overall_locus(tmp_dir):
     """test pharokka overall locus tag prefix"""
     input_fasta: Path = f"{standard_data}/SAOMS1.fasta"