Change the default extension behaviour to --noextend

Following discussion in Issue #342.

pyani/anim.py

@@ -141,7 +141,7 @@ def generate_nucmer_jobs(
     nucmer_exe: Path = pyani_config.NUCMER_DEFAULT,
     filter_exe: Path = pyani_config.FILTER_DEFAULT,
     maxmatch: bool = False,
-    extend: bool = False,
+    noextend: bool = False,
     jobprefix: str = "ANINUCmer",
 ):
     """Return list of Jobs describing NUCmer command-lines for ANIm.
@@ -151,14 +151,14 @@ def generate_nucmer_jobs(
     :param nucmer_exe:  str, location of the nucmer binary
     :param filter_exe:
     :param maxmatch:  Boolean flag indicating to use NUCmer's -maxmatch option
-    :param extend:  Boolean flag indicating whether to use NUCmer's --(no)extend (False: --noextend; True: --extend)
+    :param noextend:  Boolean flag indicating whether to use NUCmer's --(no)extend (True: --noextend; False: --extend)
     :param jobprefix:
 
     Loop over all FASTA files, generating Jobs describing NUCmer command lines
     for each pairwise comparison.
     """
     ncmds, fcmds = generate_nucmer_commands(
-        filenames, outdir, nucmer_exe, filter_exe, maxmatch, extend
+        filenames, outdir, nucmer_exe, filter_exe, maxmatch, noextend
     )
     joblist = []
     for idx, ncmd in enumerate(ncmds):
@@ -177,15 +177,15 @@ def generate_nucmer_commands(
     nucmer_exe: Path = pyani_config.NUCMER_DEFAULT,
     filter_exe: Path = pyani_config.FILTER_DEFAULT,
     maxmatch: bool = False,
-    extend: bool = False,
+    noextend: bool = False,
 ) -> Tuple[List, List]:
     """Return list of NUCmer command-lines for ANIm.
 
     :param filenames:  a list of paths to input FASTA files
     :param outdir:  path to output directory
     :param nucmer_exe:  location of the nucmer binary
     :param maxmatch:  Boolean flag indicating to use NUCmer's -maxmatch option
-    :param extend:  Boolean flag indicating whether to use NUCmer's --(no)extend (False: --noextend; True: --extend)
+    :param noextend:  Boolean flag indicating whether to use NUCmer's --(no)extend (True: --noextend; False: --extend)
 
     The first element returned is a list of NUCmer commands, and the
     second a corresponding list of delta_filter_wrapper.py commands.
@@ -202,7 +202,7 @@ def generate_nucmer_commands(
     for idx, fname1 in enumerate(filenames[:-1]):
         for fname2 in filenames[idx + 1 :]:
             ncmd, dcmd = construct_nucmer_cmdline(
-                fname1, fname2, outdir, nucmer_exe, filter_exe, maxmatch, extend
+                fname1, fname2, outdir, nucmer_exe, filter_exe, maxmatch, noextend
             )
             nucmer_cmdlines.append(ncmd)
             delta_filter_cmdlines.append(dcmd)
@@ -218,7 +218,7 @@ def construct_nucmer_cmdline(
     nucmer_exe: Path = pyani_config.NUCMER_DEFAULT,
     filter_exe: Path = pyani_config.FILTER_DEFAULT,
     maxmatch: bool = False,
-    extend: bool = False,
+    noextend: bool = False,
 ) -> Tuple[str, str]:
     """Return a tuple of corresponding NUCmer and delta-filter commands.
 
@@ -229,7 +229,7 @@ def construct_nucmer_cmdline(
     :param filter_exe:
     :param maxmatch:  Boolean flag indicating whether to use NUCmer's -maxmatch
     option. If not, the -mum option is used instead
-    :param extend:  Boolean flag indicating whether to use NUCmer's --(no)extend (False: --noextend; True: --extend)
+    :param noextend:  Boolean flag indicating whether to use NUCmer's --(no)extend (True: --noextend; False: --extend)
 
     The split into a tuple was made necessary by changes to SGE/OGE.
     The delta-filter command must now be run as a dependency of the NUCmer
@@ -252,10 +252,10 @@ def construct_nucmer_cmdline(
         mode = "--maxmatch"
     else:
         mode = "--mum"
-    if extend:
-        ext = " --extend"
-    else:
+    if noextend:
         ext = " --noextend"
+    else:
+        ext = " --extend"
     nucmercmd = f"{nucmer_exe} {mode} {ext} -p {outprefix} {fname2} {fname2}"
     # There's a subtle pathlib.Path issue, here. We must use string concatenation to add suffixes
     # to the outprefix files, as using path.with_suffix() instead can replace part of the filestem

pyani/pyani_orm.py

@@ -274,7 +274,7 @@ class Comparison(Base):
             "version",
             "fragsize",
             "maxmatch",
-            "extend",
+            "noextend",
         ),
     )
 
@@ -290,7 +290,7 @@ class Comparison(Base):
     version = Column(String)
     fragsize = Column(Integer)
     maxmatch = Column(Boolean)
-    extend = Column(Boolean)
+    noextend = Column(Boolean)
 
     query = relationship(
         "Genome", foreign_keys=[query_id], back_populates="query_comparisons"
@@ -344,7 +344,7 @@ def get_comparison_dict(session: Any) -> Dict[Tuple, Any]:
     :param session:      live SQLAlchemy session of pyani database
 
     Returns Comparison objects, keyed by (_.query_id, _.subject_id,
-    _.program, _.version, _.fragsize, _.maxmatch, _.extend) tuple
+    _.program, _.version, _.fragsize, _.maxmatch, _.noextend) tuple
     """
     return {
         (
@@ -354,7 +354,7 @@ def get_comparison_dict(session: Any) -> Dict[Tuple, Any]:
             _.version,
             _.fragsize,
             _.maxmatch,
-            _.extend,
+            _.noextend,
         ): _
         for _ in session.query(Comparison).all()
     }
@@ -416,7 +416,7 @@ def filter_existing_comparisons(
     version,
     fragsize: Optional[int] = None,
     maxmatch: Optional[bool] = False,
-    extend: Optional[bool] = False,
+    noextend: Optional[bool] = False,
 ) -> List:
     """Filter list of (Genome, Genome) comparisons for those not in the session db.
 
@@ -427,7 +427,7 @@ def filter_existing_comparisons(
     :param version:       version of program for comparison
     :param fragsize:      fragment size for BLAST databases
     :param maxmatch:      maxmatch used with nucmer comparison
-    :param extend:        extend used with nucmer comparison
+    :param noextend:        noextend used with nucmer comparison
 
     When passed a list of (Genome, Genome) comparisons as comparisons, check whether
     the comparison exists in the database and, if so, associate it with the passed run.
@@ -448,7 +448,7 @@ def filter_existing_comparisons(
                         version,
                         fragsize,
                         maxmatch,
-                        extend,
+                        noextend,
                     )
                 ]
             )

pyani/scripts/parsers/anim_parser.py

@@ -111,18 +111,18 @@ def build(
         default=False,
         help="override MUMmer to allow all NUCmer matches",
     )
-    extend = parser.add_mutually_exclusive_group()
-    extend.add_argument(
-        "--extend",
-        dest="extend",
-        action="store_true",
-        default=False,
-        help="override default to allow overlapping NUCmer matches",
-    )
-    extend.add_argument(
+    # extend = parser.add_mutually_exclusive_group()
+    # extend.add_argument(
+    #     "--extend",
+    #     dest="extend",
+    #     action="store_true",
+    #     default=True,
+    #     help="override default to allow overlapping NUCmer matches",
+    # )
+    parser.add_argument(
         "--noextend",
-        dest="extend",
-        action="store_false",
+        dest="noextend",
+        action="store_true",
         default=False,
         help="disallow overlapping NUCmer matches",
     )

pyani/scripts/subcommands/subcmd_anim.py

@@ -128,7 +128,7 @@ class ProgParams(NamedTuple):
 
     fragsize: str
     maxmatch: bool
-    extend: bool
+    noextend: bool
 
 
 def subcmd_anim(args: Namespace) -> None:
@@ -252,7 +252,7 @@ def subcmd_anim(args: Namespace) -> None:
         nucmer_version,
         None,
         args.maxmatch,
-        args.extend,
+        args.noextend,
     )
     logger.info(
         "\t...after check, still need to run %s comparisons", len(comparisons_to_run)
@@ -338,7 +338,7 @@ def generate_joblist(
             args.nucmer_exe,
             args.filter_exe,
             args.maxmatch,
-            args.extend,
+            args.noextend,
         )
         logger.debug("Commands to run:\n\t%s\n\t%s", ncmd, dcmd)
         outprefix = ncmd.split()[4]  # prefix for NUCmer output
@@ -447,7 +447,7 @@ def update_comparison_results(
                 version=nucmer_version,
                 fragsize=None,
                 maxmatch=args.maxmatch,
-                extend=args.extend,
+                noextend=args.noextend,
             )
         )