[WIP] add support for sourmash sketch fromfile functionality. (#1884)

* upgrade ComputerParameters with __repr__ and __eq__

* cleanup and refactor

* add tests for new behavior

* finish tests

* add ComputeParameters.to_param_str

* fix spelling

* a fix, and some tests

* add tests for to_param_str

src/sourmash/command_compute.py

@@ -328,6 +328,60 @@ def __init__(self, ksizes, seed, protein, dayhoff, hp, dna, num_hashes, track_ab
         self.track_abundance = track_abundance
         self.scaled = scaled
 
+    def to_param_str(self):
+        "Convert object to equivalent params str."
+        pi = []
+
+        if self.dna:
+            pi.append("dna")
+        elif self.protein:
+            pi.append("protein")
+        elif self.hp:
+            pi.append("hp")
+        elif self.dayhoff:
+            pi.append("dayhoff")
+        else:
+            assert 0            # must be one of the previous
+
+        if self.dna:
+            kstr = [f"k={k}" for k in self.ksizes]
+        else:
+            # for protein, divide ksize by three.
+            kstr = [f"k={k//3}" for k in self.ksizes]
+        assert kstr
+        pi.extend(kstr)
+
+        if self.num_hashes != 0:
+            pi.append(f"num={self.num_hashes}")
+        elif self.scaled != 0:
+            pi.append(f"scaled={self.scaled}")
+        else:
+            assert 0
+
+        if self.track_abundance:
+            pi.append("abund")
+        # noabund is default
+
+        if self.seed != 42:
+            pi.append(f"seed={self.seed}")
+        # self.seed
+
+        return ",".join(pi)
+
+    def __repr__(self):
+        return f"ComputeParameters({self.ksizes}, {self.seed}, {self.protein}, {self.dayhoff}, {self.hp}, {self.dna}, {self.num_hashes}, {self.track_abundance}, {self.scaled})"
+
+    def __eq__(self, other):
+        return (self.ksizes == other.ksizes and
+                self.seed == other.seed and
+                self.protein == other.protein and
+                self.dayhoff == other.dayhoff and
+                self.hp == other.hp and
+                self.dna == other.dna and
+                self.num_hashes == other.num_hashes and
+                self.track_abundance == other.track_abundance and
+                self.scaled == other.scaled)
+
     @staticmethod
     def from_args(args):
         ptr = lib.computeparams_new()

src/sourmash/command_sketch.py

@@ -82,8 +82,7 @@ def _parse_params_str(params_str):
 
 class _signatures_for_sketch_factory(object):
     "Build sigs on demand, based on args input to 'sketch'."
-    def __init__(self, params_str_list, default_moltype, mult_ksize_by_3):
-
+    def __init__(self, params_str_list, default_moltype):
         # first, set up defaults per-moltype
         defaults = {}
         for moltype, pstr in DEFAULTS.items():
@@ -94,7 +93,7 @@ def __init__(self, params_str_list, default_moltype, mult_ksize_by_3):
 
         # next, fill out params_list
         self.params_list = []
-        self.mult_ksize_by_3 = mult_ksize_by_3
+        self.mult_ksize_by_3 = True
 
         if params_str_list:
             # parse each params_str passed in, using default_moltype if none
@@ -103,17 +102,21 @@ def __init__(self, params_str_list, default_moltype, mult_ksize_by_3):
                 moltype, params = _parse_params_str(params_str)
                 if moltype and moltype != 'dna' and default_moltype == 'dna':
                     raise ValueError(f"Incompatible sketch type ({default_moltype}) and parameter override ({moltype}) in '{params_str}'; maybe use 'sketch translate'?")
-                elif moltype == 'dna' and default_moltype != 'dna':
+                elif moltype == 'dna' and default_moltype and default_moltype != 'dna':
                     raise ValueError(f"Incompatible sketch type ({default_moltype}) and parameter override ({moltype}) in '{params_str}'")
                 elif moltype is None:
+                    if default_moltype is None:
+                        raise ValueError(f"No default moltype and none specified in param string")
                     moltype = default_moltype
 
                 self.params_list.append((moltype, params))
         else:
+            if default_moltype is None:
+                raise ValueError(f"No default moltype and none specified in param string")
             # no params str? default to a single sig, using default_moltype.
             self.params_list.append((default_moltype, {}))
 
-    def get_compute_params(self):
+    def get_compute_params(self, *, split_ksizes=False):
         for moltype, params_d in self.params_list:
             # get defaults for this moltype from self.defaults:
             default_params = self.defaults[moltype]
@@ -134,26 +137,33 @@ def get_compute_params(self):
             if not ksizes:
                 ksizes = def_ksizes
 
-            if self.mult_ksize_by_3:
+            # 'command sketch' adjusts k-mer sizes by 3 if non-DNA sketch.
+            if self.mult_ksize_by_3 and not def_dna:
                 ksizes = [ k*3 for k in ksizes ]
 
-            params_obj = ComputeParameters(ksizes,
-                                           params_d.get('seed', def_seed),
-                                           def_protein,
-                                           def_dayhoff,
-                                           def_hp,
-                                           def_dna,
-                                           params_d.get('num', def_num),
-                                           params_d.get('track_abundance',
-                                                        def_abund),
-                                           params_d.get('scaled', def_scaled))
-
-            yield params_obj
-
-    def __call__(self):
+            make_param = lambda ksizes: ComputeParameters(ksizes,
+                                            params_d.get('seed', def_seed),
+                                            def_protein,
+                                            def_dayhoff,
+                                            def_hp,
+                                            def_dna,
+                                            params_d.get('num', def_num),
+                                            params_d.get('track_abundance',
+                                                         def_abund),
+                                            params_d.get('scaled', def_scaled))
+
+            if split_ksizes:
+                for ksize in ksizes:
+                    params_obj = make_param([ksize])
+                    yield params_obj
+            else:
+                params_obj = make_param(ksizes)
+                yield params_obj
+
+    def __call__(self, *, split_ksizes=False):
         "Produce a new set of signatures built to match the param strings."
         sigs = []
-        for params in self.get_compute_params():
+        for params in self.get_compute_params(split_ksizes=split_ksizes):
             sig = SourmashSignature.from_params(params)
             sigs.append(sig)
 
@@ -214,8 +224,7 @@ def dna(args):
 
     try:
         signatures_factory = _signatures_for_sketch_factory(args.param_string,
-                                                            'dna',
-                                                            mult_ksize_by_3=False)
+                                                            'dna')
     except ValueError as e:
         error(f"Error creating signatures: {str(e)}")
         sys.exit(-1)
@@ -244,8 +253,7 @@ def protein(args):
 
     try:
         signatures_factory = _signatures_for_sketch_factory(args.param_string,
-                                                            moltype,
-                                                            mult_ksize_by_3=True)
+                                                            moltype)
     except ValueError as e:
         error(f"Error creating signatures: {str(e)}")
         sys.exit(-1)
@@ -274,8 +282,7 @@ def translate(args):
 
     try:
         signatures_factory = _signatures_for_sketch_factory(args.param_string,
-                                                            moltype,
-                                                            mult_ksize_by_3=True)
+                                                            moltype)
     except ValueError as e:
         error(f"Error creating signatures: {str(e)}")
         sys.exit(-1)

src/sourmash/index/__init__.py

@@ -341,7 +341,7 @@ def select(self, ksize=None, moltype=None, scaled=None, num=None,
 
 def select_signature(ss, *, ksize=None, moltype=None, scaled=0, num=0,
                      containment=False, abund=None, picklist=None):
-    "Check that the given signature matches the specificed requirements."
+    "Check that the given signature matches the specified requirements."
     # ksize match?
     if ksize and ksize != ss.minhash.ksize:
         return False