[MRG] Add FrozenMinHash (#1508)

* have the 'find' function for SBTs return signatures * fix majority of tests * comment & then fix test * torture the tests into working * split find and _find_nodes to take different kinds of functions * redo 'find' on index * refactor lca_db to use new find * refactor SBT to use new find * comment/cleanup * refactor out common code * fix up gather * use 'passes' properly * attempted cleanup * minor fixes * get a start on correct downsampling * adjust tree downsampling for regular minhashes, too * remove now-unused search functions in sbtmh * refactor categorize to use new find * cleanup and removal * remove redundant code in lca_db * remove redundant code in SBT * add notes * remove more unused code * refactor most of the test_sbt tests * fix one minor issue * fix jaccard calculation in sbt * check for compatibility of search fn and query signature * switch tests over to jaccard similarity, not containment * fix test * remove test for unimplemented LCA_Database.find method * document threshold change; update test * refuse to run abund signatures * flatten sigs internally for gather * reinflate abundances for saving * fix problem where sbt indices coudl be created with abund signatures * more * split flat and abund search * make ignore_abundance work again for categorize * turn off best-only, since it triggers on self-hits. * add test: 'sourmash index' flattens sigs * add note about something to test * fix typo; still broken tho * location is now a property * move search code into search.py * remove redundant scaled checking code * best-only now works properly for two tests * 'fix' tests by removing v1 and v2 SBT compatibility * simplify (?) downsampling code * require keyword args in MinHash.downsample(...) * fix bug with downsample * require keyword args in MinHash.downsample(...) * fix test to use proper downsampling, reverse order to match scaled * add test for revealed bug * remove unnecessary comment * flatten subject MinHash, too * add testme comment * clean up sbt find * clean up lca find * add IndexSearchResult namedtuple for search and gather results * add more tests for Index classes * add tests for subj & query num downsampling * tests for Index.search_abund * refactor a bit * refactor make_jaccard_search_query; start tests * even more tests * test collect, best_only * more search tests * remove unnec space * add minor comment * deal with status == None on SystemExit * upgrade and simplify categorize * restore test * merge * fix abundance search in SBT for categorize * code cleanup and refactoring; check for proper error messages * add explicit test for incompatible num * refactor MinHash.downsample * deal with status == None on SystemExit * fix test * fix comment mispelling * properly pass kwargs; fix search_sbt_index * add simple tests for SBT load and search API * allow arbitrary kwargs for LCA_DAtabase.find * add testing of passthru-kwargs * re-enable test * add notes to update docstrings * docstring updates * fix test * fix location reporting in prefetch * fix prefetch location by fixing MultiIndex * temporary prefetch_gather intervention * 'gather' only returns best match * turn prefetch on by default, for now * better tests for gather --save-unassigned * remove unused print * remove unnecessary check-me comment * clear out docstring * SBT search doesn't work on v1 and v2 SBTs b/c no min_n_below * start adding tests * test some basic prefetch stuff * update index for prefetch * add fairly thorough tests * fix my dumb mistake with gather * simplify, refactor, fix * fix remaining tests * propogate ValueErrors better * fix tests * flatten prefetch queries * fix for genome-grist alpha test * fix threshold bugarooni * fix gather/prefetch interactions * fix sourmash prefetch return value * minor fixes * pay proper attention to threshold * cleanup and refactoring * remove unnecessary 'scaled' * minor cleanup * added LazyLinearLindex and prefetch --linear * fix abundance problem * save matches to a directory * test for saving matches to a directory * add a flexible progressive signature output class * add tests for .sig.gz and .zip outputs * update save_signatures code; add tests; use in gather and search too * update comment * cleanup and refactor of SaveSignaturesToLocation code * docstrings & cleanup * add 'run' and 'runtmp' test fixtures * remove unnecessary track_abundance fixture call * restore original; * linear and prefetch fixtures + runtmp * fix use of runtmp * copy over SaveSignaturesToLocation code from other branch * docs for sourmash prefetch * more doc * minor edits * Re-implement the actual gather protocol with a cleaner interface. (#1489) * initial refactor of CounterGather stuff * refactor into peek and consume * move next method over to query specific class * replace gather implementation with new CounterGather * many more tests for CounterGather * remove scaled arg from peek * open-box test for counter internal data structures * add num query & subj tests * add repr; add tests; support stdout * refactor signature saving to use new sourmash_args collection saving * specify utf-8 encoding for output * add flexible output to compute/sketch * add test to trigger rust panic * test search --save-matches * add --save-prefetch to sourmash gather * remove --no-prefetch option :) * added --save-prefetch functionality * add back a mostly-functioning --no-prefetch argument :) * add --no-prefetch back in * check for JSON in first byte of LCA DB file * start adding linear tests * use fixtures to test prefetch and linear more thoroughly * comments, etc * upgrade docs for --linear and --prefetch * 'fix' issue and test * fix a last test ;) * Update doc/command-line.md Co-authored-by: Tessa Pierce Ward <[email protected]> * Update src/sourmash/cli/sig/rename.py Co-authored-by: Tessa Pierce Ward <[email protected]> * Update tests/test_sourmash_args.py Co-authored-by: Tessa Pierce Ward <[email protected]> * Update tests/test_sourmash_args.py Co-authored-by: Tessa Pierce Ward <[email protected]> * Update tests/test_sourmash_args.py Co-authored-by: Tessa Pierce Ward <[email protected]> * Update tests/test_sourmash_args.py Co-authored-by: Tessa Pierce Ward <[email protected]> * Update tests/test_sourmash_args.py Co-authored-by: Tessa Pierce Ward <[email protected]> * Update doc/command-line.md Co-authored-by: Tessa Pierce Ward <[email protected]> * write tests for LazyLinearIndex * add some basic prefetch tests * properly test linear! * add more tests for LazyLinearIndex * test zipfile bool * remove unnecessary try/except; comment * fix signatures() call * fix --prefetch snafu; doc * do not overwrite signature even if duplicate md5sum (#1497) * try adding loc to return values from Index.find * made use of new IndexSearchResult.find throughout * adjust note * provide signatures_with_location on all Index objects * cleanup and fix * Update doc/command-line.md Co-authored-by: Tessa Pierce Ward <[email protected]> * Update doc/command-line.md Co-authored-by: Tessa Pierce Ward <[email protected]> * fix bug around --save-prefetch with multiple databases * comment/doc minor updates * initial trial implementation of ImmutableMinHash * fix tests * provide our own pickle for ImmutableMinHash * ok, a few more plcaes to change. * rename to FrozenMinHash per luiz * finish renaming, add some tests * thanks, I hate the old behavior * copy.copy is no longer needed * docs and an explicit 'frozen' method * switch to using 'to_frozen' and 'to_mutable' Co-authored-by: Luiz Irber <[email protected]> Co-authored-by: Tessa Pierce Ward <[email protected]>
sourmash-bio · May 15, 2021 · 9712009 · 9712009
1 parent 4c48f39
commit 9712009
Show file tree

Hide file tree

Showing 8 changed files with 152 additions and 8 deletions.
diff --git a/src/sourmash/commands.py b/src/sourmash/commands.py
@@ -1106,7 +1106,8 @@ def prefetch(args):
 
     # iterate over signatures in db one at a time, for each db;
     # find those with sufficient overlap
-    noident_mh = copy.copy(query_mh)
+    noident_mh = query_mh.to_mutable()
+
     did_a_search = False        # track whether we did _any_ search at all!
     for dbfilename in args.databases:
         notify(f"loading signatures from '{dbfilename}'")
@@ -1164,7 +1165,7 @@ def prefetch(args):
         notify(f"saved {matches_out.count} matches to CSV file '{args.output}'")
         csvout_fp.close()
 
-    matched_query_mh = copy.copy(query_mh)
+    matched_query_mh = query_mh.to_mutable()
     matched_query_mh.remove_many(noident_mh.hashes)
     notify(f"of {len(query_mh)} distinct query hashes, {len(matched_query_mh)} were found in matches above threshold.")
     notify(f"a total of {len(noident_mh)} query hashes remain unmatched.")

diff --git a/src/sourmash/minhash.py b/src/sourmash/minhash.py
@@ -588,7 +588,7 @@ def __add__(self, other):
             if self.num != other.num:
                 raise TypeError(f"incompatible num values: self={self.num} other={other.num}")
 
-        new_obj = self.__copy__()
+        new_obj = self.to_mutable()
         new_obj += other
         return new_obj
 
@@ -645,3 +645,107 @@ def moltype(self):                    # TODO: test in minhash tests
             return 'hp'
         else:
             return 'DNA'
+
+    def to_mutable(self):
+        "Return a copy of this MinHash that can be changed."
+        return self.__copy__()
+
+    def to_frozen(self):
+        "Return a frozen copy of this MinHash that cannot be changed."
+        new_mh = self.__copy__()
+        new_mh.__class__ = FrozenMinHash
+        return new_mh
+
+
+class FrozenMinHash(MinHash):
+    def add_sequence(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def add_kmer(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def add_many(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def remove_many(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def add_hash(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def add_hash_with_abundance(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def clear(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def remove_many(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def set_abundances(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def add_protein(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def downsample(self, *, num=None, scaled=None):
+        if scaled and self.scaled == scaled:
+            return self
+        if num and self.num == num:
+            return self
+
+        return MinHash.downsample(self, num=num, scaled=scaled).to_frozen()
+
+    def flatten(self):
+        if not self.track_abundance:
+            return self
+        return MinHash.flatten(self).to_frozen()
+
+    def __iadd__(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def merge(self, *args, **kwargs):
+        raise TypeError('FrozenMinHash does not support modification')
+
+    def to_mutable(self):
+        "Return a copy of this MinHash that can be changed."
+        mut = MinHash.__new__(MinHash)
+        state_tup = self.__getstate__()
+
+        # is protein/hp/dayhoff?
+        if state_tup[2] or state_tup[3] or state_tup[4]:
+            state_tup = list(state_tup)
+            # adjust ksize.
+            state_tup[1] = state_tup[1] * 3
+        mut.__setstate__(state_tup)
+        return mut
+
+    def to_frozen(self):
+        "Return a frozen copy of this MinHash that cannot be changed."
+        return self
+
+    def __setstate__(self, tup):
+        "support pickling via __getstate__/__setstate__"
+        (n, ksize, is_protein, dayhoff, hp, mins, _, track_abundance,
+         max_hash, seed) = tup
+
+        self.__del__()
+
+        hash_function = (
+            lib.HASH_FUNCTIONS_MURMUR64_DAYHOFF if dayhoff else
+            lib.HASH_FUNCTIONS_MURMUR64_HP if hp else
+            lib.HASH_FUNCTIONS_MURMUR64_PROTEIN if is_protein else
+            lib.HASH_FUNCTIONS_MURMUR64_DNA
+        )
+
+        scaled = _get_scaled_for_max_hash(max_hash)
+        self._objptr = lib.kmerminhash_new(
+            scaled, ksize, hash_function, seed, track_abundance, n
+        )
+        if track_abundance:
+            MinHash.set_abundances(self, mins)
+        else:
+            MinHash.add_many(self, mins)
+
+    def __copy__(self):
+        return self
diff --git a/src/sourmash/search.py b/src/sourmash/search.py
@@ -354,6 +354,7 @@ def gather_databases(query, counters, threshold_bp, ignore_abundance):
 
         # construct a new query, subtracting hashes found in previous one.
         new_query_mh = query.minhash.downsample(scaled=cmp_scaled)
+        new_query_mh = new_query_mh.to_mutable()
         new_query_mh.remove_many(set(found_mh.hashes))
         new_query = SourmashSignature(new_query_mh)
 

diff --git a/src/sourmash/signature.py b/src/sourmash/signature.py
@@ -9,7 +9,7 @@
 
 from .logging import error
 from . import MinHash
-from .minhash import to_bytes
+from .minhash import to_bytes, FrozenMinHash
 from ._lowlevel import ffi, lib
 from .utils import RustObject, rustcall, decode_str
 
@@ -42,7 +42,7 @@ def __init__(self, minhash, name="", filename=""):
 
     @property
     def minhash(self):
-        return MinHash._from_objptr(
+        return FrozenMinHash._from_objptr(
             self._methodcall(lib.signature_first_mh)
         )
 

diff --git a/tests/test_index.py b/tests/test_index.py
@@ -1326,6 +1326,7 @@ def is_found(ss, xx):
 
 def _consume_all(query_mh, counter, threshold_bp=0):
     results = []
+    query_mh = query_mh.to_mutable()
 
     last_intersect_size = None
     while 1:
@@ -1891,7 +1892,7 @@ def test_counter_gather_3_test_consume():
 
     ## round 1
 
-    cur_query = copy.copy(query_ss.minhash)
+    cur_query = query_ss.minhash.to_mutable()
     (sr, intersect_mh) = counter.peek(cur_query)
     assert sr.signature == match_ss_1
     assert len(intersect_mh) == 10

diff --git a/tests/test__minhash.py → tests/test_minhash.py b/tests/test__minhash.py → tests/test_minhash.py
@@ -42,6 +42,7 @@
 import sourmash
 from sourmash.minhash import (
     MinHash,
+    FrozenMinHash,
     hash_murmur,
     _get_scaled_for_max_hash,
     _get_max_hash_for_scaled,
@@ -1908,3 +1909,39 @@ def test_max_containment_equal():
     assert mh2.contained_by(mh1) == 1
     assert mh1.max_containment(mh2) == 1
     assert mh2.max_containment(mh1) == 1
+
+
+def test_frozen_and_mutable_1(track_abundance):
+    # mutable minhashes -> mutable minhashes creates new copy
+    mh1 = MinHash(0, 21, scaled=1, track_abundance=track_abundance)
+    mh2 = mh1.to_mutable()
+
+    mh1.add_hash(10)
+    assert 10 not in mh2.hashes
+
+
+def test_frozen_and_mutable_2(track_abundance):
+    # check that mutable -> frozen are separate
+    mh1 = MinHash(0, 21, scaled=1, track_abundance=track_abundance)
+    mh1.add_hash(10)
+
+    mh2 = mh1.to_frozen()
+    assert 10 in mh2.hashes
+    mh1.add_hash(11)
+    assert 11 not in mh2.hashes
+
+
+def test_frozen_and_mutable_3(track_abundance):
+    # check that mutable -> frozen -> mutable are all separate from each other
+    mh1 = MinHash(0, 21, scaled=1, track_abundance=track_abundance)
+    mh1.add_hash(10)
+
+    mh2 = mh1.to_frozen()
+    assert 10 in mh2.hashes
+    mh1.add_hash(11)
+    assert 11 not in mh2.hashes
+
+    mh3 = mh2.to_mutable()
+    mh3.add_hash(12)
+    assert 12 not in mh2.hashes
+    assert 12 not in mh1.hashes
diff --git a/tests/test_prefetch.py b/tests/test_prefetch.py
@@ -295,7 +295,7 @@ def test_prefetch_nomatch_hashes(runtmp, linear_gather):
     ss47 = sourmash.load_one_signature(sig47, ksize=31)
     ss63 = sourmash.load_one_signature(sig63, ksize=31)
 
-    remain = ss47.minhash
+    remain = ss47.minhash.to_mutable()
     remain.remove_many(ss63.minhash.hashes)
 
     ss = sourmash.load_one_signature(nomatch_out)

diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py
@@ -3111,7 +3111,7 @@ def test_gather_f_match_orig(runtmp, linear_gather, prefetch_gather):
     print(runtmp.last_result.err)
 
     combined_sig = sourmash.load_one_signature(testdata_combined, ksize=21)
-    remaining_mh = copy.copy(combined_sig.minhash)
+    remaining_mh = combined_sig.minhash.to_mutable()
 
     def approx_equal(a, b, n=5):
         return round(a, n) == round(b, n)