[MRG] Better molecule type checks

sourmash/_minhash.pyx

@@ -502,17 +502,11 @@ cdef class MinHash(object):
     def is_molecule_type(self, molecule):
         if molecule.upper() == 'DNA' and not self.is_protein:
             return True
-        if self.is_protein:
-            if self.dayhoff:
-                if molecule == 'dayhoff':
-                    return True
-            else:
-                if molecule == 'protein':
-                    return True
-            if self.hp:
-                if molecule == 'hp':
-                    return True
-                else:
-                    if molecule == 'protein':
-                        return True
+        elif self.is_protein and molecule == 'protein' and not any((self.dayhoff, self.hp)):
+            return True
+        elif self.dayhoff and molecule == 'dayhoff':
+            return True
+        elif self.hp and molecule == 'hp':
+            return True
+
         return False

sourmash/signature.py

@@ -228,6 +228,11 @@ def load_signatures(data, ksize=None, select_moltype=None,
             if not ksize or ksize == sig.minhash.ksize:
                 if not select_moltype or \
                      sig.minhash.is_molecule_type(select_moltype):
+                    if select_moltype == 'protein':
+                        if any(sig.minhash.is_molecule_type(t) for t in ('dayhoff', 'hp')):
+                            # dayhoff and hp are also protein MHs. only yield
+                            # sig if it is exactly one of (protein, hp, dayhoff)
+                            continue
                     yield sig
     except Exception as e:
         if not quiet:

sourmash/sourmash_args.py

@@ -116,12 +116,12 @@ def add_ksize_arg(parser, default):
 def get_moltype(sig, require=False):
     if sig.minhash.is_molecule_type('DNA'):
         moltype = 'DNA'
-    elif sig.minhash.is_molecule_type('protein'):
-        moltype = 'protein'
     elif sig.minhash.is_molecule_type('dayhoff'):
         moltype = 'dayhoff'
     elif sig.minhash.is_molecule_type('hp'):
         moltype = 'hp'
+    elif sig.minhash.is_molecule_type('protein'):
+        moltype = 'protein'
     else:
         raise ValueError('unknown molecule type for sig {}'.format(sig.name()))
 
@@ -136,14 +136,14 @@ def calculate_moltype(args, default=None):
         args.dna = False
 
     moltype = default
-    if args.protein:
-        moltype = 'protein'
-    elif args.dna:
+    if args.dna:
         moltype = 'DNA'
     elif args.dayhoff:
         moltype = 'dayhoff'
     elif args.hp:
         moltype = 'hp'
+    elif args.protein:
+        moltype = 'protein'
 
     return moltype
 

tests/test-data/protein_781.sig

@@ -0,0 +1 @@
+[{"class":"sourmash_signature","email":"","filename":"smash-testing/gingivalis/protein/GCA_000007585.1_ASM758v1_protein.faa.gz","hash_function":"0.murmur64","license":"CC0","signatures":[{"ksize":7,"max_hash":9223372036854776,"md5sum":"8f14e45fceea167a5a36dedd4bea2543","mins":[],"molecule":"protein","num":0,"seed":42},{"ksize":7,"max_hash":9223372036854776,"md5sum":"8f14e45fceea167a5a36dedd4bea2543","mins":[],"molecule":"dayhoff","num":0,"seed":42},{"ksize":7,"max_hash":9223372036854776,"md5sum":"8f14e45fceea167a5a36dedd4bea2543","mins":[],"molecule":"hp","num":0,"seed":42},{"ksize":11,"max_hash":9223372036854776,"md5sum":"eddce6d9ac96be04ed806aadf53665d1","mins":[935333424279453,2538868037911012,7421288836408751,7960286979232677,8654912015719540],"molecule":"protein","num":0,"seed":42},{"ksize":11,"max_hash":9223372036854776,"md5sum":"6512bd43d9caa6e02c990b0a82652dca","mins":[],"molecule":"dayhoff","num":0,"seed":42},{"ksize":11,"max_hash":9223372036854776,"md5sum":"6512bd43d9caa6e02c990b0a82652dca","mins":[],"molecule":"hp","num":0,"seed":42},{"ksize":17,"max_hash":9223372036854776,"md5sum":"4e7f2da275e0d3cd3488a7429f23c0e7","mins":[80545341491115,95893197637407,115032912017982,167876181889216,186411802953277,222466650340651,224967183012543,258505356847424,309875701424311,355213055946019,386676749766432,412910340994277,462537020181146,494965971291721,559141879168033,561484232050194,644615490355418,658172460965864,720535257532265,738352407205548,745810431880043,759181896175271,850588167607652,887659205846183,894164001336358,905078595321889,970165616477383,1017856994095351,1028412790624984,1050795138079130,1139932302760059,1186388344819559,1192818915503467,1198212766664640,1216892715424691,1219438185071604,1237070334261946,1387123735448234,1434001421971507,1485329804804021,1506460396271450,1557881761202533,1621319275541247,1652996636263092,1759458369106525,1775445012461498,1778569708504615,1790264270235488,1814476471419496,1836560547212168,1860873491028851,1896569881953525,1897420327685705,1923345118834304,1936637912433824,1937255081379236,1947138500658091,1975618333674647,2144882621679500,2149108682537798,2161921385516085,2246818310352884,2290340663993180,2304543670495485,2364205861776990,2412514993466726,2452585910741483,2509528096806449,2539884144415183,2541107353815135,2572053948720929,2622479875739911,2647527190109029,2713096700045735,2761919595787895,2867643251943479,2925231867832341,3025758098634438,3033763278178401,3058704182312610,3115261468695424,3166876962072314,3233211247123021,3235567354197305,3243245537683617,3259305016866742,3337410579699057,3418776874767941,3423000771650184,3507216917735704,3595029584959389,3634370995551791,3768235701772236,3775046865943208,3817698542949254,3828452511096857,3833691931514236,4038649211585583,4067919805126295,4097280795487840,4221222492196035,4343951716797518,4367658693942699,4450087885545040,4509903538197388,4513107976808259,4527368785345773,4562209560900537,4639168970839038,4668382471614239,4669352267366042,4679521416287799,4686839507440048,4709562456621538,4724594069568581,4736749713837036,4738083948924482,4759958931942220,4789425451192135,4800497165006063,4820147941509539,4850297769952409,4850600607797904,4868447772682418,4905552855041575,4971930424454368,4985072012605862,4995739741362592,5001422416309153,5009161631707149,5030854929253622,5035217786452507,5065729136452008,5077023046760465,5082191099848633,5176553408615803,5187575110109033,5315950415531956,5380346145125625,5432557230189792,5443962862203433,5504634862131301,5523415209316411,5539462263412859,5578575768148920,5594872593367517,5602170740228452,5627969550666066,5645214919396423,5715244891476417,5716776196844718,5756975294595510,5791158195561112,5804298783161609,5859298762196680,5941703205411035,5984207756172447,6006605546729755,6040624656956813,6079431920736680,6120850189740657,6143463234120488,6403824852243549,6434823327466671,6452924095770729,6486607607852558,6493745783442873,6609514638731456,6621397331436691,6639512072137206,6651392661523258,6663467668433959,6746635771795261,6774460282204914,6798792706747163,6818258524917823,6853148606664897,6862857851511771,6863419022655845,6884221467246173,6960794347010868,6971091824735669,6996177331699958,7020119488788226,7041050337195108,7093433891425227,7105809197035780,7123502524719655,7152363307939419,7180066834856704,7230192109807876,7268204104636229,7369432586890070,7369545607316536,7452432790013634,7475586378544421,7518091663474830,7555974865996135,7567184934833446,7598164152364795,7691459572863761,7709831060098954,7733841383672718,7823392534007031,7863676561152009,7870327771274750,7886730508543846,7920363556752832,7939090045786917,7956077051018542,8006111745484961,8014778875958321,8022584532939757,8066519196340294,8068684551622667,8139161380118085,8156857187140640,8161593522327026,8243833392562765,8267006323898637,8308586921720912,8354821843549256,8375847106291424,8417181145027020,8463616731079599,8649752374463547,8676699653973820,8678492387990270,8746431528629889,8764389844740277,8806802453026237,8846826235070247,8937418166974287,8969593290271317,8982504059107137,9012010336229099,9027180495854695,9045704090610147,9104390213566336,9118607030191614,9198853303101481],"molecule":"protein","num":0,"seed":42},{"ksize":17,"max_hash":9223372036854776,"md5sum":"61b7ea9355dd355ea5d6670c919a45cf","mins":[1816309557216154,3456445761862780,7650346105396480],"molecule":"dayhoff","num":0,"seed":42},{"ksize":17,"max_hash":9223372036854776,"md5sum":"70efdf2ec9b086079795c442636b55fb","mins":[],"molecule":"hp","num":0,"seed":42}],"version":0.4}]

tests/test_bugs.py

@@ -0,0 +1,16 @@
+from __future__ import print_function, unicode_literals
+from . import sourmash_tst_utils as utils
+
+def test_bug_781():
+    with utils.TempDirectory() as location:
+        testdata1 = utils.get_test_data('protein_781.sig')
+
+        status, out, err = utils.runscript('sourmash',
+                                           ['compare',
+                                            '--protein', '--no-dna', '--no-dayhoff',
+                                            '--no-hp',  '-k', '11', '-o', 'testing',
+                                            testdata1],
+                                           in_directory=location)
+        print(out)
+        print(err)
+        assert status == 0

tests/test_sourmash_compute.py

@@ -493,7 +493,7 @@ def test_do_sourmash_compute_multik_with_dayhoff_hp_dna_protein():
             assert sum(x.minhash.is_molecule_type('dayhoff') for x in siglist) == 2
             assert sum(x.minhash.is_molecule_type('hp') for x in siglist) == 2
             # 2 = dayhoff, 2 = hp = 4 protein
-            assert sum(x.minhash.is_molecule_type('protein') for x in siglist) == 4
+            assert sum(x.minhash.is_molecule_type('protein') for x in siglist) == 2
 
 
 def test_do_sourmash_compute_multik_with_nothing():