Merge pull request #148 from mobiusklein/feature/proforma_mod_cache

Add modification caching; Constant terminal mods for ProForma

pyteomics/proforma.py

@@ -271,6 +271,29 @@ def __init__(self, name, **kwargs):
         self.name = name.lower()
         self.symbol = self.name[0]
         self._database = None
+        self._cache = {}
+
+    def clear_cache(self):
+        """Clear the modification definition cache"""
+        self._cache.clear()
+
+    def enable_caching(self, flag=True):
+        """
+        Enable or disable caching of modification definitions.
+
+        If `flag` is :const:`False`, this will also dispose of any
+        existing cached values.
+
+        Parameters
+        ----------
+        flag : :class:`bool`
+            Whether or not to disable the cache
+        """
+        if flag:
+            if not self._cache:
+                self._cache = {}
+        else:
+            self._cache = None
 
     def load_database(self):
         raise NotImplementedError()
@@ -316,9 +339,19 @@ def parse_identifier(self, identifier):
             id = None
         return name, id
 
-    def resolve(self, name=None, id=None, **kwargs):
+    def _resolve_impl(self, name=None, id=None, **kwargs):
         raise NotImplementedError()
 
+    def resolve(self, name=None, id=None, **kwargs):
+        if self._cache is None:
+            return self._resolve_impl(name, id, **kwargs)
+        cache_key = (name, id, frozenset(kwargs.items()))
+        if cache_key in self._cache:
+            return self._cache[cache_key].copy()
+        value = self._resolve_impl(name, id, **kwargs)
+        self._cache[cache_key] = value
+        return  value.copy()
+
     def __call__(self, name=None, id=None, **kwargs):
         return self.resolve(name, id, **kwargs)
 
@@ -343,7 +376,7 @@ def load_database(self):
             return obo_cache.resolve("http://www.unimod.org/obo/unimod.obo")
         return Unimod()
 
-    def resolve(self, name=None, id=None, **kwargs):
+    def _resolve_impl(self, name=None, id=None, **kwargs):
         strict = kwargs.get("strict", self.strict)
         exhaustive = kwargs.get("exhaustive", True)
         if name is not None:
@@ -398,7 +431,7 @@ def __init__(self, **kwargs):
     def load_database(self):
         return load_psimod()
 
-    def resolve(self, name=None, id=None, **kwargs):
+    def _resolve_impl(self, name=None, id=None, **kwargs):
         if name is not None:
             defn = self.database[name]
         elif id is not None:
@@ -443,7 +476,7 @@ def __init__(self, **kwargs):
     def load_database(self):
         return load_xlmod()
 
-    def resolve(self, name=None, id=None, **kwargs):
+    def _resolve_impl(self, name=None, id=None, **kwargs):
         if name is not None:
             defn = self.database[name]
         elif id is not None:
@@ -562,7 +595,7 @@ def get_mass_from_term(self, term, raw_mass):
              "Only a rough approximation is available.") % (term, ))
         return rough_mass
 
-    def resolve(self, name=None, id=None, **kwargs):
+    def _resolve_impl(self, name=None, id=None, **kwargs):
         if name is not None:
             term = self.database[name]
         elif id is not None:
@@ -613,7 +646,7 @@ def parse_identifier(self, identifier):
         """
         return identifier, None
 
-    def resolve(self, name=None, id=None, **kwargs):
+    def _resolve_impl(self, name=None, id=None, **kwargs):
         defn = None
         for resolver in self.resolvers:
             try:
@@ -1251,6 +1284,56 @@ def process_tag_tokens(tokens):
     return main_tag
 
 
+class ModificationTarget(object):
+    def __init__(self, aa, n_term=False, c_term=False):
+        self.aa = aa
+        self.n_term = n_term
+        self.c_term = c_term
+
+    def __eq__(self, other):
+        if isinstance(other, str):
+            return str(self) == other
+        else:
+            return (
+                self.aa == other.aa
+                and self.n_term == other.n_term
+                and self.c_term == other.c_term
+            )
+
+    def __ne__(self, other):
+        if isinstance(other, str):
+            return str(self) != other
+        else:
+            return (
+                self.aa != other.aa
+                or self.n_term != other.n_term
+                or self.c_term != other.c_term
+            )
+
+    def __hash__(self):
+        return hash(str(self))
+
+    def __str__(self):
+        buffer = []
+        if self.n_term:
+            buffer.append('N-term')
+        if self.c_term:
+            buffer.append('C-term')
+        if self.aa:
+            buffer.append(self.aa)
+        return ':'.join(buffer)
+
+    def __repr__(self):
+        return str(self)
+
+    def is_valid(self, aa, n_term, c_term):
+        if (n_term and self.n_term) or (c_term and self.c_term):
+            if (self.aa and aa == self.aa) or self.aa is None:
+                return True
+            return False
+        return self.aa == aa or self.aa is None
+
+
 class ModificationRule(object):
     '''Define a fixed modification rule which dictates a modification tag is
     always applied at one or more amino acid residues.
@@ -1267,6 +1350,53 @@ class ModificationRule(object):
     def __init__(self, modification_tag, targets=None):
         self.modification_tag = modification_tag
         self.targets = targets
+        self._validate_targets()
+
+    def is_valid(self, aa, n_term, c_term):
+        return any(target.is_valid(aa, n_term, c_term) for target in self.targets)
+
+    def _validate_targets(self):
+        validated_targets = []
+        if self.targets is None:
+            self.targets = []
+        elif not isinstance(self.targets, list):
+            self.targets = [self.targets]
+        for target in self.targets:
+            if target in VALID_AA:
+                validated_targets.append(ModificationTarget(target, False, False))
+            elif target in ("N-term", "C-term"):
+                n_term = target == "N-term"
+                c_term = target == "C-term"
+                validated_targets.append(ModificationTarget(None, n_term, c_term))
+            elif target.startswith(("N-term:", "C-term:")):
+                tokens = target.split(":")
+                if len(tokens) == 2:
+                    if tokens[1] in VALID_AA:
+                        n_term = tokens[0] == "N-term"
+                        c_term = tokens[0] == "C-term"
+                        validated_targets.append(ModificationTarget(tokens[1], n_term, c_term))
+                    else:
+                        raise PyteomicsError(
+                            "Modification rule {0} has an invalid amino acid specific terminal target {2} in {1}".format(
+                                self,
+                                target,
+                                tokens[1]
+                            )
+                        )
+                else:
+                    raise PyteomicsError(
+                        "Modification rule {0} has an empty amino acid specific terminal target {1}".format(
+                            self, target
+                        )
+                    )
+            else:
+                raise PyteomicsError(
+                    "Modification rule {0} has an invalid target {1}".format(
+                        self, target
+                    )
+                )
+
+        self.targets = validated_targets
 
     def __eq__(self, other):
         if other is None:
@@ -1277,7 +1407,7 @@ def __ne__(self, other):
         return not self == other
 
     def __str__(self):
-        targets = ','.join(self.targets)
+        targets = ','.join(map(str, self.targets))
         return "<[{self.modification_tag}]@{targets}>".format(self=self, targets=targets)
 
     def __repr__(self):
@@ -1609,6 +1739,7 @@ class ParserStateEnum(Enum):
     inter_chain_cross_link_start = 20
     chimeric_start = 21
     interval_initial = 22
+    post_global_terminal = 23
     done = 999
 
 
@@ -1628,6 +1759,7 @@ class ParserStateEnum(Enum):
 UNLOCALIZED_COUNT = ParserStateEnum.unlocalized_count
 POST_GLOBAL = ParserStateEnum.post_global
 POST_GLOBAL_AA = ParserStateEnum.post_global_aa
+POST_GLOBAL_TERM = ParserStateEnum.post_global_terminal
 POST_INTERVAL_TAG = ParserStateEnum.post_interval_tag
 CHARGE_START = ParserStateEnum.charge_state_start
 CHARGE_NUMBER = ParserStateEnum.charge_state_number
@@ -1636,6 +1768,7 @@ class ParserStateEnum(Enum):
 DONE = ParserStateEnum.done
 
 VALID_AA = set("QWERTYIPASDFGHKLCVNMXUOJZB")
+TERMINAL_SPEC_CHARS = set('N-term') | set('C-term') | set("ncT: ")
 
 def parse(sequence):
     '''Tokenize a ProForma sequence into a sequence of amino acid+tag positions, and a
@@ -1678,7 +1811,7 @@ def parse(sequence):
     current_tag = TagParser()
     current_interval = None
     current_unlocalized_count = NumberParser()
-    current_aa_targets = TokenBuffer()
+    current_aa_targets = StringParser()
 
     charge_buffer = None
     adduct_buffer = None
@@ -1868,13 +2001,13 @@ def parse(sequence):
                 depth = 1
                 tag = current_tag()[0]
                 multiplicity = current_unlocalized_count()
-                for i in range(multiplicity):
+                for _ in range(multiplicity):
                     unlocalized_modifications.append(tag)
             elif c == '?':
                 state = BEFORE
                 tag = current_tag()[0]
                 multiplicity = current_unlocalized_count()
-                for i in range(multiplicity):
+                for _ in range(multiplicity):
                     unlocalized_modifications.append(tag)
             else:
                 raise ProFormaError(
@@ -1887,14 +2020,25 @@ def parse(sequence):
                     ("Error In State {state}, fixed modification detected without "
                      "target amino acids found at index {i}").format(**locals()), i, state)
         elif state == POST_GLOBAL_AA:
-            if c in VALID_AA:
+            if c in VALID_AA or c in TERMINAL_SPEC_CHARS:
                 current_aa_targets.append(c)
             elif c == ',':
                 # the next character should be another amino acid
-                pass
+                current_aa_targets.bound()
             elif c == '>':
-                fixed_modifications.append(
-                    ModificationRule(current_tag()[0], current_aa_targets()))
+                try:
+                    v = current_aa_targets()
+                    fixed_modifications.append(
+                        ModificationRule(current_tag()[0], v))
+                except PyteomicsError as err:
+                    raise ProFormaError(
+                        (
+                            "Error In State {state}, fixed modification detected invalid "
+                            "target found at index {i}: {err}"
+                        ).format(state=state, i=i, err=err),
+                        i,
+                        state,
+                    )
                 state = BEFORE
             else:
                 raise ProFormaError(
@@ -2164,19 +2308,20 @@ def mass(self):
         mass = 0.0
 
         fixed_modifications = self.properties['fixed_modifications']
-        fixed_rules = {}
-        for rule in fixed_modifications:
-            for aa in rule.targets:
-                fixed_rules[aa] = rule.modification_tag.mass
 
-        for position in self.sequence:
+        n_term_v = 0
+        c_term_v = len(self) - 1
+        for i, position in enumerate(self.sequence):
             aa = position[0]
             try:
                 mass += std_aa_mass[aa]
             except KeyError:
                 warnings.warn("%r does not have an exact mass" % (aa, ))
-            if aa in fixed_rules:
-                mass += fixed_rules[aa]
+            n_term = i == n_term_v
+            c_term = i == c_term_v
+            for rule in fixed_modifications:
+                if rule.is_valid(aa, n_term, c_term):
+                    mass += rule.modification_tag.mass
             tags = position[1]
             if tags:
                 for tag in tags:
@@ -2261,10 +2406,6 @@ def fragments(self, ion_shift, charge=1, reverse=None, include_labile=True, incl
         mass += ion_shift
 
         fixed_modifications = self.properties['fixed_modifications']
-        fixed_rules = {}
-        for rule in fixed_modifications:
-            for aa in rule.targets:
-                fixed_rules[aa] = rule.modification_tag.mass
 
         intervals = self.intervals
         if intervals:
@@ -2298,8 +2439,12 @@ def fragments(self, ion_shift, charge=1, reverse=None, include_labile=True, incl
 
         if not reverse:
             iterator = (iter(range(0, n - 1)))
+            n_term_v = 0
+            c_term_v = n - 1
         else:
             iterator = (reversed(range(1, n)))
+            n_term_v = n - 1
+            c_term_v = 0
 
         for i in iterator:
             position = self.sequence[i]
@@ -2310,8 +2455,11 @@ def fragments(self, ion_shift, charge=1, reverse=None, include_labile=True, incl
             except KeyError:
                 warnings.warn("%r does not have an exact mass" % (aa, ))
 
-            if aa in fixed_rules:
-                mass += fixed_rules[aa]
+            n_term = i == n_term_v
+            c_term = i == c_term_v
+            for rule in fixed_modifications:
+                if rule.is_valid(aa, n_term, c_term):
+                    mass += rule.modification_tag.mass
 
             tags = position[1]
             if tags: