Refactor and update dependencies in snap module

snap/deciphon_snap/amino.py

@@ -4,8 +4,7 @@
 __all__ = ["AminoInterval", "make_amino_interval"]
 
 
-class AminoInterval(PyInterval):
-    ...
+class AminoInterval(PyInterval): ...
 
 
 def make_amino_interval(x: DomTBLCoord):

snap/deciphon_snap/fasta.py

@@ -21,12 +21,10 @@ def __len__(self):
         return len(self.root)
 
     @overload
-    def __getitem__(self, i: int) -> FASTAItem:
-        ...
+    def __getitem__(self, i: int) -> FASTAItem: ...
 
     @overload
-    def __getitem__(self, i: slice) -> FASTAList:
-        ...
+    def __getitem__(self, i: slice) -> FASTAList: ...
 
     def __getitem__(self, i: int | slice):
         if isinstance(i, slice):

snap/deciphon_snap/gff.py

@@ -4,7 +4,6 @@
 
 from pydantic import BaseModel, RootModel
 
-
 __all__ = ["GFFItem", "GFFList"]
 
 
@@ -34,12 +33,10 @@ def __len__(self):
         return len(self.root)
 
     @overload
-    def __getitem__(self, i: int) -> GFFItem:
-        ...
+    def __getitem__(self, i: int) -> GFFItem: ...
 
     @overload
-    def __getitem__(self, i: slice) -> GFFList:
-        ...
+    def __getitem__(self, i: slice) -> GFFList: ...
 
     def __getitem__(self, i: int | slice):
         if isinstance(i, slice):

snap/deciphon_snap/hit.py

@@ -39,7 +39,7 @@ def matches(self):
         assert self._interval is not None
         assert self._match_list is not None
         matches: list[Match] = []
-        offset = self._interval.pyinterval.start
+        offset = self._interval.py.start
         for x in self._match_list[self.match_list_interval.slice]:
             y = Match(raw=x.raw, start=x.start, end=x.end, position=offset)
             if y.is_match_state or y.is_insert_state:
@@ -58,12 +58,10 @@ def __len__(self):
         return len(self.root)
 
     @overload
-    def __getitem__(self, i: int) -> Hit:
-        ...
+    def __getitem__(self, i: int) -> Hit: ...
 
     @overload
-    def __getitem__(self, i: slice) -> HitList:
-        ...
+    def __getitem__(self, i: slice) -> HitList: ...
 
     def __getitem__(self, i: int | slice):
         if isinstance(i, slice):

snap/deciphon_snap/hmmer.py

@@ -1,11 +1,12 @@
 from __future__ import annotations
 
 import os
+from io import StringIO
 from tempfile import NamedTemporaryFile
 
 from h3result.h3result import H3Result as H3ResultRaw
-from hmmer_tables.domtbl import read_domtbl, DomTBL
-from hmmer_tables.tbl import read_tbl, TBL
+from hmmer_tables.domtbl import DomTBL, read_domtbl
+from hmmer_tables.tbl import TBL, read_tbl
 from pydantic import BaseModel, ConfigDict
 
 __all__ = ["H3Result"]
@@ -45,11 +46,11 @@ def domains_table(self) -> str:
 
     @property
     def tbl(self) -> TBL:
-        return read_tbl(stream=self.targets_table.split("\n"))
+        return read_tbl(stream=StringIO(self.targets_table))
 
     @property
     def domtbl(self) -> DomTBL:
-        return read_domtbl(stream=self.domains_table.split("\n"))
+        return read_domtbl(stream=StringIO(self.domains_table))
 
     def __str__(self):
         items = []

snap/deciphon_snap/match.py

@@ -105,12 +105,10 @@ def __len__(self):
         return len(self.root)
 
     @overload
-    def __getitem__(self, i: int) -> Match:
-        ...
+    def __getitem__(self, i: int) -> Match: ...
 
     @overload
-    def __getitem__(self, i: slice) -> MatchList:
-        ...
+    def __getitem__(self, i: slice) -> MatchList: ...
 
     def __getitem__(self, i: int | slice):
         if isinstance(i, slice):
@@ -142,8 +140,7 @@ def amino(self):
         return "".join(x.amino for x in iter(self))
 
 
-class MatchListInterval(PyInterval):
-    ...
+class MatchListInterval(PyInterval): ...
 
 
 class MatchListIntervalBuilder:

snap/deciphon_snap/prod.py

@@ -94,12 +94,10 @@ def __len__(self):
         return len(self.root)
 
     @overload
-    def __getitem__(self, i: int) -> Prod:
-        ...
+    def __getitem__(self, i: int) -> Prod: ...
 
     @overload
-    def __getitem__(self, i: slice) -> ProdList:
-        ...
+    def __getitem__(self, i: slice) -> ProdList: ...
 
     def __getitem__(self, i: int | slice):
         if isinstance(i, slice):

snap/deciphon_snap/query_interval.py

@@ -5,8 +5,7 @@
 __all__ = ["QueryInterval", "QueryIntervalBuilder"]
 
 
-class QueryInterval(PyInterval):
-    ...
+class QueryInterval(PyInterval): ...
 
 
 class QueryIntervalBuilder:

snap/deciphon_snap/snap_file.py

@@ -38,7 +38,9 @@ def __init__(self, filesystem):
                 window = int(row["window"])
                 hit = int(row["hit"])
                 profile = str(row["profile"])
-                with fs.open(f"{hmmer_dir}/{seq_id}/{window}/{hit}/{profile}.h3r", "rb") as f2:
+                with fs.open(
+                    f"{hmmer_dir}/{seq_id}/{window}/{hit}/{profile}.h3r", "rb"
+                ) as f2:
                     h3r = H3Result(raw=read_h3result(fileno=f2.fileno()))
                 window_start = int(row["window_start"])
                 window_stop = int(row["window_stop"])

snap/deciphon_snap/view.py

@@ -1,10 +1,11 @@
 from functools import partial
+from io import StringIO
 from itertools import accumulate, chain
 from typing import Optional
 
-import tabulate
 from hmmer_tables.query import DomAnnot, read_query
 from pydantic import BaseModel
+from tabulate import simple_separated_format, tabulate
 
 from deciphon_snap.match import Match, MatchList
 from deciphon_snap.prod import H3Result, Prod
@@ -37,7 +38,7 @@ def make_deciphon_steps(match_list: MatchList):
 
 
 def make_hmmer_annot(h3result: H3Result):
-    hmmer_query = read_query(stream=h3result.domains.splitlines())
+    hmmer_query = read_query(stream=StringIO(h3result.domains))
     assert len(hmmer_query.domains) == 1
     return hmmer_query.domains[0]
 
@@ -196,11 +197,9 @@ def grab_query(x, i):
             [None, None, "".join(score[sl]) + pad, "PP"],
         ]
         table += row + [[None, None, None, None]]
-    tablefmt = tabulate.simple_separated_format(" ")
-    txt += str(
-        tabulate.tabulate(
-            table, tablefmt=tablefmt, colalign=("right", "right", "left", "left")
-        )
+    tablefmt = simple_separated_format(" ")
+    txt += tabulate(
+        table, tablefmt=tablefmt, colalign=("right", "right", "left", "left")
     )
     txt = txt.replace("&", "") + "\n"
     return txt

snap/pyproject.toml

@@ -1,25 +1,25 @@
 [tool.poetry]
 name = "deciphon-snap"
-version = "0.11.2"
+version = "0.11.3"
 description = "Reader for Deciphon snap files."
 authors = ["Danilo Horta <[email protected]>"]
 license = "MIT"
 readme = "README.md"
 packages = [{ include = "deciphon_snap" }]
 
 [tool.poetry.dependencies]
-fsspec = { version = ">=2024.2.0" }
 python = "^3.9"
-h3result = ">=0.3.1"
-tabulate = "^0"
-fasta-reader = "^3.0.2"
-deciphon-intervals = "^0.1.1"
-prettytable = "^3.9.0"
-pydantic = "^2.6.1"
-hmmer-tables = "^0.6.0"
+fsspec = ">=2024.5.0"
+h3result = "^0.3"
+tabulate = "^0.9"
+fasta-reader = "^3.0"
+deciphon-intervals = "^0.1"
+prettytable = "^3.10"
+pydantic = "^2.7"
+hmmer-tables = "^0.6"
 
 [tool.poetry.group.dev.dependencies]
-pytest = ">=7.3.2"
+pytest = "^8.2"
 
 [build-system]
 requires = ["poetry-core"]