Repository: cogent3/cogent3
Pull request #1319 (2023-03-14 22:51:25)

DEP: remove usages of deprecated Sequence.translate


Patch:
diff --git a/src/cogent3/core/moltype.py b/src/cogent3/core/moltype.py
index 975887151..99328fc46 100644
--- a/src/cogent3/core/moltype.py
+++ b/src/cogent3/core/moltype.py
@@ -887,16 +887,16 @@ class MolType(object):
         Always tries to return same type as item: if item looks like a dict,
         will return list of keys.
         """
+        if isinstance(item, (list, tuple)):
+            data = "".join(item)
+        else:
+            data = str(item)
+
         if not self.complements:
             raise TypeError(
                 "Tried to complement sequence using alphabet without complements."
             )
-        try:
-            return item.translate(self.ComplementTable)
-        except (AttributeError, TypeError):
-            item = iterable(item)
-            get = self.complements.get
-            return item.__class__([get(i, i) for i in item])
+        return item.__class__(data.translate(self.ComplementTable))
 
     def rc(self, item):
         """Returns reverse complement of item w/ data from self.complements.
@@ -1044,16 +1044,13 @@ class MolType(object):
 
     def degap(self, sequence):
         """Deletes all gap characters from sequence."""
-        try:
-            trans = dict([(i, None) for i in map(ord, self.gaps)])
-            return sequence.__class__(sequence.translate(trans))
-        except AttributeError:
-            gap = self.gaps
-
-            def not_gap(x):
-                return x not in gap
+        if isinstance(sequence, (tuple, list)):
+            data = "".join(sequence)
+        else:
+            data = str(sequence)
 
-            return sequence.__class__(list(filter(not_gap, sequence)))
+        trans = dict([(i, None) for i in map(ord, self.gaps)])
+        return sequence.__class__(data.translate(trans))
 
     def gap_indices(self, sequence):
         """Returns list of indices of all gaps in the sequence, or []."""
diff --git a/src/cogent3/parse/gff.py b/src/cogent3/parse/gff.py
index d1ad463c9..4a7ef79a1 100644
--- a/src/cogent3/parse/gff.py
+++ b/src/cogent3/parse/gff.py
@@ -1,4 +1,8 @@
-#!/usr/bin/env python
+import collections.abc as abc
+import functools
+import os
+import typing
+
 from pathlib import Path
 
 from cogent3.util.io import open_
@@ -19,29 +23,42 @@ __email__ = "pm67nz@gmail.com"
 __status__ = "Production"
 
 
-def gff_parser(f):
+@functools.singledispatch
+def gff_parser(
+    f: typing.Union[str, os.PathLike, abc.Sequence, typing.IO], attribute_parser=None
+) -> typing.Iterable[dict]:
     """parses a gff file
+
     Parameters
     -----------
     f
         accepts string path or pathlib.Path or file-like object (e.g. StringIO)
+    attribute_parser
+        callback function for custom handling of attributes field. Defaults to
+        a function that converts Attributes field into a dict based on the gff
+        version.
 
     Returns
     -------
     dict
         contains each of the 9 parameters specified by gff3, and comments.
     """
+    yield from _gff_parser(f, attribute_parser=attribute_parser)
 
-    # calling a separate function to ensure file closes correctly
-    f = f if not isinstance(f, Path) else str(f)
-    if isinstance(f, str):
-        with open_(f) as infile:
-            yield from _gff_parser(infile)
-    else:
-        yield from _gff_parser(f)
+
+@gff_parser.register
+def _(f: str, attribute_parser=None) -> typing.Iterable[dict]:
+    with open_(f) as infile:
+        yield from _gff_parser(infile, attribute_parser=attribute_parser)
 
 
-def _gff_parser(f):
+@gff_parser.register
+def _(f: os.PathLike, attribute_parser=None) -> typing.Iterable[dict]:
+    with open_(f) as infile:
+        yield from _gff_parser(infile, attribute_parser=attribute_parser)
+
+
+def _gff_parser(f, attribute_parser=None):
     """parses a gff file"""
 
     gff3_header = "gff-version 3"
@@ -51,10 +68,8 @@ def _gff_parser(f):
         gff3 = gff3_header in f.readline()
         f.seek(0)
 
-    if gff3:
-        attribute_parser = parse_attributes_gff3
-    else:
-        attribute_parser = parse_attributes_gff2
+    if attribute_parser is None:
+        attribute_parser = parse_attributes_gff3 if gff3 else parse_attributes_gff2
 
     for line in f:
         # comments and blank lines
diff --git a/src/cogent3/parse/rdb.py b/src/cogent3/parse/rdb.py
index 352aaf0df..6b99475dc 100644
--- a/src/cogent3/parse/rdb.py
+++ b/src/cogent3/parse/rdb.py
@@ -119,7 +119,7 @@ def create_acceptable_sequence(sequence):
     trans_table = dict([(ord(c), None) for c in "{}[]()^"])
     trans_table[ord("o")] = ord("?")
     # strip out secondary structure annotation {}[]()^
-    return sequence.translate(trans_table)  # should be accepted by RnaSequence
+    return str(sequence).translate(trans_table)  # should be accepted by RnaSequence
 
 
 def RdbParser(
diff --git a/src/cogent3/parse/sequence.py b/src/cogent3/parse/sequence.py
index e8ae305f5..17779afe5 100644
--- a/src/cogent3/parse/sequence.py
+++ b/src/cogent3/parse/sequence.py
@@ -17,7 +17,7 @@ from cogent3.parse import (
     tinyseq,
 )
 from cogent3.parse.record import FileFormatError
-from cogent3.util.io import open_, get_format_suffixes
+from cogent3.util.io import get_format_suffixes, open_
 
 
 __author__ = "Cath Lawrence"


Test patch:
diff --git a/tests/test_parse/test_gff.py b/tests/test_parse/test_gff.py
index 10398a50f..691e1bf2c 100644
--- a/tests/test_parse/test_gff.py
+++ b/tests/test_parse/test_gff.py
@@ -148,6 +148,12 @@ class GffTest(TestCase):
         # 15 total lines, but 2 comments
         self.assertEqual(i + 1, 15 - 2)
 
+    def test_custom_attr_func(self):
+        """user provided attr parser"""
+        gff3_path = os.path.join("data/c_elegans_WS199_shortened_gff.gff3")
+        for result in gff_parser(gff3_path, attribute_parser=lambda x, y: x):
+            self.assertIsInstance(result["Attributes"], str)
+
 
 if __name__ == "__main__":
     main()