Changed several parsers avoid using next.

tempfile.NamedTemporaryFiles do not support __next__.

Bio/AlignIO/MafIO.py

@@ -140,10 +140,8 @@ def MafIterator(handle, seq_count=None):
 
     while True:
         # allows parsing of the last bundle without duplicating code
-        try:
+        line = handle.readline()
-            line = next(handle)
+
-        except StopIteration:
-            line = ""
         try:
             # Will be in binary mode if called via the indexing code
             # (which needs the raw offsets for cross platform indexing)

Bio/SeqIO/FastaIO.py

@@ -194,9 +194,8 @@ class FastaIterator(SequenceIterator):
         if alphabet is not None:
             raise ValueError("The alphabet argument is no longer supported")
         super().__init__(source, fmt="Fasta")
-        try:
+        line = self.stream.readline()
-            line = next(self.stream)
+        if not line:
-        except StopIteration:
             line = None
         else:
             if not line.startswith(">"):

Bio/SeqIO/PirIO.py

@@ -144,16 +144,22 @@ class PirIterator(SequenceIterator):
         line = self._line
         if line is None:
             raise StopIteration
-        stream = self.stream
+
         pir_type = line[1:3]
         if pir_type not in _pir_mol_type or line[3] != ";":
             raise ValueError(
                 "Records should start with '>XX;' where XX is a valid sequence type"
             )
+
         identifier = line[4:].strip()
-        description = next(stream).strip()
+        description = self.stream.readline()
+        if description == "":
+            raise StopIteration
+        else:
+            description = description.strip()
+
         lines = []
-        for line in stream:
+        for line in self.stream:
             if line[0] == ">":
                 self._line = line
                 break

Bio/SeqIO/QualityIO.py

@@ -933,9 +933,9 @@ def FastqGeneralIterator(source: _TextIOSource) -> Iterator[tuple[str, str, str]
     with as_handle(source) as handle:
         if handle.read(0) != "":
             raise StreamModeError("Fastq files must be opened in text mode") from None
-        try:
+
-            line = next(handle)
+        line = handle.readline()
-        except StopIteration:
+        if line == "":
             return  # Premature end of file, or just empty?
 
         while True:
@@ -1031,15 +1031,11 @@ class FastqIteratorAbstractBaseClass(SequenceIterator[str]):
 
     def __next__(self) -> SeqRecord:
         """Parse the file and generate SeqRecord objects."""
+
         line = self.line
         if line is None:
-            try:
+            line = self.stream.readline()
-                line = next(self.stream)
+        if not line:
-            except StopIteration:  # empty file?
-                self.line = None
-            else:
-                self.line = line
-        if line is None:
             raise StopIteration
         if line[0] != "@":
             raise ValueError("Records in Fastq files should start with '@' character")

CONTRIB.rst

@@ -301,7 +301,7 @@ please open an issue on GitHub or mention it on the mailing list.
 - Sebastian Bassi <https://about.me/bassi>
 - Sergei Lebedev <https://github.com/superbobry>
 - Sergio Valqui <https://github.com/svalqui>
-- Seth Sims <seth.sims at gmail>
+- Seth Sims <https://github.com/xzy3>
 - She Zhang <https://github.com/shz66>
 - Shoichiro Kawauchi <https://github.com/lacrosse91>
 - Shuichiro MAKIGAKI <https://github.com/shuichiro-makigaki>

Tests/test_SeqIO.py

@@ -10,6 +10,8 @@ import unittest
 import warnings
 from io import BytesIO
 from io import StringIO
+from tempfile import NamedTemporaryFile
+from contextlib import ExitStack
 
 from Bio import AlignIO
 from Bio import BiopythonParserWarning
@@ -301,6 +303,7 @@ class TestSeqIO(SeqIOTestBaseClass):
         else:
             debug = False
         unequal_length = len({len(_) for _ in records}) != 1
+
         for fmt in test_write_read_alignment_formats:
             if fmt not in possible_unknown_seq_formats and len(records[0].seq) > 100:
                 try:
@@ -318,12 +321,30 @@ class TestSeqIO(SeqIOTestBaseClass):
             if molecule_type is not None:
                 for record in records1:
                     record.annotations["molecule_type"] = molecule_type
+
+            for test_type in ("IO", "NamedTemporaryFile"):
+                with ExitStack() as exit_stack:
                     # Going to write to a handle...
                     mode = self.get_mode(fmt)
+                    if test_type == "IO":
                         if mode == "t":
-                handle = StringIO()
+                            handle = exit_stack.enter_context(StringIO())
                         elif mode == "b":
-                handle = BytesIO()
+                            handle = exit_stack.enter_context(BytesIO())
+
+                    elif test_type == "NamedTemporaryFile":
+                        file_mode = "wb+"
+                        encoding = None
+                        if mode == "t":
+                            encoding = "utf8"
+                            file_mode = "w+"
+
+                        handle = exit_stack.enter_context(
+                            NamedTemporaryFile(mode=file_mode, encoding=encoding)
+                        )
+
+                    else:
+                        self.fail(f"test type is not recognized: {test_type}")
 
                     if unequal_length and fmt in AlignIO._FormatToWriter:
                         msg = "Sequences must all be the same length"
@@ -338,7 +359,9 @@ class TestSeqIO(SeqIOTestBaseClass):
                         # Should fail.
                         if debug:
                             try:
-                        SeqIO.write(sequences=records1, handle=handle, format=fmt)
+                                SeqIO.write(
+                                    sequences=records1, handle=handle, format=fmt
+                                )
                             except (ValueError, TypeError) as e:
                                 messages[fmt] = str(e)
                         else:
@@ -347,9 +370,12 @@ class TestSeqIO(SeqIOTestBaseClass):
                                 with warnings.catch_warnings():
                                     # e.g. data loss
                                     warnings.simplefilter("ignore", BiopythonWarning)
-                            SeqIO.write(sequences=records1, handle=handle, format=fmt)
+                                    SeqIO.write(
+                                        sequences=records1, handle=handle, format=fmt
+                                    )
                             self.assertTrue(
-                        isinstance(cm.exception, (ValueError, TypeError)), msg=message
+                                isinstance(cm.exception, (ValueError, TypeError)),
+                                msg=message,
                             )
                             self.assertEqual(str(cm.exception), msg, msg=message)
 
@@ -427,7 +453,9 @@ class TestSeqIO(SeqIOTestBaseClass):
                             self.assertEqual(r1_id, r2.id, f"'{r1.id}' vs '{r2.id}'")
                         elif fmt == "maf":
                             self.assertEqual(
-                        r1.id.replace(" ", "_"), r2.id, f"'{r1.id}' vs '{r2.id}'"
+                                r1.id.replace(" ", "_"),
+                                r2.id,
+                                f"'{r1.id}' vs '{r2.id}'",
                             )
                         elif fmt in ["fasta", "fasta-2line"]:
                             self.assertEqual(r1.id.split()[0], r2.id)
@@ -446,7 +474,10 @@ class TestSeqIO(SeqIOTestBaseClass):
                             warnings.simplefilter("ignore", BiopythonWarning)
                             SeqIO.write(records1[0], handle, fmt)
                             if mode == "t":
-                        self.assertEqual(handle.getvalue(), records1[0].format(fmt))
+                                self.assertEqual(
+                                    handle.getvalue(), records1[0].format(fmt)
+                                )
+
         if debug:
             self.fail(
                 f"Update {t_format} test to use this dict:\nmessages = {messages!r}"