# HG changeset patch
# User peterjc
# Date 1703155678 0
# Node ID 85ef5f5a0562255559e669033e47d7838480435c
# Parent  83a19df00eab17c676e2604f6ed15a39ca47d08b
v0.2.9  - Fixed file open mode for Python 3.11 onwards.

diff -r 83a19df00eab -r 85ef5f5a0562 tools/seq_filter_by_id/README.rst
--- a/tools/seq_filter_by_id/README.rst	Thu Nov 30 09:58:56 2023 +0000
+++ b/tools/seq_filter_by_id/README.rst	Thu Dec 21 10:47:58 2023 +0000
@@ -96,6 +96,7 @@
         - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
 v0.2.8  - Bumped Biopython dependency version for Python 3 fixes.
+v0.2.9  - Fixed file open mode for Python 3.11 onwards.
 ======= ======================================================================
 
 
diff -r 83a19df00eab -r 85ef5f5a0562 tools/seq_filter_by_id/seq_filter_by_id.py
--- a/tools/seq_filter_by_id/seq_filter_by_id.py	Thu Nov 30 09:58:56 2023 +0000
+++ b/tools/seq_filter_by_id/seq_filter_by_id.py	Thu Dec 21 10:47:58 2023 +0000
@@ -21,7 +21,7 @@
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
 https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
-This script is copyright 2010-2017 by Peter Cock, The James Hutton Institute
+This script is copyright 2010-2023 by Peter Cock, The James Hutton Institute
 (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
 See accompanying text file for licence details (MIT license).
 
@@ -113,7 +113,7 @@
 options, args = parser.parse_args()
 
 if options.version:
-    print("v0.2.7")
+    print("v0.2.9")
     sys.exit(0)
 
 in_file = options.input
@@ -247,7 +247,7 @@
     print("Have %i unique identifiers from list" % len(ids))
 for tabular_file, columns in identifiers:
     file_ids = set()
-    handle = open(tabular_file, "rU")
+    handle = open(tabular_file)
     if len(columns) > 1:
         # General case of many columns
         for line in handle:
diff -r 83a19df00eab -r 85ef5f5a0562 tools/seq_filter_by_id/seq_filter_by_id.xml
--- a/tools/seq_filter_by_id/seq_filter_by_id.xml	Thu Nov 30 09:58:56 2023 +0000
+++ b/tools/seq_filter_by_id/seq_filter_by_id.xml	Thu Dec 21 10:47:58 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.8">
+<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.9">
     <description>from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.81">biopython</requirement>