peterjc · peterjc · Dec 21, 2023 · Dec 21, 2023 · Dec 21, 2023 · Dec 21, 2023
diff --git a/tools/fasta_filter_by_id/README.rst b/tools/fasta_filter_by_id/README.rst
@@ -53,6 +53,7 @@ v0.0.5  - Explicit dependency on ``galaxy_sequence_utils``.
         - Use standard MIT license (was previously using the MIT/BSD style
           Biopython Licence Agreement).
 v0.0.6  - Python 3 compatible print function.
+v0.0.7  - Fix file open mode for Python 3.11 onwards.
 ======= ======================================================================
 
 

diff --git a/tools/fasta_filter_by_id/fasta_filter_by_id.py b/tools/fasta_filter_by_id/fasta_filter_by_id.py
@@ -16,7 +16,7 @@
 in column one, and the ID of the match from the database is in column two.
 Here sensible values for the column numbers would therefore be "1" or "2".
 
-This tool is copyright 2010-2017 by Peter Cock, The James Hutton Institute
+This tool is copyright 2010-2023 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See accompanying text file for licence details (MIT license).
 """
@@ -26,7 +26,7 @@
 import sys
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print("v0.0.6")
+    print("v0.0.7")
     sys.exit(0)
 
 from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
@@ -45,7 +45,7 @@
 
 # Read tabular file and record all specified identifiers
 ids = set()
-handle = open(tabular_file, "rU")
+handle = open(tabular_file)
 if len(columns) > 1:
     # General case of many columns
     for line in handle:
@@ -66,7 +66,7 @@
 handle.close()
 
 # Write filtered FASTA file based on IDs from tabular file
-reader = fastaReader(open(in_file, "rU"))
+reader = fastaReader(open(in_file))
 if out_positive_file != "-" and out_negative_file != "-":
     print("Generating two FASTA files")
     positive_writer = fastaWriter(open(out_positive_file, "w"))

diff --git a/tools/fasta_filter_by_id/fasta_filter_by_id.xml b/tools/fasta_filter_by_id/fasta_filter_by_id.xml
@@ -1,4 +1,4 @@
-<tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.6" hidden="true">
+<tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.7" hidden="true">
     <description>from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>

diff --git a/tools/fastq_filter_by_id/README.rst b/tools/fastq_filter_by_id/README.rst
@@ -54,6 +54,7 @@ v0.0.5  - Explicit dependency on ``galaxy_sequence_utils``.
         - Use standard MIT license (was previously using the MIT/BSD style
           Biopython Licence Agreement).
 v0.0.6  - Python 3 compatible print function.
+v0.0.7  - Fix file open mode for Python 3.11 onwards.
 ======= ======================================================================
 
 

diff --git a/tools/fastq_filter_by_id/fastq_filter_by_id.py b/tools/fastq_filter_by_id/fastq_filter_by_id.py
@@ -16,7 +16,7 @@
 in column one, and the ID of the match from the database is in column two.
 Here sensible values for the column numbers would therefore be "1" or "2".
 
-This tool is copyright 2010-2017 by Peter Cock, The James Hutton Institute
+This tool is copyright 2010-2023 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See accompanying text file for licence details (MIT license).
 """
@@ -26,7 +26,7 @@
 import sys
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print("v0.0.6")
+    print("v0.0.7")
     sys.exit(0)
 
 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
@@ -45,7 +45,7 @@
 
 # Read tabular file and record all specified identifiers
 ids = set()
-handle = open(tabular_file, "rU")
+handle = open(tabular_file)
 if len(columns) > 1:
     # General case of many columns
     for line in handle:
@@ -66,7 +66,7 @@
 handle.close()
 
 # Write filtered FASTQ file based on IDs from tabular file
-reader = fastqReader(open(in_file, "rU"))
+reader = fastqReader(open(in_file))
 if out_positive_file != "-" and out_negative_file != "-":
     print("Generating two FASTQ files")
     positive_writer = fastqWriter(open(out_positive_file, "w"))

diff --git a/tools/fastq_filter_by_id/fastq_filter_by_id.xml b/tools/fastq_filter_by_id/fastq_filter_by_id.xml
@@ -1,4 +1,4 @@
-<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.6" hidden="true">
+<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.7" hidden="true">
     <description>from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>

diff --git a/tools/predictnls/README.rst b/tools/predictnls/README.rst
@@ -70,6 +70,7 @@ v0.0.9  - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
         - Python 3 compatible print function.
         - Record version of the Python script.
+v0.0.10 - Fix file open mode for Python 3.11 onwards.
 ======= ======================================================================
 
 

diff --git a/tools/predictnls/predictnls.py b/tools/predictnls/predictnls.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright 2011-2013 by Peter Cock, James Hutton Institute (formerly SCRI), UK
+# Copyright 2011-2023 by Peter Cock, James Hutton Institute (formerly SCRI), UK
 #
 # Licenced under the GPL (GNU General Public Licence) version 3.
 #
@@ -56,7 +56,7 @@
 import sys
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print("v0.0.9")
+    print("v0.0.10")
     sys.exit(0)
 
 if len(sys.argv) == 4:
@@ -88,7 +88,7 @@
 
 def load_re(filename):
     """Parse the 5+ column tabular NLS motif file."""
-    handle = open(filename, "rU")
+    handle = open(filename)
     for line in handle:
         line = line.rstrip("\n")
         if not line:

diff --git a/tools/predictnls/predictnls.xml b/tools/predictnls/predictnls.xml
@@ -1,4 +1,4 @@
-<tool id="predictnls" name="PredictNLS" version="0.0.9">
+<tool id="predictnls" name="PredictNLS" version="0.0.10">
     <description>Find nuclear localization signals (NLSs) in protein sequences</description>
     <version_command>
 python $__tool_directory__/predictnls.py --version

diff --git a/tools/seq_filter_by_id/README.rst b/tools/seq_filter_by_id/README.rst
@@ -96,6 +96,7 @@ v0.2.7  - Python 3 compatible print function.
         - 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 --git a/tools/seq_filter_by_id/seq_filter_by_id.py b/tools/seq_filter_by_id/seq_filter_by_id.py
@@ -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 @@ def clean_name(name):
     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 --git a/tools/seq_filter_by_id/seq_filter_by_id.xml b/tools/seq_filter_by_id/seq_filter_by_id.xml
@@ -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>

diff --git a/tools/seq_primer_clip/README.rst b/tools/seq_primer_clip/README.rst
@@ -1,7 +1,7 @@
 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
 ===========================================================
 
-This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2023 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -74,6 +74,8 @@ v0.0.14 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
 v0.0.15 - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only)
 v0.0.16 - Python 3 compatible print function.
+v0.0.17 - Use Python 3 style dictionary iteration.
+v0.0.18 - Fix file open mode for Python 3.11 onwards.
 ======= ======================================================================
 
 

diff --git a/tools/seq_primer_clip/seq_primer_clip.py b/tools/seq_primer_clip/seq_primer_clip.py
@@ -22,7 +22,7 @@
 Note that only the trim/clip values in the SFF file are changed, not the flow
 information of the full read sequence.
 
-This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This script is copyright 2011-2023 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/BSD style).
 
@@ -34,7 +34,7 @@
 import sys
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print("v0.0.17")
+    print("v0.0.18")
     sys.exit(0)
 
 from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
@@ -201,7 +201,7 @@ def load_primers_as_re(primer_fasta, mm, rc=False):
     Read primer file and record all specified sequences.
     """
     primers = set()
-    in_handle = open(primer_fasta, "rU")
+    in_handle = open(primer_fasta)
     reader = fastaReader(in_handle)
     count = 0
     for record in reader:
@@ -293,7 +293,7 @@ def process(records):
     writer.write_file(process(SffIterator(in_handle)))
     # End of SFF code
 elif seq_format.lower().startswith("fastq"):
-    in_handle = open(in_file, "rU")
+    in_handle = open(in_file)
     out_handle = open(out_file, "w")
     reader = fastqReader(in_handle)
     writer = fastqWriter(out_handle)
@@ -338,7 +338,7 @@ def process(records):
                 else:
                     short_neg += 1
 elif seq_format.lower() == "fasta":
-    in_handle = open(in_file, "rU")
+    in_handle = open(in_file)
     out_handle = open(out_file, "w")
     reader = fastaReader(in_handle)
     writer = fastaWriter(out_handle)

diff --git a/tools/seq_primer_clip/seq_primer_clip.xml b/tools/seq_primer_clip/seq_primer_clip.xml
@@ -1,4 +1,4 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.16">
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.18">
     <description>Trim off 5' or 3' primers</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>

diff --git a/tools/seq_rename/README.rst b/tools/seq_rename/README.rst
@@ -1,7 +1,7 @@
 Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences
 =========================================================
 
-This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2023 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -85,6 +85,7 @@ v0.0.8  - Updated to point at Biopython 1.67 (latest version in Tool Shed).
 v0.0.9  - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
         - Python 3 compatible print function.
+v0.0.10 - Fix file open mode for Python 3.11 onwards.
 ======= ======================================================================
 
 

diff --git a/tools/seq_rename/seq_rename.py b/tools/seq_rename/seq_rename.py
@@ -17,7 +17,7 @@
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
 https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
-This script is copyright 2011-2017 by Peter Cock, The James Hutton Institute UK.
+This script is copyright 2011-2023 by Peter Cock, The James Hutton Institute UK.
 All rights reserved. See accompanying text file for licence details (MIT
 license).
 """
@@ -27,7 +27,7 @@
 import sys
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print("v0.0.9")
+    print("v0.0.10")
     sys.exit(0)
 
 # Parse Command Line
@@ -67,7 +67,7 @@ def parse_ids(tabular_file, old_col, new_col):
 
     Internal white space in the new column is taken as desired output.
     """
-    handle = open(tabular_file, "rU")
+    handle = open(tabular_file)
     old_warn = False
     new_warn = False
     for line in handle:
@@ -144,13 +144,13 @@ def rename_seqrecords(records, mapping):
     ):
         from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
 
-        reader = fastaReader(open(in_file, "rU"))
+        reader = fastaReader(open(in_file))
         writer = fastaWriter(open(out_file, "w"))
         marker = ">"
     elif seq_format.lower().startswith("fastq"):
         from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
 
-        reader = fastqReader(open(in_file, "rU"))
+        reader = fastqReader(open(in_file))
         writer = fastqWriter(open(out_file, "w"))
         marker = "@"
     else:

diff --git a/tools/seq_rename/seq_rename.xml b/tools/seq_rename/seq_rename.xml
@@ -1,4 +1,4 @@
-<tool id="seq_rename" name="Rename sequences" version="0.0.9">
+<tool id="seq_rename" name="Rename sequences" version="0.0.10">
     <description>with ID mapping from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>

diff --git a/tools/seq_select_by_id/README.rst b/tools/seq_select_by_id/README.rst
@@ -1,7 +1,7 @@
 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
 ===============================================================
 
-This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2023 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -91,6 +91,7 @@ v0.0.12 - Python style changes (internal change only).
         - Python 3 compatible print function.
 v0.0.13 - Python 3 compatible exception handling.
 v0.0.14 - Script works on Python 2 and 3 (fixed output file mode).
+v0.0.15 - Fixed file open mode for Python 3.11 onwards.
 ======= ======================================================================
 
 

diff --git a/tools/seq_select_by_id/seq_select_by_id.py b/tools/seq_select_by_id/seq_select_by_id.py
@@ -16,7 +16,7 @@
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
 https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
-This script is copyright 2011-2017 by Peter Cock, The James Hutton Institute UK.
+This script is copyright 2011-2023 by Peter Cock, The James Hutton Institute UK.
 All rights reserved. See accompanying text file for licence details (MIT
 license).
 """
@@ -26,7 +26,7 @@
 import sys
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print("v0.0.14")
+    print("v0.0.15")
     sys.exit(0)
 
 # Parse Command Line
@@ -71,7 +71,7 @@ def parse_ids(tabular_file, col):
     non-trailing white space (only the first word will be used as
     the identifier).
     """
-    handle = open(tabular_file, "rU")
+    handle = open(tabular_file)
     warn = False
     for line in handle:
         if line.strip() and not line.startswith("#"):

diff --git a/tools/seq_select_by_id/seq_select_by_id.xml b/tools/seq_select_by_id/seq_select_by_id.xml
@@ -1,4 +1,4 @@
-<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.14">
+<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.15">
     <description>from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.67">biopython</requirement>

diff --git a/tools/venn_list/README.rst b/tools/venn_list/README.rst
@@ -1,7 +1,7 @@
 Galaxy tool to draw a Venn Diagram with up to 3 sets
 ====================================================
 
-This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2023 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -54,6 +54,7 @@ History
 ======= ======================================================================
 Version Changes
 ------- ----------------------------------------------------------------------
+v0.1.2  - Fixed file open mode for Python 3.11 onwards.
 v0.1.1  - Removed legacy ``tool_dependencies.xml`` file (the legacy Galaxy
           packages did not cover matplotlib_venn anyway).
 v0.1.0  - Now uses Python library matplotlib_venn to draw the diagram