Mercurial > repos > peterjc > seq_filter_by_id
changeset 12:85ef5f5a0562 draft default tip
v0.2.9 - Fixed file open mode for Python 3.11 onwards.
| author | peterjc |
|---|---|
| date | Thu, 21 Dec 2023 10:47:58 +0000 |
| parents | 83a19df00eab |
| children | |
| files | tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.py tools/seq_filter_by_id/seq_filter_by_id.xml |
| diffstat | 3 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- 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. ======= ======================================================================
--- 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:
--- 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>