From 782e2e2060eb1700579ac05fd141df9d34098738 Mon Sep 17 00:00:00 2001 From: Aaron Petkau Date: Wed, 26 Oct 2022 15:00:27 -0500 Subject: [PATCH 1/2] Print error even if blast error message does not match pattern --- staramr/blast/JobHandler.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/staramr/blast/JobHandler.py b/staramr/blast/JobHandler.py index 00915062..ccd8efeb 100644 --- a/staramr/blast/JobHandler.py +++ b/staramr/blast/JobHandler.py @@ -286,5 +286,7 @@ def _make_blast_db(self, path: str, file: str) -> None: subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True) except subprocess.CalledProcessError as e: err_msg = str(e.stderr.strip()) - err_msg = re.findall('REF\|(.*?)\'', err_msg)[0] + err_msg_match = re.findall('REF\|(.*?)\'', err_msg) + if len(err_msg_match) > 0: + err_msg = err_msg_match[0] raise Exception('Could not run makeblastdb on file {}, error {}'.format(file, err_msg)) From d0556ab953879604b925abf19ad46f06e2e78778 Mon Sep 17 00:00:00 2001 From: Aaron Petkau Date: Wed, 26 Oct 2022 15:07:55 -0500 Subject: [PATCH 2/2] Updated changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 44628900..143d8755 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,7 @@ # Version 0.9.1 -* Fixed a bug that occured when parsing some plasmid FASTA record IDs. +* Fixed a bug that occured when parsing some plasmid FASTA record IDs ([PR 159](https://github.com/phac-nml/staramr/pull/159)). +* Fixed issue where sometimes the extraction of error messages from `makeblastdb` was crashing leading to less useful errors ([PR 160](https://github.com/phac-nml/staramr/pull/160)). # Version 0.9.0