bump Pyrodigal to 3.4.0

oschwengers · May 21, 2024 · 41b801f · 41b801f
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commit 41b801f
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -111,7 +111,7 @@ Bakta requires the following 3rd party software tools which must be installed an
 - Aragorn (1.2.38) <http://dx.doi.org/10.1093/nar/gkh152> <http://130.235.244.92/ARAGORN>
 - INFERNAL (1.1.4) <https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtt509> <http://eddylab.org/infernal>
 - PILER-CR (1.06) <https://doi.org/10.1186/1471-2105-8-18> <http://www.drive5.com/pilercr>
-- Pyrodigal (2.1.0) <https://doi.org/10.21105/joss.04296> <https://github.com/althonos/pyrodigal>
+- Pyrodigal (3.4.0) <https://doi.org/10.21105/joss.04296> <https://github.com/althonos/pyrodigal>
 - PyHMMER (0.10.0) <https://doi.org/10.21105/joss.04296> <https://github.com/althonos/pyhmmer>
 - Diamond (2.0.14) <https://doi.org/10.1038/nmeth.3176> <https://github.com/bbuchfink/diamond>
 - Blast+ (2.12.0) <https://www.ncbi.nlm.nih.gov/pubmed/2231712> <https://blast.ncbi.nlm.nih.gov>

diff --git a/bakta/features/cds.py b/bakta/features/cds.py
@@ -119,7 +119,7 @@ def create_cdss(genes, contig):
             partial_cdss_per_sequence.append(cds)
         else:
             cdss_per_sequence.append(cds)
-        aa = gene.translate(translation_table=cfg.translation_table).upper()
+        aa = gene.translate(translation_table=cfg.translation_table, strict=False).upper()
         if('truncated' not in cds or cds['truncated'] == bc.FEATURE_END_5_PRIME):
             aa = aa[:-1]  # discard trailing asterisk
         cds['aa'] = aa

diff --git a/bakta/utils.py b/bakta/utils.py
@@ -42,7 +42,7 @@ def print_version(self):
 DEPENDENCY_ARAGORN = (Version(1, 2, 41), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Aragorn', ('aragorn', '-h'), ['skip-tmrna'])
 DEPENDENCY_CMSCAN = (Version(1, 1, 4), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'CMscan', ('cmscan', '-h'), ['--skip-rrna', '--skip-ncrna', '--skip-ncrna-region'])
 DEPENDENCY_PILERCR = (Version(1, 6), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'PilerCR', ('pilercr', '-options'), ['--skip-crispr'])
-DEPENDENCY_PYRODIGAL = (Version(3, 1, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyrodigal', ('pyrodigal', '--version'), ['--skip-cds'])
+DEPENDENCY_PYRODIGAL = (Version(3, 4, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyrodigal', ('pyrodigal', '--version'), ['--skip-cds'])
 DEPENDENCY_PYHMMER = (Version(0, 10, 4), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyhmmer', ('python', '-c', 'import pyhmmer; print(pyhmmer.__version__)'), ['--skip-cds', '--skip-sorf'])
 DEPENDENCY_DIAMOND = (Version(2, 1, 8), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Diamond', ('diamond', 'help'), ['--skip-cds', '--skip-sorf'])
 DEPENDENCY_DEEPSIG = (Version(1, 2, 5), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'DeepSig', ('deepsig', '--version'), ['--gram ?'])

diff --git a/environment.yml b/environment.yml
@@ -9,7 +9,7 @@ dependencies:
   - requests>=2.25.1
   - alive-progress>=3.0.1
   - pyyaml>=6.0
-  - pyrodigal>=3.1.0
+  - pyrodigal>=3.4.0
   - trnascan-se>=2.0.11
   - aragorn>=1.2.41
   - infernal>=1.1.4

diff --git a/setup.py b/setup.py
@@ -31,7 +31,7 @@
         'requests >= 2.25.1',
         'alive-progress >= 3.0.1',
         'PyYAML >= 6.0',
-        'pyrodigal >= 3.0.1',
+        'pyrodigal >= 3.4.0',
         'pyhmmer >= 0.10.0'
     ],
     entry_points={