Update dependencies

.github/workflows/cd-pypi.yml

@@ -6,11 +6,11 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v6
       with:
-        python-version: '3.11'
+        python-version: '3.13'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/ci-lint.yml

@@ -15,11 +15,11 @@ jobs:
     runs-on: 'ubuntu-latest'
     strategy:
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.13']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Display Python version
@@ -28,6 +28,6 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 . --count --select=E9,F63,F7,F82 --ignore=F824 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-line-length=240 --statistics
+        flake8 . --count --ignore=F824 --exit-zero --max-line-length=240 --statistics

.github/workflows/ci-package.yml

@@ -15,12 +15,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-latest', 'macos-latest']
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        os: ['ubuntu-latest']
+        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Display Python version

.github/workflows/ci-test.yml

@@ -18,11 +18,11 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: ['ubuntu-latest', 'macos-latest']
-        python-version: ['3.11']
+        os: ['ubuntu-latest']
+        python-version: ['3.13']
     steps:
-    - uses: actions/checkout@v2
-    - uses: mamba-org/setup-micromamba@v1
+    - uses: actions/checkout@v6
+    - uses: mamba-org/setup-micromamba@v3
       with:
         micromamba-version: 'latest'
         environment-name: 'platon'

README.md

@@ -89,12 +89,13 @@ $ python3 -m pip install --user cb-platon
 
 Platon requires the following 3rd party executables which must be installed & executable:
 
+- Pyrodigal (3.7.1) <https://doi.org/10.21105/joss.04296> <https://github.com/althonos/pyrodigal>
 - Prodigal (2.6.3) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848648> <https://github.com/hyattpd/Prodigal>
-- Diamond (2.0.6) <https://pubmed.ncbi.nlm.nih.gov/25402007> <http://www.diamondsearch.org>
-- Blast+ (2.10.1) <https://www.ncbi.nlm.nih.gov/pubmed/2231712> <https://blast.ncbi.nlm.nih.gov>
-- MUMmer (4.0.0-beta2) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC395750/> <https://github.com/gmarcais/mummer>
-- HMMER (3.3.1) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695513/> <http://hmmer.org/>
-- INFERNAL (1.1.4) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810854> <http://eddylab.org/infernal>
+- Diamond (2.2.0) <https://pubmed.ncbi.nlm.nih.gov/25402007> <http://www.diamondsearch.org>
+- Blast+ (2.17.0) <https://www.ncbi.nlm.nih.gov/pubmed/2231712> <https://blast.ncbi.nlm.nih.gov>
+- MUMmer (4.0.1) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC395750/> <https://github.com/gmarcais/mummer>
+- HMMER (3.4) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695513/> <http://hmmer.org/>
+- INFERNAL (1.1.5) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810854> <http://eddylab.org/infernal>
 
 ### Database download
 

db-scripts/build-hmms.nf

@@ -21,7 +21,7 @@ process extractNRP {
     errorStrategy 'ignore'
     cpus 1
     memory '1 GB'
-    conda 'seqtk=1.3 muscle=5.1 hmmer=3.3.2'
+    conda 'seqtk=1.5 muscle=5.3 hmmer=3.4.0'
 
     input:
     val(cluster) from chGeneCluster

db-scripts/compute-rds-thresholds.nf

@@ -39,7 +39,7 @@ process searchProts {
     maxRetries 3
     cpus 4
     memory '4 GB'
-    conda 'prodigal=2.6.3 diamond=2.0.14'
+    conda 'pyrodigal=3.7.1 diamond=2.2.0'
 
     input:
     set val(type), val(id), val(subSequence) from chContigs
@@ -50,7 +50,7 @@ process searchProts {
     script:
     """
     echo '>${id}\n${subSequence}' > seq.fna
-    prodigal -i seq.fna -a cdss.faa -p meta
+    pyrodigal -i seq.fna -a cdss.faa -p meta
     if [ -s cdss.faa ]
     then
         diamond blastp --query cdss.faa --db ${pcDb} --fast --threads ${task.cpus} --out output.tsv --max-target-seqs 1 --id 90 --query-cover 80 --subject-cover 80

db-scripts/count-protein-hits.nf

@@ -29,7 +29,7 @@ process callORFs {
 
     errorStrategy 'ignore'
     maxRetries 3
-    conda 'prodigal=2.6.3'
+    conda 'pyrodigal=3.7.1'
 
     input:
     set val(type), file('replicon.fna') from chInput
@@ -40,11 +40,11 @@ process callORFs {
     script:
     if( type == 'p' )
         """
-        prodigal -i replicon.fna -a cdss.faa -p meta
+        pyrodigal -i replicon.fna -a cdss.faa -p meta
         """
     else
         """
-        prodigal -i replicon.fna -a cdss.faa
+        pyrodigal -i replicon.fna -a cdss.faa
         """
 }
 
@@ -55,7 +55,7 @@ process searchProts {
     maxRetries 3
     cpus 4
     memory '12 GB'
-    conda 'diamond=2.0.14'
+    conda 'diamond=2.2.0'
 
     input:
     set val(type), file(cdss) from chAA

environment.yml

@@ -2,12 +2,11 @@ name: platon
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - biopython>=1.78
-  - prodigal>=2.6.3
-  - diamond>=2.0.14
-  - blast>=2.12.0
-  - hmmer>=3.3.1
-  - infernal>=1.1.4
-  - mummer4>=4.0.0rc1
+  - biopython>=1.87
+  - pyrodigal>=3.7.1
+  - diamond>=2.2.0
+  - blast>=2.17.0
+  - hmmer>=3.4
+  - infernal>=1.1.5
+  - mummer4>=4.0.1

platon.cwl

@@ -17,7 +17,7 @@ hints:
   SoftwareRequirement:
     packages:
       platon:
-      version: [ "1.7.0" ]
+      version: [ "1.8.0" ]
 
 requirements:
   ResourceRequirement:

platon/__init__.py

@@ -1 +1 @@
-__version__ = '1.7'
+__version__ = '1.8'

platon/functions.py

@@ -1,6 +1,5 @@
 import logging
 import subprocess as sp
-
 import platon.config as cfg
 import platon.constants as pc
 
@@ -455,7 +454,7 @@ def predict_orfs(contigs, filteredDraftGenomePath):
     proteins_path = cfg.tmp_path.joinpath('proteins.faa')
     gff_path = cfg.tmp_path.joinpath('prodigal.gff')
     cmd = [
-        'prodigal',
+        'pyrodigal',
         '-i', str(filteredDraftGenomePath),
         '-a', str(proteins_path),
         '-c',  # closed ends
@@ -491,7 +490,7 @@ def predict_orfs(contigs, filteredDraftGenomePath):
         for line in fh:
             if(line[0] != '#'):
                 cols = line.split('\t')
-                orf_id = cols[8].split(';')[0].split('=')[1].split('_')[1]
+                orf_id = cols[8].split(';')[0].split('=')[1].split('_')[-1]
                 orf = {
                     'start': int(cols[3]),
                     'end': int(cols[4]),

platon/utils.py

@@ -23,12 +23,12 @@ def print_version(self):
 VERSION_MAX_DIGIT = 1000000000000
 VERSION_REGEX = re.compile(r'(\d+)\.(\d+)(?:\.(\d+))?')  # regex to search for version number in tool output. Takes missing patch version into consideration.
 DEPENDENCIES = [  # List of dependencies: tuples for: min version, max version, tool name & command line parameter, dependency check exclusion options
-    (Version(2,6,3), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('prodigal', '-v')),
-    (Version(2,0,14), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('diamond', 'help')),
-    (Version(2,12,0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('blastn', '-version')),
-    (Version(3,3,1), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('hmmsearch', '-h')),
-    (Version(4,0,0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('nucmer', '-V')),
-    (Version(1,1,2), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('cmscan', '-h'))
+    (Version(3,7,1), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('pyrodigal', '-V')),
+    (Version(2,2,0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('diamond', 'help')),
+    (Version(2,17,0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('blastn', '-version')),
+    (Version(3,4,0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('hmmsearch', '-h')),
+    (Version(4,0,1), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('nucmer', '-V')),
+    (Version(1,1,5), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('cmscan', '-h'))
 ]
 
 

setup.py

@@ -22,11 +22,12 @@
     author_email='oliver.schwengers@computational.bio.uni-giessen.de',
     url='https://github.com/oschwengers/platon',
     packages=['platon'],
-    python_requires='>=3.8',
+    python_requires='>=3.10',
     include_package_data=True,
     zip_safe=False,
     install_requires=[
-        'biopython >= 1.78'
+        'biopython >= 1.87',
+        'pyrodigal >= 3.7.1'
     ],
     entry_points={
         'console_scripts': [
@@ -36,10 +37,11 @@
     classifiers=[
         'Operating System :: POSIX :: Linux',
         'Programming Language :: Python :: 3 :: Only',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
+        'Programming Language :: Python :: 3.14',
         'Development Status :: 5 - Production/Stable',
         'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
         'Topic :: Scientific/Engineering :: Bio-Informatics',