Merge pull request #369 from gbouras13/dev

v1.7.4 with `--trna_scan_model`

.github/workflows/ci.yaml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest]
+        os: [macos-13, ubuntu-latest] #macos-latest/macos-14 is M1 - some deps
         python-version: ["3.9"]
 
     steps:
@@ -22,25 +22,26 @@ jobs:
           fetch-depth: 0
 
       # Setup env
-      - uses: "conda-incubator/setup-miniconda@v2"
+      - uses: "conda-incubator/setup-miniconda@v3"
         with:
           activate-environment: pharokka_env
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           auto-activate-base: false
-          miniforge-variant: Mambaforge
           channels: conda-forge,bioconda,defaults
           channel-priority: strict
           auto-update-conda: true
       - name: Install pharokka 
         shell: bash -l {0}
         run: |
-          mamba install python=${{ matrix.python-version }}
+          conda install python=${{ matrix.python-version }}
           python -m pip install --upgrade pip
           pip install -e .
       - name: Run tests and collect coverage
         run: pytest --cov=./ --cov-report=xml
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
+        with:
+          version: v0.7.3
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/release.yaml

@@ -12,13 +12,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: 3.9
         activate-environment: pharokka_env
         environment-file: environment.yml
         auto-activate-base: false
-        miniforge-variant: Mambaforge
         channels: conda-forge,bioconda,defaults
         channel-priority: strict
         auto-update-conda: true

HISTORY.md

@@ -1,6 +1,13 @@
 History
 =======
 
+1.7.4 (2024-11-23)
+------------------
+
+* Adds `--trna_scan_model`  parameter with two accepted options: `--trna_scan_model general` (this will be run by default - what Pharokka has always been running) and `--trna_scan_model bacterial`. See the [tRNAscan-SE paper](https://doi.org/10.1093/nar/gkab688) for more information.
+* Bumps the `dnaapler` dependency to v1.0.1 due to a breaking dependency change in `dnaapler`.
+
+
 1.7.3 (2024-07-10)
 ------------------
 

README.md

@@ -66,6 +66,7 @@ If you don't want to install `pharokka` or `phold` locally, you can run `pharokk
   - [Source](#source)
 - [Database Installation](#database-installation)
 - [Beginner Conda Installation](#beginner-conda-installation)
+- [Beginner Conda Installation](#beginner-conda-installation-1)
 - [Usage](#usage)
 - [Version Log](#version-log)
 - [System](#system)
@@ -294,35 +295,49 @@ which will create a directory called "pharokka_v1.4.0_databases" containing the
 
 If you are new to using the command-line, please install conda using the following instructions.
 
-1. Install [Anaconda](https://www.anaconda.com/products/distribution). I would recommend [miniconda](https://docs.conda.io/en/latest/miniconda.html).
-2. Assuming you are using a Linux x86_64 machine (for other architectures, please replace the URL with the appropriate one on the [miniconda](https://docs.conda.io/en/latest/miniconda.html) website).
 
-`curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh`
+# Beginner Conda Installation
+
+If you are new to using the command-line, please install conda using the following instructions.
+
+1. Install Conda - I would recommend [miniforge](https://github.com/conda-forge/miniforge).
+2. Assuming you are using a Linux x86_64 machine (for other architectures, please replace the URL with the appropriate one on the [miniforge](https://github.com/conda-forge/miniforge) repository).
+
+`wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-Linux-x86_64.sh`
+
+For Mac Intel:
+
+`wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-MacOSX-x86_64.sh`
 
-For Mac (Intel, will also work with M1):
+For Mac M1/M2/M3/M4
 
-`curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh`
+`wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-MacOSX-arm64.sh`
 
-3. Install miniconda and follow the prompts.
+3. Install miniforge and follow the prompts.
 
-`sh Miniconda3-latest-Linux-x86_64.sh`
+`sh Miniforge3-24.9.2-0-Linux-x86_64.sh`
 
 4. After installation is complete, you should add the following channels to your conda configuration:
 
-```
+```bash
 conda config --add channels defaults
 conda config --add channels bioconda
 conda config --add channels conda-forge
 ```
 
-5. After this, conda should be installed (you may need to restart your terminal). It is recommended that mamba is also installed, as it will solve the enviroment quicker than conda:
+ 5. Finally, I would recommend installing pharokka into a fresh environment. For example to create an environment called pharokkaENV with pharokka installed:
 
-`conda install mamba`
+```bash
+conda create -n pharokkaENV pharokka
+conda activate pharokkaENV
+install_databases.py -h
+pharokka.py -h
+```
 
- 6. Finally, I would recommend installing `pharokka` into a fresh environment. For example to create an environment called pharokkaENV with `pharokka` installed:
+If you have a Mac with Apple Silicon (M1-M4), try
 
-```
-mamba create -n pharokkaENV pharokka
+```bash
+conda create --platform osx-64 -n pharokkaENV pharokka
 conda activate pharokkaENV
 install_databases.py -h
 pharokka.py -h
@@ -399,6 +414,8 @@ options:
                         extra commands to pass to MINced (please omit the leading hyphen for the first argument). You will need to use quotation marks e.g. --minced_args "minNR 2 -minRL 21"
   --mash_distance MASH_DISTANCE
                         mash distance for the search against INPHARED. Defaults to 0.2.
+  --trna_scan_model {general,bacterial}
+                        tRNAscan-SE model
   -V, --version         Print pharokka Version
   --citation            Print pharokka Citation
   ```

bin/input_commands.py

@@ -161,6 +161,13 @@ def get_input():
         default=0.2,
         type=float,
     )
+    parser.add_argument(
+        "--trna_scan_model",
+        help="tRNAscan-SE model",
+        choices=["general", "bacterial"],
+        default="general",
+        type=str,
+    )
     parser.add_argument(
         "-V",
         "--version",
@@ -408,17 +415,22 @@ def check_dependencies(skip_mash):
     else:
         raise ValueError("MMseqs2 version not found")
 
-    mmseqs_major_version = int(mmseqs_version.split(".")[0])
-    mmseqs_minor_version = mmseqs_version.split(".")[1]
+    # Ryan Wick's code from Dnaapler - for prebuilt binary on github
+    if mmseqs_version.startswith("45111b6"):
+        logger.info(f"MMseqs2 version found is {mmseqs_version}")
+    else:
 
-    logger.info(
-        f"MMseqs2 version found is v{mmseqs_major_version}.{mmseqs_minor_version}"
-    )
+        mmseqs_major_version = int(mmseqs_version.split(".")[0])
+        mmseqs_minor_version = mmseqs_version.split(".")[1]
+
+        logger.info(
+            f"MMseqs2 version found is v{mmseqs_major_version}.{mmseqs_minor_version}"
+        )
 
-    if mmseqs_major_version != 13:
-        logger.error("MMseqs2 is the wrong version. Please install v13.45111")
-    if mmseqs_minor_version != '45111':
-        logger.error("MMseqs2 is the wrong version. Please install v13.45111")
+        if mmseqs_major_version != 13:
+            logger.error("MMseqs2 is the wrong version. Please install v13.45111")
+        if mmseqs_minor_version != '45111':
+            logger.error("MMseqs2 is the wrong version. Please install v13.45111")
 
     logger.info("MMseqs2 version is ok.")
 
@@ -574,8 +586,8 @@ def check_dependencies(skip_mash):
         f"Dnaapler version found is v{dnaapler_major_version}.{dnaapler_minor_version}.{dnaapler_minorest_version}"
     )
 
-    if dnaapler_minor_version < 2:
-        logger.error("Dnaapler is the wrong version. Please re-install pharokka.")
+    if dnaapler_major_version < 1:
+        logger.error("Dnaapler is the wrong version. Please install Dnaapler v1.0.1 or higher.")
 
     logger.info("Dnaapler version is ok.")
 

bin/pharokka.py

@@ -303,11 +303,11 @@ def main():
     if args.skip_extra_annotations is False:
         if args.meta == True:
             logger.info("Starting tRNA-scanSE. Applying meta mode.")
-            run_trnascan_meta(input_fasta, out_dir, args.threads, num_fastas)
+            run_trnascan_meta(input_fasta, out_dir, args.threads, num_fastas, args.trna_scan_model)
             concat_trnascan_meta(out_dir, num_fastas)
         else:
             logger.info("Starting tRNA-scanSE.")
-            run_trna_scan(input_fasta, args.threads, out_dir, logdir)
+            run_trna_scan(input_fasta, args.threads, out_dir, logdir, args.trna_scan_model)
         # run minced and aragorn
         run_minced(input_fasta, out_dir, prefix, args.minced_args, logdir)
         run_aragorn(input_fasta, out_dir, prefix, logdir)

bin/processes.py

@@ -197,7 +197,7 @@ def concat_phanotate_meta(out_dir, num_fastas):
                 outfile.write(infile.read())
 
 
-def run_trnascan_meta(filepath_in, out_dir, threads, num_fastas):
+def run_trnascan_meta(filepath_in, out_dir, threads, num_fastas, trna_scan_model):
     """
     Runs trnascan to output gffs one contig per thread
     :param filepath_in: input filepath
@@ -210,12 +210,17 @@ def run_trnascan_meta(filepath_in, out_dir, threads, num_fastas):
     input_tmp_dir = os.path.join(out_dir, "input_split_tmp")
     commands = []
 
+    if trna_scan_model == "general":
+        model = "G"
+    else: # bacterial
+        model = "B"
+
     for i in range(1, num_fastas + 1):
         in_file = "input_subprocess" + str(i) + ".fasta"
         out_file = "trnascan_tmp" + str(i) + ".gff"
         filepath_in = os.path.join(input_tmp_dir, in_file)
         filepath_out = os.path.join(input_tmp_dir, out_file)
-        cmd = "tRNAscan-SE " + filepath_in + " --thread 1 -G -Q -j " + filepath_out
+        cmd = f"tRNAscan-SE {filepath_in} --thread 1 -{model} -Q -j {filepath_out}"
         commands.append(cmd)
 
     n = int(threads)  # the number of parallel processes you want
@@ -632,7 +637,7 @@ def translate_fastas(out_dir, gene_predictor, coding_table, genbank_file):
     # for genbank do nothing
 
 
-def run_trna_scan(filepath_in, threads, out_dir, logdir):
+def run_trna_scan(filepath_in, threads, out_dir, logdir, trna_scan_model):
     """
     Runs trna scan
     :param filepath_in: input filepath
@@ -643,11 +648,16 @@ def run_trna_scan(filepath_in, threads, out_dir, logdir):
 
     out_gff = os.path.join(out_dir, "trnascan_out.gff")
 
+    if trna_scan_model == "general":
+        model = "G"
+    else: # bacterial
+        model = "B"
+
     trna = ExternalTool(
         tool="tRNAscan-SE",
         input=f"{filepath_in}",
         output=f"{out_gff}",
-        params=f"--thread {threads} -G -Q -j",
+        params=f"--thread {threads} -{model} -Q -j",
         logdir=logdir,
         outfile="",
     )

bin/version.py

@@ -1 +1 @@
-__version__ = "1.7.3"
+__version__ = "1.7.4"

docs/install.md

@@ -10,11 +10,11 @@ conda install -c bioconda pharokka
 
 This will install all the dependencies along with `pharokka`. The dependencies are listed in environment.yml.
 
-If conda is taking a long time to solve the environment, try using mamba:
+If you have a MacOS system with M1/M2/M3 Apple Silicon, try this 
 
 ```bash
-conda install mamba
-mamba install -c bioconda pharokka
+conda create --platform osx-64 --name pharokkaENV -c bioconda pharokka
+conda activate pharokkaENV
 ```
 
 ## Pip
@@ -100,18 +100,22 @@ which will create a directory called "pharokka_v1.4.0_databases" containing the
 
 If you are new to using the command-line, please install conda using the following instructions.
 
-1. Install [Anaconda](https://www.anaconda.com/products/distribution). I would recommend [miniconda](https://docs.conda.io/en/latest/miniconda.html).
-2. Assuming you are using a Linux x86_64 machine (for other architectures, please replace the URL with the appropriate one on the [miniconda](https://docs.conda.io/en/latest/miniconda.html) website).
+1. Install Conda - I would recommend [miniforge](https://github.com/conda-forge/miniforge).
+2. Assuming you are using a Linux x86_64 machine (for other architectures, please replace the URL with the appropriate one on the [miniforge](https://github.com/conda-forge/miniforge) repository).
+
+`wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-Linux-x86_64.sh`
+
+For Mac Intel:
 
-`curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh`
+`wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-MacOSX-x86_64.sh`
 
-For Mac (Intel, will also work with M1):
+For Mac M1/M2/M3/M4
 
-`curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh`
+`wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-MacOSX-arm64.sh`
 
-3. Install miniconda and follow the prompts.
+3. Install miniforge and follow the prompts.
 
-`sh Miniconda3-latest-Linux-x86_64.sh`
+`sh Miniforge3-24.9.2-0-Linux-x86_64.sh`
 
 4. After installation is complete, you should add the following channels to your conda configuration:
 
@@ -121,15 +125,20 @@ conda config --add channels bioconda
 conda config --add channels conda-forge
 ```
 
-5. After this, conda should be installed (you may need to restart your terminal). It is recommended that mamba is also installed, as it will solve the enviroment quicker than conda:
+ 5. Finally, I would recommend installing pharokka into a fresh environment. For example to create an environment called pharokkaENV with pharokka installed:
 
-`conda install mamba`
+```bash
+conda create -n pharokkaENV pharokka
+conda activate pharokkaENV
+install_databases.py -h
+pharokka.py -h
+```
 
- 6. Finally, I would recommend installing pharokka into a fresh environment. For example to create an environment called pharokkaENV with pharokka installed:
+If you have a Mac with Apple Silicon (M1-M4), try
 
 ```bash
-mamba create -n pharokkaENV pharokka
+conda create --platform osx-64 -n pharokkaENV pharokka
 conda activate pharokkaENV
 install_databases.py -h
 pharokka.py -h
-```
+```

docs/run.md

@@ -159,6 +159,8 @@ Note 2 things: (1) that you need to leave off the leading hyphen (i.e. `"minNR 2
 pharokka.py -i <fasta file> -o <output folder> -d <path/to/database_dir> -t <threads>  --minced_args "minNR 2 -minRL 21"
 ```
 
+As of v1.7.4 you can specify the bacterial `tRNAscan-SE` model using `--trna_scan_model bacterial`. Otherwise, `pharokka` uses the general model by default. See the [tRNAscan-SE paper](https://doi.org/10.1093/nar/gkab688) for more information.
+
 
 ```bash
 usage: pharokka.py [-h] [-i INFILE] [-o OUTDIR] [-d DATABASE] [-t THREADS] [-f] [-p PREFIX] [-l LOCUSTAG] [-g GENE_PREDICTOR] [-m] [-s]
@@ -217,6 +219,8 @@ options:
                         extra commands to pass to MINced (please omit the leading hyphen for the first argument). You will need to use quotation marks e.g. --minced_args "minNR 2 -minRL 21"
   --mash_distance MASH_DISTANCE
                         mash distance for the search against INPHARED. Defaults to 0.2.
+  --trna_scan_model {general,bacterial}
+                        tRNAscan-SE model
   -V, --version         Print pharokka Version
   --citation            Print pharokka Citation
   ```

environment.yml

@@ -12,7 +12,7 @@ dependencies:
   - minced >=0.4.2
   - aragorn >=1.2.41
   - mash >=2.2
-  - dnaapler >=0.4.0
+  - dnaapler >=1.0.1
   - pyrodigal >=3.1.0
   - pyrodigal-gv >=0.2.0
   - pycirclize >=0.3.1

setup.py

@@ -18,8 +18,8 @@ def package_files(directory):
     long_description = fh.read()
 
 setup(
-    name="Pharokka",
-    version="1.7.3",
+    name="pharokka",
+    version="1.7.4",
     author="George Bouras",
     author_email="[email protected]",
     description="Fast phage annotation tool",