bbmapy 0.0.5__tar.gz → 0.0.41__tar.gz

bbmapy-0.0.41/MANIFEST.in

@@ -0,0 +1,3 @@
+include bbmapy/__init__.py
+recursive-include bbmapy *
+recursive-include vendor *

bbmapy-0.0.41/PKG-INFO

@@ -0,0 +1,163 @@
+Metadata-Version: 2.2
+Name: bbmapy
+Version: 0.0.41
+Summary: A Python wrapper for BBTools
+Project-URL: Homepage, https://github.com/urineri/bbmapy
+Project-URL: Repository, https://github.com/urineri/bbmapy.git
+Project-URL: BBTools Repository, https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: rich
+
+# bbmapy
+
+A Python wrapper for BBTools.  
+Current BBMap version: 0.0.41
+
+## Installation
+1. Lazy way - Clone this repository, download bbmap, and install the package:
+   ```
+   git clone https://github.com/urineri/bbmapy.git
+   cd bbmapy
+   cd vendor
+   rm bb* -rf
+   wget https://sourceforge.net/projects/bbmap/files/latest/download -O bbtools.tar.gz
+   tar -xf bbtools.tar.gz
+   cd ..
+   pip install -e .
+   generate-bbmapy-commands
+   ```
+   The above should be automatically done or just not needed if you are installing from pip (pypi)
+   
+2. Unlazy way - is commented out below this line, that's how much it isn't suggested.
+<!-- Add the BBTools submodule:
+   ```
+   git submodule add https://bitbucket.org/berkeleylab/jgi-bbtools.git vendor/bbtools
+   ```
+
+3. Initialize and update the submodule:
+   ```
+   git submodule init
+   git submodule update
+   ```
+
+4. Install the package:
+   ```
+   pip install .
+   ```
+
+5. Generate the commands:
+   ```
+   generate-bbmapy-commands
+   ```
+6. Now actually delete the git submodule in vendor and replace it with the sourceforge version (i.e. the lazy way):
+```
+cd vendor/
+rm bb* -rf
+wget https://sourceforge.net/projects/bbmap/files/latest/download -O bbtools.tar.gz
+tar -xf bbtools.tar.gz
+
+``` -->
+<!-- 
+Note: Steps 2 and 3 are only necessary if you're setting up the project for the first time or if the submodule hasn't been added yet. If you're cloning the repository and the submodule has already been added, you can use: -->
+<!-- 
+```
+git clone --recurse-submodules https://github.com/yourusername/bbmapy.git
+```
+
+This will clone the repository and initialize the submodule in one step... I think? -->
+
+
+
+## Dependencies
+- Java  
+- BBmap  (the above steps should download it to the vendor subdirectory...).  
+If you rather this to use your own bbmap etc, go to the base.py script and comment out line 51, then uncomment line 52.
+- rich (for pretty printing)
+
+## Usage
+
+After installation, you can use bbmapy in your Python scripts like this:
+
+```python
+from bbmapy import bbduk
+
+# Basic usage
+bbduk(
+    in_file="input.fastq",
+    out="output.fastq",
+    ktrim="r",
+    k="23",
+    mink="11",
+    hdist="1",
+    tbo=True,
+    tpe=True,
+    minlen="45",
+    ref="adapters",
+    ftm="5",
+    maq="6",
+    maxns="1",
+    ordered=True,
+    threads="4",
+    overwrite="t",
+    stats="stats.txt"
+)
+```
+### Using Java flags alongside other arguments
+```python
+bbduk(
+    Xmx="2g",  # Set maximum heap size
+    da=True,   # Enable assertions
+    eoom=True, # Enable out-of-memory termination
+    in_file="input.fastq",
+    out="output.fastq",
+    ktrim="r",
+    k="23"
+)
+```
+
+### To capture output
+You need to set `capture_output=True` in the function call, AND out="stdout.fastq" (or any other file format you like). 
+```python
+stdout, stderr = bbduk(
+    capture_output=True,
+    Xmx="2g",
+    in_file="input.fastq",
+    out="stdout.fastq",
+    # ... other parameters ...
+)
+```
+
+#### Notes:
+ * `in` can be a protected word in python and other code, it is replaced by `in_file` in function calls. `in1`, `in2` are still valid.
+ * Java flags (such as `Xmx`, `Xms`, `da`, `ea`, `eoom`) are automatically recognized and handled appropriately. Include them in your function calls just like any other argument.
+ * the `capture_output` argument might be switched (stderr --> out and vice verse). 
+ * Flags (i.e. argument that do not take value in the OG bbmap version) are set with Boolean values. e.g.:
+ ``` 
+ flag : True
+ ```
+ Not to be mistaken for lower case, fouble qouted `"true"` and `"false"` for boolian arguments to be passed to bbtools, e.g.:
+ ```
+ argument : "true"
+ ```
+ 
+### Citation
+BBMerge manuscript: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185056
+Please cite this paper if you use bbmap in your work.
+
+
+
+## License
+
+This project is only a wrapper, please see the actual bbtools repository for (license)[https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/license.txt] etc.  
+Neither the developers of bbtools nor of bbmapy take any responsibility for how you use this code. All accountability is on you.
+
+## Acknowledgments
+
+This project only (crudely) wraps BBTools (a.k.a bbmap), which is developed by Brian Bushnell.  
+If you use bbmapy and things don't quite work like you'd like, don't expect the developer of bbmap to help you with this whacky python wrapper.  
+If 
+Please see the [BBTools website](https://jgi.doe.gov/data-and-tools/bbtools/) for more information about the underlying tools.  

bbmapy-0.0.41/README.md

@@ -0,0 +1,149 @@
+# bbmapy
+
+A Python wrapper for BBTools.  
+Current BBMap version: 0.0.41
+
+## Installation
+1. Lazy way - Clone this repository, download bbmap, and install the package:
+   ```
+   git clone https://github.com/urineri/bbmapy.git
+   cd bbmapy
+   cd vendor
+   rm bb* -rf
+   wget https://sourceforge.net/projects/bbmap/files/latest/download -O bbtools.tar.gz
+   tar -xf bbtools.tar.gz
+   cd ..
+   pip install -e .
+   generate-bbmapy-commands
+   ```
+   The above should be automatically done or just not needed if you are installing from pip (pypi)
+   
+2. Unlazy way - is commented out below this line, that's how much it isn't suggested.
+<!-- Add the BBTools submodule:
+   ```
+   git submodule add https://bitbucket.org/berkeleylab/jgi-bbtools.git vendor/bbtools
+   ```
+
+3. Initialize and update the submodule:
+   ```
+   git submodule init
+   git submodule update
+   ```
+
+4. Install the package:
+   ```
+   pip install .
+   ```
+
+5. Generate the commands:
+   ```
+   generate-bbmapy-commands
+   ```
+6. Now actually delete the git submodule in vendor and replace it with the sourceforge version (i.e. the lazy way):
+```
+cd vendor/
+rm bb* -rf
+wget https://sourceforge.net/projects/bbmap/files/latest/download -O bbtools.tar.gz
+tar -xf bbtools.tar.gz
+
+``` -->
+<!-- 
+Note: Steps 2 and 3 are only necessary if you're setting up the project for the first time or if the submodule hasn't been added yet. If you're cloning the repository and the submodule has already been added, you can use: -->
+<!-- 
+```
+git clone --recurse-submodules https://github.com/yourusername/bbmapy.git
+```
+
+This will clone the repository and initialize the submodule in one step... I think? -->
+
+
+
+## Dependencies
+- Java  
+- BBmap  (the above steps should download it to the vendor subdirectory...).  
+If you rather this to use your own bbmap etc, go to the base.py script and comment out line 51, then uncomment line 52.
+- rich (for pretty printing)
+
+## Usage
+
+After installation, you can use bbmapy in your Python scripts like this:
+
+```python
+from bbmapy import bbduk
+
+# Basic usage
+bbduk(
+    in_file="input.fastq",
+    out="output.fastq",
+    ktrim="r",
+    k="23",
+    mink="11",
+    hdist="1",
+    tbo=True,
+    tpe=True,
+    minlen="45",
+    ref="adapters",
+    ftm="5",
+    maq="6",
+    maxns="1",
+    ordered=True,
+    threads="4",
+    overwrite="t",
+    stats="stats.txt"
+)
+```
+### Using Java flags alongside other arguments
+```python
+bbduk(
+    Xmx="2g",  # Set maximum heap size
+    da=True,   # Enable assertions
+    eoom=True, # Enable out-of-memory termination
+    in_file="input.fastq",
+    out="output.fastq",
+    ktrim="r",
+    k="23"
+)
+```
+
+### To capture output
+You need to set `capture_output=True` in the function call, AND out="stdout.fastq" (or any other file format you like). 
+```python
+stdout, stderr = bbduk(
+    capture_output=True,
+    Xmx="2g",
+    in_file="input.fastq",
+    out="stdout.fastq",
+    # ... other parameters ...
+)
+```
+
+#### Notes:
+ * `in` can be a protected word in python and other code, it is replaced by `in_file` in function calls. `in1`, `in2` are still valid.
+ * Java flags (such as `Xmx`, `Xms`, `da`, `ea`, `eoom`) are automatically recognized and handled appropriately. Include them in your function calls just like any other argument.
+ * the `capture_output` argument might be switched (stderr --> out and vice verse). 
+ * Flags (i.e. argument that do not take value in the OG bbmap version) are set with Boolean values. e.g.:
+ ``` 
+ flag : True
+ ```
+ Not to be mistaken for lower case, fouble qouted `"true"` and `"false"` for boolian arguments to be passed to bbtools, e.g.:
+ ```
+ argument : "true"
+ ```
+ 
+### Citation
+BBMerge manuscript: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185056
+Please cite this paper if you use bbmap in your work.
+
+
+
+## License
+
+This project is only a wrapper, please see the actual bbtools repository for (license)[https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/license.txt] etc.  
+Neither the developers of bbtools nor of bbmapy take any responsibility for how you use this code. All accountability is on you.
+
+## Acknowledgments
+
+This project only (crudely) wraps BBTools (a.k.a bbmap), which is developed by Brian Bushnell.  
+If you use bbmapy and things don't quite work like you'd like, don't expect the developer of bbmap to help you with this whacky python wrapper.  
+If 
+Please see the [BBTools website](https://jgi.doe.gov/data-and-tools/bbtools/) for more information about the underlying tools.