Metadata-Version: 2.1
Name: pyrodigal
Version: 0.2.1
Summary: Python interface to Prodigal, an ORF finder for genomes, progenomes and metagenomes.
Home-page: https://github.com/althonos/pyrodigal
Author: Martin Larralde
Author-email: martin.larralde@embl.de
License: GPLv3
Project-URL: Bug Tracker, https://github.com/althonos/pyrodigal/issues
Project-URL: Changelog, https://github.com/althonos/pyrodigal/blob/master/CHANGELOG.md
Description: # 🔥 Pyrodigal
        
        *Python interface to [Prodigal](https://github.com/hyattpd/Prodigal/), an ORF
        finder for genomes, progenomes and metagenomes.*
        
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        ## 🗺️ Overview
        
        Pyrodigal is a Python module that provides bindings to Prodigal using
        [Cython](https://cython.org/). It directly interacts with the Prodigal
        internals, which has the following advantages:
        
        - **single dependency**: Pyrodigal is distributed as a Python package, so you
          can add it as a dependency to your project, and stop worrying about the
          Prodigal binary being present on the end-user machine.
        - **no intermediate files**: everything happens in memory, in a Python object
          you fully control, so you don't have to manually import and export sequences
          to pass to the Prodigal CLI.
        - **no input formatting**: sequences are manipulated directly as strings, which
          leverages the issue of formatting your input to FASTA for Prodigal.
        - **lower memory usage**: Pyrodigal is slightly more conservative when it comes
          to using memory, which can help process very large sequences.
        
        ### 📋 Features
        
        The library now features everything needed to run Prodigal in metagenomic mode.
        It does not yet support single mode, which requires more configuration from
        the user but offers more flexibility.
        
        **Roadmap**:
        
        - [x] Metagenomic mode
        - [x] Single mode
        - [ ] External training file support (`-t` flag)
        - [ ] Region masking (`-m` flag)
        
        ### 📋 Memory
        
        Contrary to the Prodigal command line, Pyrodigal attempts to be more conservative
        about memory usage. This means that most of the allocations will be lazy, and
        that some functions will reallocate their results to exact-sized arrays when
        it's possible. This leads to Pyrodigal using about 30% less memory, but with
        some more overhead
        
        ### 🧶 Thread-safety
        
        `pyrodigal.Pyrodigal` instances are not thread-safe: concurrent `find_genes`
        calls will overwrite the internal memory used for dynamic programming and
        could lead to unexpected crashes. A solution to process sequences in parallel
        is to use a consumer/worker pattern, and have on `Pyrodigal` instance in each
        worker. Using a pool spawning `Pyrodigal` instances on the fly is also fine,
        but prevents recycling internal buffers:
        ```python
        with multiprocessing.pool.ThreadPool() as pool:
            pool.map(lambda s: Pyrodigal(meta=True).find_genes(s), sequences)
        ```
        
        ## 💡 Example
        
        Using [Biopython](https://biopython.org/), load a sequence from a GenBank file,
        use Prodigal to find all genes it contains, and print the proteins in FASTA
        format:
        ```python
        record = Bio.SeqIO.read("sequence.fa", "genbank")
        p = pyrodigal.Pyrodigal(meta=True)
        
        for i, gene in enumerate(p.find_genes(str(record.seq))):
            print(f"> {record.id}_{i+1}")
            print(textwrap.fill(record.translate()))
        ```
        
        To use `Pyrodigal` in single mode, you must explicitly call `Pyrodigal.train` 
        with the sequence you want to use for training before trying to find genes:
        ```python
        p = pyrodigal.Pyrodigal()
        p.train(str(record.seq))
        genes = p.find_genes(str(record.seq))
        ```
        
        ## 📜 License
        
        This library, like the original Prodigal software, is provided under the
        [GNU General Public License v3.0](https://choosealicense.com/licenses/gpl-3.0/).
        
Keywords: bioinformatics,genome,orf,gene,prodigal
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: C
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Description-Content-Type: text/markdown
