Treffer: althonos/pyrodigal: v0.2.4

🔥 Pyrodigal Python interface to Prodigal, an ORF finder for genomes, progenomes and metagenomes. 🗺️ Overview Pyrodigal is a Python module that provides bindings to Prodigal using Cython. 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: Metagenomic mode 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: with ...