From 31adc27e6c5fb2d2f6eb30eaf91b1d227b08da52 Mon Sep 17 00:00:00 2001 From: Aleksei Korzhenkov Date: Fri, 3 Feb 2023 17:39:13 +0300 Subject: [PATCH] Cleanup and v0.1.0 release --- README.md | 4 ++-- pyyamb/__init__.py | 2 +- pyyamb/pyyamb.py | 7 +++---- setup.py | 1 + 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 02c5ef8..7037827 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # pyYAMB -![Python versions](https://img.shields.io/pypi/pyversions/pyyamb.svg) -![PyPI version](https://img.shields.io/pypi/v/pyyamb.svg) +[![Python versions](https://img.shields.io/pypi/pyversions/pyyamb.svg)](https://pypi.org/project/pyYAMB/) +[![PyPI version](https://img.shields.io/pypi/v/pyyamb.svg)](https://pypi.org/project/pyYAMB/) pyYAMB is an implementation of [YAMB](https://github.com/laxeye/YAMB/) (Yet another metagenome binner) on Python (>=3.8). Originally YAMB was described in the preprint https://www.biorxiv.org/content/10.1101/521286.abstract and it's main point is the use of tSNE and HDBSCAN to process tetramer frequencies and coverage depth of metagenome fragments. pyYAMB strives for parallel computing wherever possible, currently coverage depth extraction is single threaded and takes the most time. diff --git a/pyyamb/__init__.py b/pyyamb/__init__.py index db4e81a..b794fd4 100644 --- a/pyyamb/__init__.py +++ b/pyyamb/__init__.py @@ -1 +1 @@ -__version__ = '0.1.0b0' +__version__ = '0.1.0' diff --git a/pyyamb/pyyamb.py b/pyyamb/pyyamb.py index 819263d..b12df93 100755 --- a/pyyamb/pyyamb.py +++ b/pyyamb/pyyamb.py @@ -16,23 +16,22 @@ from pyyamb.map import sort_mapping_file from pyyamb.utils import write_records_to_fasta from pyyamb.tetra import kmer_freq_table +from pyyamb import __version__ def parse_args(): logger = logging.getLogger() parser = argparse.ArgumentParser(prog="pyYAMB", - description="pyYAMB metagenome binner", + description=f"pyYAMB metagenome binner ver. {__version__}", formatter_class=argparse.ArgumentDefaultsHelpFormatter) general_args = parser.add_argument_group(title="General options", description="") general_args.add_argument("--task", required=True, - choices=["all", "cut", "tetra", "clustering", "map", "make_bins"], + choices=["all", "cut", "tetra", "map", "clustering", "make_bins"], help="Task of pipeline: cut (discard short contigs and cut longer), " + "map (map reads or process mapping file)") general_args.add_argument("-o", "--output", type=str, required=True, help="Output directory") - '''general_args.add_argument("--mapper", help="Mapping software, currently minimap2 only", - choices=["minimap2"], default="minimap2")''' general_args.add_argument("--min-length", default=1000, type=int, help="Minimum contig length") general_args.add_argument("--fragment-length", default=10000, type=int, diff --git a/setup.py b/setup.py index 03db99e..3993819 100644 --- a/setup.py +++ b/setup.py @@ -1,3 +1,4 @@ +import pyyamb import setuptools with open("README.md", "r") as fh: