From dd34c30acfd35cd8a056ca437a150c595b65edde Mon Sep 17 00:00:00 2001 From: asistradition Date: Sun, 4 Oct 2020 13:08:23 -0400 Subject: [PATCH] Update README and setup --- README.md | 27 +++++++++++++++++++++------ setup.py | 10 +++++----- 2 files changed, 26 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index b2a449c..190a176 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,29 @@ -# srrTomat0 - -[![Travis](https://travis-ci.org/cskokgibbs/srrTomat0.svg?branch=master)](https://travis-ci.org/cskokgibbs/srrTomat0) +# inferelator-prior This is a set of pipelines to create expression and prior matrices for network inference. They are designed to create -data that is compatible with the [inferelator](https://github.com/flatironinstitute/inferelator) package. In addition to +data that is compatible with the [inferelator](https://github.com/flatironinstitute/inferelator) package. + +### Usage + + python -m inferelator_prior.network_from_motifs + usage: network_from_motifs.py -m motif_PWM_file.meme + -f genome_fasta_file.fasta + -g genome_annotation_file.gtf + -o ~/output/path/prefix + --species {yeast,fly,mouse,human}] + +This requires a motif PWM database (`-m PATH`), +a genome to search (both sequence as a FASTA `-f PATH` and annotations `-g PATH`), +and an output prefix for several files (`-o PATH`). +In addition, default settings for a specific species can be set with (`--species`). + +### Requirements + +In addition to python dependencies, this package also requires [STAR](https://github.com/alexdobin/STAR), [sra-tools](http://ncbi.github.io/sra-tools/), [bedtools](https://bedtools.readthedocs.io/en/latest/), -[samtools](http://www.htslib.org/), -[homer](http://homer.ucsd.edu/homer/), and +[samtools](http://www.htslib.org/), and [fimo](http://meme-suite.org/doc/fimo.html). diff --git a/setup.py b/setup.py index 2d441f9..0be4204 100644 --- a/setup.py +++ b/setup.py @@ -3,24 +3,24 @@ install_requires = ["numpy", "pandas", "HTSeq", "pybedtools", "scipy", "pathos"] tests_require = ["coverage", "nose", "pysam"] -version = "0.1.1" +version = "0.2.0" # Description from README.md base_dir = os.path.dirname(os.path.abspath(__file__)) long_description = "\n\n".join([open(os.path.join(base_dir, "README.md"), "r").read()]) setup( - name="srrTomat0", + name="inferelator_prior", version=version, - description="SRR Pipelines: Building matrixes from read data", + description="Inferelator-Prior Network Generation Tool", long_description=long_description, long_description_content_type="text/markdown", - url="https://github.com/flatironinstitute/srrTomat0", + url="https://github.com/flatironinstitute/inferelator-prior", author="Chris Jackson", author_email="cj59@nyu.edu", maintainer="Chris Jackson", maintainer_email="cj59@nyu.edu", - packages=find_packages(include=["srrTomat0", "srrTomat0.*"]), + packages=find_packages(include=["inferelator_prior", "inferelator_prior.*"]), zip_safe=False, install_requires=install_requires, tests_require=tests_require,