diff --git a/README.md b/README.md index 8db9564a7f1ba4c595eec1224015f731f62cc19e..e40105028d8f54d7e023775ceca042a5177f6f33 100644 --- a/README.md +++ b/README.md @@ -6,11 +6,11 @@ We hope that others would find use for this transcript_structure generator that # Installation -To install the Python virtual environment, run +To install package, run ``` -conda env create --file environment.yml -conda activate transcript-structure-generator +pip install "setuptools>=62.1.0" +pip install . ``` # Usage @@ -27,45 +27,17 @@ Output: - id of original transcript (without intron inclusions) - count -To install package, run - -``` -pip install "setuptools>=62.1.0" -pip install . -``` -To generate the sampled transcripts, open a new shell, activate your environment and run +To generate the sampled transcripts, run ``` -conda activate transcript-structure-generator - -transcript-generator --prob-inclusion <probability_inclusion> [--log "INFO"] <transcripts_file> <annotations_file> +transcript-structure-generator --prob-inclusion <probability_inclusion> [--log "INFO"] <transcripts_file> <annotations_file> ``` where the transcripts file should be csv-formatted, the annotation file gtf-formatted and the inclusion probability for introns a float in the range [0,1]. The log parameter is optional and can be one of `["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"]`. The default is `INFO`. Sample Transcripts and Annotation files can be found in the repository under main/tests/resources. -# Development - -To perform all tests, make sure your environment corresponds to the `environment.yml` file and run - -``` -pytest tests -``` - -To build Docker image, run - -``` -docker build -t transcript-app . -``` - -Afterwards, you can use the Docker image like so - -``` -docker run transcript-app --prob_inclusion <probability_inclusion> [--log "INFO"] <transcripts_file> <annotations_file> -``` - # License MIT license, Copyright (c) 2021 Zavolan Lab, Biozentrum, University of Basel