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Commit 9d68856d authored by Mate Balajti's avatar Mate Balajti
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refactor: update readme

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1 merge request!48refactor: setup.py, CI
...@@ -6,11 +6,11 @@ We hope that others would find use for this transcript_structure generator that ...@@ -6,11 +6,11 @@ We hope that others would find use for this transcript_structure generator that
# Installation # Installation
To install the Python virtual environment, run To install package, run
``` ```
conda env create --file environment.yml pip install "setuptools>=62.1.0"
conda activate transcript-structure-generator pip install .
``` ```
# Usage # Usage
...@@ -27,45 +27,17 @@ Output: ...@@ -27,45 +27,17 @@ Output:
- id of original transcript (without intron inclusions) - id of original transcript (without intron inclusions)
- count - 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-structure-generator --prob-inclusion <probability_inclusion> [--log "INFO"] <transcripts_file> <annotations_file>
transcript-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`. 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. 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 # License
MIT license, Copyright (c) 2021 Zavolan Lab, Biozentrum, University of Basel MIT license, Copyright (c) 2021 Zavolan Lab, Biozentrum, University of Basel
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