diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index dd408e1..b8f3852 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.8', '3.9', '3.10'] + python-version: ['3.10'] steps: - name: Checkout github repo (+ download lfs dependencies) diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..709654c --- /dev/null +++ b/docs/README.md @@ -0,0 +1,82 @@ +# iAnnotateSV: Annotation of structural variants detected from NGS + +Author: [Ronak H Shah](http://github.com/rhshah) + +Contributors : [Gowtham Jayakumaran](https://github.com/andurill) and [Ian Johonson](https://github.com/ionox0) + +Contact: + +Source code: + +License: [Apache License 2.0](http://www.apache.org/licenses/LICENSE-2.0) + +[![image](https://img.shields.io/pypi/v/iAnnotateSV.svg)](https://pypi.python.org/pypi/iAnnotateSV) +[![image](https://zenodo.org/badge/18929/rhshah/iAnnotateSV.svg)](https://zenodo.org/badge/latestdoi/18929/rhshah/iAnnotateSV) + +iAnnotateSV is a Python library and command-line software toolkit to +annotate and visualize structural variants detected from Next Generation +DNA sequencing data. This works for majority is just re-writing of a +tool called dRanger_annotate written in matlab by Mike Lawrence at Broad +Institue. But it also has some additional functionality and control over +the annotation w.r.t the what transcripts to be used for annotation. It +is designed for use with hybrid capture, including both whole-exome and +custom target panels, and short-read sequencing platforms such as +Illumina. + +## Citation + +We are in the process of publishing a manuscript describing iAnnotateSV +as part of the Structural Variant Detection framework. If you use this +software in a publication, for now, please cite our website +[iAnnotateSV](http://github.com/rhshah/iAnnotateSV). + +## Acknowledgements + +I would like to thanks Mike Lawrence from Broad Institute for sharing his code and Michael Berger for his insights into the dRanger_annotate tool. + +## Required Packages + +We require that you install: + +python: [v3.10](https://www.python.org/downloads/release/) + +pandas: [v2.2.2](http://pandas.pydata.org/) + +biopython: [v1.84](http://biopython.org/wiki/Main_Page) + +Pillow: [v10.4.0](https://pypi.python.org/pypi/Pillow/) + +openpyxl: [v3.1.5](https://pypi.python.org/pypi/openpyxl/) + +reportlab: [v3.6.13](https://pypi.python.org/pypi/reportlab/) + +coloredlogs: [v15.0.1](https://pypi.python.org/pypi/coloredlogs) + +## Utilities + +[Generate Fusion Peptides](./generate_fusion_peptides/README.md) - Helen +Xie + +## Quick Usage + +If you know python I have created a small test script in /iAnnotateSV/test directory it runs a test on existing code and compares the result with the output file. + +Else To Run: + +- If you want to run with default options: + + ```bash + python /path/to/iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000 + ``` + +- If you want to run with your own transcripts: + + ```bash + python path/to/path/to/iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000 -c canonicalTranscripts.txt + ``` + +- If you want to run with your own transcripts & make plots (making plots is a test module only): + + ```bash + python path/to/iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000 -c canonicalTranscripts.txt -u uniprot.txt -p + ``` diff --git a/pyproject.toml b/pyproject.toml index f0bdceb..9e32203 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "iAnnotateSV" version = "1.3.0" description = "iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Generation DNA sequencing data." authors = ["Ronak Shah "] -readme = "See README" +readme = "docs/README.md" packages = [{include = "iAnnotateSV"}] include = [ "iAnnotateSV/data/*",