Merge branch 'release/1.3.0'

.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)

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:   <[email protected]>
+
+Source code:   <http://github.com/rhshah/iAnnotateSV>
+
+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
+    ```

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 <[email protected]>"]
-readme = "See README"
+readme = "docs/README.md"
 packages = [{include = "iAnnotateSV"}]
 include = [
     "iAnnotateSV/data/*",