Metadata-Version: 2.1
Name: sma-finder
Version: 1.0.2
Summary: A tool for diagnosing spinal muscular atrophy (SMA) using exome or genome sequencing data
Home-page: https://github.com/broadinstitute/sma_finder
License: MIT
Keywords: Spinal Muscular Atrophy,SMA,SMN,SMN1,SMN2
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: pandas (>=1.3.5)
Requires-Dist: pysam (>=0.18.0)
Requires-Dist: scipy (>=1.7.3)

sma_finder.py: A tool for diagnosing spinal muscular atrophy (SMA) based on exome or genome sequencing data. 

### Install

```
python3 -m pip install sma-finder
```


### Usage

```
usage: sma_finder [-h] -R REFERENCE_FASTA -g {37,38,T2T} [-o OUTPUT_TSV] [-v]
                  cram_or_bam_path [cram_or_bam_path ...]

positional arguments:
  cram_or_bam_path      One or more CRAM or BAM file paths

optional arguments:
  -h, --help            show this help message and exit
  -R REFERENCE_FASTA, --reference-fasta REFERENCE_FASTA
                        Reference genome FASTA file path
  -g {37,38,T2T}, --genome-version {37,38,T2T}
                        Reference genome version
  -o OUTPUT_TSV, --output-tsv OUTPUT_TSV
                        Output tsv file path
  -v, --verbose         Whether to print extra details during the run

```

