seqslab-report-parser 0.2.4
Atgenomix SeqsLab Report Parser
License: Apache License, Version 2.0
Requires Python: >=3.8

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This package provides a unified command line interface to Atgenomix SeqsLab, a cloud-native biomedical informatics (BioMed IT) platform.

<!-- TABLE OF CONTENTS -->
<details open="open">
  <summary>Table of Contents</summary>
  <ol>
    <li>
      <a href="#getting-started">Getting Started</a>
      <ul>
        <li><a href="#prerequisites">Prerequisites</a></li>
        <li><a href="#install-the-seqslab-cli">Install the SeqsLab CLI</a> </li>
        <li><a href="#basic-commands">Basic Commands</a></li>
      </ul>
    <li><a href="#getting-help">Getting Help</a></li>
    <li><a href="#contributing">Contributing</a></li>
    <li><a href="#more-resources">More Resources</a></li>
  </ol>
</details>

## Getting Started

### Prerequisites

* Python 3.8 or later

* [PyMuPDF](https://github.com/pymupdf/PyMuPDF)
* [pyfaidx](https://github.com/mdshw5/pyfaidx/)
* [pyhgvs](https://github.com/counsyl/hgvs)


### Install the SeqsLab Report Parser
  ```bash
  pip install seqslab-report-parser
  ```

### Basic Commands
#### Parse PDF Report (single)

  ```bash
  report-parser single -i {INPUT_DIR} --ref {FASTA_PATH} --ref_fa {FASTA_IDX_PATH} --ref_gene {REF_GENE_PATH} --trans_cds {TRANSCRIPT_CDS_PATH} --ens_to_nm {ENS_TO_NM_MAPPING_PATH}
  ```

* -m: optional, generate MAF info
* -v: optional, generate VCF file

#### Parse PDF Report (batch)

  ```bash
  report-parser batch -i {INPUT_DIR} -o {OUTPUT_DIR} --ref {FASTA_PATH} --ref_fa {FASTA_IDX_PATH} --ref_gene {REF_GENE_PATH} --trans_cds {TRANSCRIPT_CDS_PATH} --ens_to_nm {ENS_TO_NM_MAPPING_PATH}
  ```

* -m: optional, generate MAF info
* -v: optional, generate VCF file

#### Generate genes.refGene

  ```bash
  report-parser gen-ref-gene --output {REF_GENE_PATH}
  ```

#### Generate Transcript CDS

  ```bash
  report-parser gen-cds --output {TRANSCRIPT_CDS_PATH} --gen_code {GEN_CODE_PATH} --ref {FASTA_PATH}
  ```

#### Help documentation
To view help documentation, use one of the following:

```bash
report-parser -h
```

## Getting Help
The best way to interact with our team is through GitHub. You can open an issue and choose from one of our templates for guidance, bug reports, or feature requests.

Please check for open similar issues before opening another one.

## More Resources


## Contributing

The repository currently does not accept contributions but will eventually be opened to the community.


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[contributors-url]: https://github.com/AnomeGAP/seqslab-cli/graphs/contributors

[stars-url]: https://github.com/AnomeGAP/seqslab-cli/stargazers

[issues-url]: https://github.com/AnomeGAP/seqslab-cli/issues

[license-url]: https://github.com/AnomeGAP/seqslab-cli/blob/main/LICENSE.txt

[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=for-the-badge&logo=linkedin&colorB=555

[linkedin-url]: https://www.linkedin.com/company/atgenomix

[product-screenshot]: https://github.com/AnomeGAP/seqslab-cli/blob/main/Atgenomix%20SeqsLab%20V3.png