This is the demo python library for converting protein coordinates to genomic coordinates. It's only a demo for my coding skill, and not supposed to be used in real world research and production.

• 'converter.py' is the main Converter Class which has the core function to convert the amino acid position to genomic postion.
• 'utils.py' is the Class which contains the static methodes for IO purpose, it also contains a read_gff3_to_df function which can read gff3 files as pandas DataFrame.
• '_main_.py' is the main entry point of the program.
• 'prototype.ipynb' is the scratch notebook I used to build up the core function and prepare the feature file.

The resource files are stored in protein2genome/resources. The gencode_CDS_DataFrame.parquet is the feature file of CDS dataframes extracted from the gencode gff3 files. Code can be found in prototype.ipynb.

Run python setup.py install to install this package.

Run python .\tests\test_protein2genome.py to run the unit test.

It can also run as python -m protein2genome -o example/test_out.tsv example/teststest_input.tsv without installation. Or you can run protein2genome command after installtion of the package.

This project is licensed under the MIT License.

• Email: [email protected]
• LinkedIn: Jiawei Gu