Protein-Chemistry is a Nextflow pipeline for extracting UniProt IDs and predicting chemical properties of proteins using Propy3. The pipeline takes input file as an argument. The input file should be a list of UniProt IDs or protein sequences in FASTA format. The output file will be a TSV file containing the protein IDs and the predicted chemical properties.
To install Protein-Chemistry, you will need to have Nextflow, UniProt, and Propy3 installed. You can install Nextflow using the following command:
conda install -c nextflow nextflow
You can install UniProt using the following command:
pip install uniprot
You can install Propy3 using the following command:
pip install propy3
Once Nextflow, UniProt, and Propy3 are installed, you can clone the Protein-Chemistry repository and run the pipeline using the following commands:
git clone https://github.com/aysanraza/protein-chemistry.git
cd protein-chemistry
nextflow run pipeline.nf
To run the Protein-Chemistry pipeline, you will need to specify the input and output files on the command line. You can do this using the following arguments:
--input_file: The path to the input file.--output_file: The path to the output file.
For example, to run the pipeline with the following input and output files:
input.txtoutput.tsv
You would use the following command:
nextflow run pipeline.nf --input_file input.txt --output_file output.tsv
Once the pipeline has finished running, you will find the output TSV file in the directory where you executed the command.
I am a Bioinformatics and Machine learning expert, practecing insilico development and analytics in the domain of biology and medicine. I am open for research collaborations, you can email me to discuss.
Thank you,
Ahsan Raza
Masters in Bioinformatics
[email protected]
Islamabad, Pakistan.
