uniprot_fasta_parser
UniProt FASTA parser written in pure python.
Development setup
Create a venv:
python -m venv venvActivate it:
source venv/bin/activateInstall dependencies:
pip install -r requirements.txtInstall the package in editable mode:
pip install -e .Install jupiter playground:
pip install jupyter
ipython kernel install --user --name=uniprot_fasta_parserTutorial on converting FASTA sequences into CSV format
Get the latest FASTA from UniProt SwissProt:
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gzThe script upfp-fasta-to-csv (installed with upfp) can be used.
upfp-fasta-to-csv -h
usage: upfp-fasta-to-csv [-h] [-g] [-c CHUNK_SIZE] fasta_filepath csv_filepath
positional arguments:
fasta_filepath path to the FASTA file.
csv_filepath path where to store the CSV file.
optional arguments:
-h, --help show this help message and exit
-g, --gzipped flag to indicate whether the FASTA is gzipped.
Defaults to False.
-c CHUNK_SIZE, --chunk_size CHUNK_SIZE
size of the chunks used when writing the CSV file.
Defaults to 10000.Provide as input the downloaded gzipped FASTA file and convert it to CSV:
upfp-fasta-to-csv uniprot_sprot.fasta.gz /path/to/file.csv -gRevert CSV to FASTA
You might want to recreate FASTA format from a CSV resulting from upfp with the script upfp-csv-to-fasta.
upfp-csv-to-fasta -h
usage: upfp-csv-to-fasta [-h] [-g] [-c CHUNK_SIZE] csv_filepath fasta_filepath
positional arguments:
csv_filepath path to the CSV file or SMI file.
fasta_filepath path where to store the FASTA file
optional arguments:
-h, --help show this help message and exit
-g, --gzipped flag to indicate whether the FASTA should be gzipped.
Defaults to False.
-c CHUNK_SIZE, --chunk_size CHUNK_SIZE
size of the chunks used when writing the FASTA file.
Defaults to 10000.
