Miscellaneous scripts not associated with any particular project
getAllGenomeFasta.py Retrieves genome-level fasta files from Downloads for every organism in a EuPathDB project (e.g., PlasmoDB). Choose between genomic sequence, transcript sequences, CDS sequences (all nucleotide) or protein sequences (amino acid). For genomic sequence, you can choose to include organisms without annotations.
Script is written in Python3 and requires the requests library. See requests documentation for installation instructions here (or use pip)
usage: getAllGenomeFasta.py [-h] --type {genomic,transcript,cds,protein}
[--includeUnannotated]
project
positional arguments:
project EuPathDB project from which you wish to download fasta
sequences, e.g., PlasmoDB, TriTrypDB
optional arguments:
-h, --help show this help message and exit
--type {genomic,transcript,cds,protein}
Type of sequence to download. Choose from genomic
sequence, transcript sequences, CDS sequences (all
nucleotide) or protein sequences (amino acid)
--includeUnannotated For genomic sequences only, include fasta from
organisms with no annotations