Data Acquisition

api evo
data collection
HPC
Gathering species and genomic data for api evo research project
Author

Shama Hasan

Published

July 14, 2026

Goals

  • Create BAT of apicomplexan species with complete genomes
  • Gather genomic / biological information from public databases
  • Download genomes
  • Write code to efficiently download all genomes to HPC at once

Methods

Gather genomic data in BAT from NCBI GenBank

  • Filter by referenced and annotated genomes to narrow taxa

Compile metadata

  • Include info about hosts, vectors, genome size, etc. to infer relationships later

Downoad genome assemblies

  • Taxon and accession number columns
  • CDS fies in FASTA format
import os
import pandas as pd 

os.chdir("/Users/shamahasan/Desktop/Apicomplexa")
print("Files will download to:", os.getcwd())

api = pd.read_csv("apicomplexa.tsv", sep="\t")
api = api[["Taxon", "Accession_Number"]]
for taxon, accession in zip(api["Taxon"], api["Accession_Number"]):
    taxon = taxon.replace(" ", "_")

    cmd = f"datasets download genome accession {accession} --include cds --filename {taxon}.WGS.CDS.zip"

    #print(cmd)
    os.system(cmd)

Upload to HPC

*See entry: “HPC Upload” for more details

Data

Present your data here. You can include:

  • Tables
  • Figures
  • Code outputs

Observations

  • 61 total taxa with complete, annotated genomes

Next Steps

References

HPC Upload