|
import pandas as pd |
|
import os |
|
from datasets import load_dataset |
|
|
|
data_dir = os.path.join(os.getcwd(), "data") |
|
|
|
species_list = ["human", "rat_SD", "mouse_BALB_c", "mouse_C57BL_6"] |
|
|
|
for species in species_list: |
|
species_url_file = os.path.join(os.getcwd(), species + "_oas_paired.txt") |
|
with open(species_url_file, "r") as f: |
|
for csv_file in f.readlines(): |
|
print(csv_file) |
|
filename = os.path.basename(csv_file) |
|
filename = os.path.splitext(filename)[0] |
|
filename = os.path.splitext(filename)[0] |
|
df = pd.read_csv( |
|
csv_file, |
|
header=1, |
|
compression="gzip", |
|
on_bad_lines="warn", |
|
) |
|
df = df[ |
|
[ |
|
"sequence_id_heavy", |
|
"sequence_heavy", |
|
"locus_heavy", |
|
"stop_codon_heavy", |
|
"productive_heavy", |
|
"rev_comp_heavy", |
|
"sequence_alignment_aa_heavy", |
|
"fwr1_aa_heavy", |
|
"cdr1_aa_heavy", |
|
"fwr2_aa_heavy", |
|
"cdr2_aa_heavy", |
|
"fwr3_aa_heavy", |
|
"cdr3_aa_heavy", |
|
"junction_aa_heavy", |
|
"sequence_id_light", |
|
"sequence_light", |
|
"locus_light", |
|
"stop_codon_light", |
|
"productive_light", |
|
"rev_comp_light", |
|
"sequence_alignment_aa_light", |
|
"fwr1_aa_light", |
|
"cdr1_aa_light", |
|
"fwr2_aa_light", |
|
"cdr2_aa_light", |
|
"fwr3_aa_light", |
|
"cdr3_aa_light", |
|
"junction_aa_light", |
|
] |
|
] |
|
df.insert(0, "run", species) |
|
output_path = os.path.join(data_dir, species) |
|
if not os.path.exists(output_path): |
|
os.makedirs(output_path, exist_ok=True) |
|
df.to_parquet( |
|
os.path.join(output_path, filename + ".parquet"), compression="gzip" |
|
) |
|
|
|
x = load_dataset(output_path) |
|
print(x.num_rows) |
|
|
|
|
