|
import os |
|
import pandas as pd |
|
import re |
|
from zipfile import ZipFile |
|
import boto3 |
|
|
|
data_dir = os.getcwd() |
|
output_path = os.getcwd() |
|
|
|
|
|
species_list = ["rat_SD"] |
|
|
|
S3_BUCKET = "aws-hcls-ml" |
|
S3_PREFIX = "oas-paired-sequence-data" |
|
s3 = boto3.client("s3") |
|
for species in species_list: |
|
print(f"Downloading {species} files") |
|
list_of_df = [] |
|
species_url_file = os.path.join(data_dir, 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) |
|
run_id = str(re.search(r"^(.*)_[Pp]aired", filename)[1]) |
|
run_data = pd.read_csv( |
|
csv_file, |
|
header=1, |
|
compression="gzip", |
|
on_bad_lines="warn", |
|
low_memory=False, |
|
) |
|
run_data = run_data[ |
|
[ |
|
"sequence_alignment_aa_heavy", |
|
"cdr1_aa_heavy", |
|
"cdr2_aa_heavy", |
|
"cdr3_aa_heavy", |
|
"sequence_alignment_aa_light", |
|
"cdr1_aa_light", |
|
"cdr2_aa_light", |
|
"cdr3_aa_light", |
|
] |
|
] |
|
run_data = run_data.dropna() |
|
|
|
def calc_cdr_coordinates(row): |
|
for i in range(1, 4): |
|
for j in ["heavy", "light"]: |
|
row[f"cdr{i}_aa_{j}_start"] = row[ |
|
f"sequence_alignment_aa_{j}" |
|
].find(row[f"cdr{i}_aa_{j}"]) |
|
row[f"cdr{i}_aa_{j}_end"] = row[f"cdr{i}_aa_{j}_start"] + len( |
|
row[f"cdr{i}_aa_{j}"] |
|
) |
|
return row |
|
|
|
run_data = run_data.apply(calc_cdr_coordinates, axis=1) |
|
run_data.insert( |
|
0, "pair_id", run_id + "_" + run_data.reset_index().index.map(str) |
|
) |
|
list_of_df.append(run_data) |
|
species_df = pd.concat(list_of_df, ignore_index=True) |
|
print(f"{species} output summary:") |
|
print(species_df.head()) |
|
print(species_df.shape) |
|
|
|
output_file_name = os.path.join(output_path, "train.csv") |
|
print(f"Creating {output_file_name}") |
|
species_df.to_csv(output_file_name, index=False, compression="zip") |
|
|
|
|
|
zip_name = species + ".zip" |
|
with ZipFile(zip_name, "w") as myzip: |
|
myzip.write("train.csv") |
|
s3.upload_file(zip_name, S3_BUCKET, os.path.join(S3_PREFIX, zip_name)) |
|
os.remove(output_file_name) |
|
os.remove(zip_name) |
|
|
|
|
