| import os |
| from Bio import SeqIO |
| from tqdm.auto import tqdm |
| import pandas as pd |
| from huggingface_hub import HfApi |
|
|
|
|
| aav_files = [ |
| "des_mut", |
| "low_vs_high", |
| "mut_des", |
| "one_vs_many", |
| "sampled", |
| "seven_vs_many", |
| "two_vs_many", |
| ] |
|
|
|
|
| meltome_files = [ |
| "human", |
| "human_cell", |
| "mixed_split", |
| ] |
|
|
|
|
| sav_files = [ |
| "human", |
| "only_savs", |
| "mixed", |
| ] |
|
|
|
|
| scl_files = [ |
| "balanced", |
| "human_hard", |
| "human_soft", |
| "mixed_hard", |
| "mixed_soft", |
| ] |
|
|
|
|
| gb1_files = [ |
| "low_vs_high", |
| "one_vs_rest", |
| "sampled", |
| "three_vs_rest", |
| "two_vs_rest", |
| ] |
|
|
|
|
| def download_wget(filename, repo): |
| if os.path.exists(f"{filename}.fasta"): |
| return |
| url = f"http://data.bioembeddings.com/public/FLIP/fasta/{repo}/{filename}.fasta" |
| os.system(f"wget {url}") |
|
|
|
|
| def upload_aav(): |
| repo = "aav" |
| for filename in aav_files: |
| download_wget(filename, repo) |
| fasta_file = f"{filename}.fasta" |
| csv_file = f"{filename}.csv" |
| db = SeqIO.index(fasta_file, "fasta") |
| output = [] |
|
|
| for _, record in tqdm(db.items()): |
| description = record.description |
| description = description.split() |
| sequence = str(record.seq) |
| seqid = description[0] |
| label = float(description[1].split("=")[1]) |
| split = description[2].split("=")[1] |
| validation = description[3].split("=")[1] |
|
|
| output.append({ |
| "seqid": seqid, |
| "label": label, |
| "sequence": sequence, |
| "split": split.lower(), |
| "validation": validation.lower(), |
| }) |
| pd.DataFrame(output).to_csv(csv_file, index=False) |
|
|
| api = HfApi() |
| api.create_repo( |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| exist_ok=True, |
| ) |
| api.upload_file( |
| path_or_fileobj=csv_file, |
| path_in_repo=csv_file, |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| ) |
| os.system(f"rm -rf {fasta_file}") |
| os.system(f"rm -rf {csv_file}") |
|
|
|
|
| def upload_meltome(): |
| repo = "meltome" |
| for filename in meltome_files: |
| download_wget(filename, repo) |
| fasta_file = f"{filename}.fasta" |
| csv_file = f"{filename}.csv" |
| db = SeqIO.index(fasta_file, "fasta") |
| output = [] |
| for _, record in tqdm(db.items()): |
| description = record.description |
| description = description.split() |
| sequence = str(record.seq) |
| seqid = description[0] |
| label = float(description[1].split("=")[1]) |
| split = description[2].split("=")[1] |
| validation = description[3].split("=")[1] |
|
|
| output.append({ |
| "seqid": seqid, |
| "label": label, |
| "sequence": sequence, |
| "split": split.lower(), |
| "validation": validation.lower(), |
| }) |
| pd.DataFrame(output).to_csv(csv_file, index=False) |
|
|
| api = HfApi() |
| api.create_repo( |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| exist_ok=True, |
| ) |
| api.upload_file( |
| path_or_fileobj=csv_file, |
| path_in_repo=csv_file, |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| ) |
| os.system(f"rm -rf {fasta_file}") |
| os.system(f"rm -rf {csv_file}") |
|
|
|
|
| def upload_sav(): |
| repo = "sav" |
| for filename in sav_files: |
| download_wget(filename, repo) |
| fasta_file = f"{filename}.fasta" |
| csv_file = f"{filename}.csv" |
| db = SeqIO.index(fasta_file, "fasta") |
| output = [] |
| for _, record in tqdm(db.items()): |
| description = record.description |
| description = description.split() |
| sequence = str(record.seq) |
| seqid = description[0] |
| |
| label = description[1].split("=")[1] |
| split = description[2].split("=")[1] |
| validation = description[3].split("=")[1] |
|
|
| output.append({ |
| "seqid": seqid, |
| "label": label, |
| "sequence": sequence, |
| "split": split.lower(), |
| "validation": validation.lower(), |
| }) |
| pd.DataFrame(output).to_csv(csv_file, index=False) |
| api = HfApi() |
| api.create_repo( |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| exist_ok=True, |
| ) |
| api.upload_file( |
| path_or_fileobj=csv_file, |
| path_in_repo=csv_file, |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| ) |
| os.system(f"rm -rf {fasta_file}") |
| os.system(f"rm -rf {csv_file}") |
|
|
|
|
| def upload_scl(): |
| repo = "scl" |
| for filename in scl_files: |
| download_wget(filename, repo) |
| fasta_file = f"{filename}.fasta" |
| csv_file = f"{filename}.csv" |
| db = SeqIO.index(fasta_file, "fasta") |
| output = [] |
| for _, record in tqdm(db.items()): |
| description = record.description |
| description = description.split() |
| sequence = str(record.seq) |
| seqid = description[0] |
| |
| label = description[1].split("=")[1] |
| split = description[2].split("=")[1] |
| validation = description[3].split("=")[1] |
|
|
| output.append({ |
| "seqid": seqid, |
| "label": label, |
| "sequence": sequence, |
| "split": split.lower(), |
| "validation": validation.lower(), |
| }) |
| pd.DataFrame(output).to_csv(csv_file, index=False) |
| api = HfApi() |
| api.create_repo( |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| exist_ok=True, |
| ) |
| api.upload_file( |
| path_or_fileobj=csv_file, |
| path_in_repo=csv_file, |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| ) |
| os.system(f"rm -rf {fasta_file}") |
| os.system(f"rm -rf {csv_file}") |
|
|
|
|
| def upload_gb1(): |
| repo = "gb1" |
| for filename in gb1_files: |
| download_wget(filename, repo) |
| fasta_file = f"{filename}.fasta" |
| csv_file = f"{filename}.csv" |
| db = SeqIO.index(fasta_file, "fasta") |
| output = [] |
| for _, record in tqdm(db.items()): |
| description = record.description |
| description = description.split() |
| sequence = str(record.seq) |
| seqid = description[0] |
| label = float(description[1].split("=")[1]) |
| split = description[2].split("=")[1] |
| validation = description[3].split("=")[1] |
|
|
| output.append({ |
| "seqid": seqid, |
| "label": label, |
| "sequence": sequence, |
| "split": split.lower(), |
| "validation": validation.lower(), |
| }) |
| pd.DataFrame(output).to_csv(csv_file, index=False) |
| api = HfApi() |
| api.create_repo( |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| exist_ok=True, |
| ) |
| api.upload_file( |
| path_or_fileobj=csv_file, |
| path_in_repo=csv_file, |
| repo_id=f"hazemessam/{repo}", |
| repo_type="dataset", |
| ) |
| os.system(f"rm -rf {fasta_file}") |
| os.system(f"rm -rf {csv_file}") |
|
|
|
|
| if __name__ == "__main__": |
| upload_gb1() |
| upload_meltome() |
| upload_sav() |
| upload_scl() |
| upload_aav() |
|
|
