| import cellxgene_census |
| import pandas as pd |
| import numpy as np |
| from data_config import VERSION |
| from typing import List |
| import os |
| import argparse |
|
|
|
|
| parser = argparse.ArgumentParser( |
| description='Download a given partition cell of the query in h5ad') |
|
|
| parser.add_argument("--query-name", |
| type=str, |
| required=True, |
| help="query name to build the index", |
| ) |
|
|
| parser.add_argument("--partition-idx", |
| type=int, |
| required=True, |
| help="partition index to download", |
| ) |
| parser.add_argument("--output-dir", |
| type=str, |
| required=True, |
| help="Directory to store the output h4ad file", |
| ) |
|
|
| parser.add_argument("--index-dir", |
| type=str, |
| required=True, |
| help="Directory to find the index file", |
| ) |
|
|
| parser.add_argument("--max-partition-size", |
| type=int, |
| required=True, |
| help="The max partition size for each partition(chunk)", |
| ) |
|
|
|
|
| args = parser.parse_args() |
|
|
| |
|
|
|
|
|
|
|
|
| def define_partition(partition_idx, id_list, partition_size) -> List[str]: |
| """ |
| This function is used to define the partition for each job |
| |
| partition_idx is the partition index, which is an integer, and 0 <= partition_idx <= len(id_list) // MAX_PARTITION_SIZE |
| """ |
| i = partition_idx * partition_size |
| return id_list[i:i + partition_size] |
|
|
|
|
| def load2list(query_name, soma_id_dir) -> List[int]: |
| """ |
| This function is used to load the idx list from file |
| """ |
| file_path = os.path.join(soma_id_dir, f"{query_name}.idx") |
| with open(file_path, 'r') as fp: |
| idx_list = fp.readlines() |
| idx_list = [int(x.strip()) for x in idx_list] |
| return idx_list |
|
|
| def download_partition(partition_idx, query_name, output_dir, index_dir, partition_size): |
| """ |
| This function is used to download the partition_idx partition of the query_name |
| """ |
| |
| id_list = load2list(query_name, index_dir) |
| id_partition = define_partition(partition_idx, id_list, partition_size) |
| with cellxgene_census.open_soma(census_version=VERSION) as census: |
| adata = cellxgene_census.get_anndata(census, |
| organism="Homo sapiens", |
| obs_coords=id_partition, |
| ) |
| |
| query_dir = os.path.join(output_dir, query_name) |
| if not os.path.exists(query_dir): |
| os.makedirs(query_dir) |
| query_adata_path = os.path.join(query_dir, f"partition_{partition_idx}.h5ad") |
| adata.write_h5ad(query_adata_path) |
| return query_adata_path |
|
|
| def del_partition(partition_idx, query_name, output_dir, index_dir, partition_size): |
| query_dir = os.path.join(output_dir, query_name) |
| query_adata_path = os.path.join(query_dir, f"partition_{partition_idx}.h5ad") |
| os.remove(query_adata_path) |
|
|
|
|
| if __name__ == "__main__": |
|
|
| download_partition(partition_idx=args.partition_idx, |
| query_name=args.query_name, |
| output_dir=args.output_dir, |
| index_dir=args.index_dir, |
| partition_size=args.max_partition_size |
| ) |
