From ed17ac59c1b4c86b1b69f0f7418d51d221685228 Mon Sep 17 00:00:00 2001 From: Starlitnightly Date: Wed, 18 Dec 2024 17:22:40 +0800 Subject: [PATCH] remove require of wget --- omicverse/externel/VIA/datasets_via.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/omicverse/externel/VIA/datasets_via.py b/omicverse/externel/VIA/datasets_via.py index 1f30533..7f0049d 100644 --- a/omicverse/externel/VIA/datasets_via.py +++ b/omicverse/externel/VIA/datasets_via.py @@ -1,7 +1,7 @@ import pandas as pd import scanpy as sc from scanpy import read -import wget + import os from scipy.io import loadmat @@ -91,7 +91,7 @@ def toy_multifurcating(foldername="./"): # read files as pandas objects data_path = foldername + "toy_multifurcating_M8_n1000d1000.csv" ids_path = foldername + "toy_multifurcating_M8_n1000d1000_ids_with_truetime.csv" - + import wget if not os.path.isfile(data_path): data_url = "https://raw.githubusercontent.com/ShobiStassen/VIA/master/Datasets/toy_multifurcating_M8_n1000d1000.csv" wget.download(data_url, data_path) @@ -133,7 +133,7 @@ def toy_disconnected(foldername="./"): # read files as pandas objects data_path = foldername + "toy_disconnected_M9_n1000d1000.csv" ids_path = foldername + "toy_disconnected_M9_n1000d1000_ids_with_truetime.csv" - + import wget if not os.path.isfile(data_path): data_url = "https://raw.githubusercontent.com/ShobiStassen/VIA/master/Datasets/toy_disconnected_M9_n1000d1000.csv" wget.download(data_url, data_path) @@ -165,7 +165,7 @@ def cell_cycle_cyto_data(foldername="./"): :return: anndata ''' - + import wget data_path = foldername + "cell_cycle_cyto.h5ad" if not os.path.isfile(data_path): ids_url = "https://raw.githubusercontent.com/ShobiStassen/VIA/master/Datasets/cell_cycle_cyto.h5ad" @@ -192,7 +192,7 @@ def scRNA_hematopoiesis(foldername="./"): # read files as pandas objects data_path = foldername + "human_cd34_bm_rep1.h5ad" ids_path = foldername + "Nover_Cor_PredFine_notLogNorm.csv" - + import wget if not os.path.isfile(data_path): data_url = "https://docs.google.com/uc?id=1ZSZbMeTQQPfPBGcnfUNDNL4om98UiNcO" gdown.download(data_url, data_path, quiet=False) @@ -243,7 +243,7 @@ def scATAC_hematopoiesis(foldername="./"): """ # read files as pandas objects data_path = foldername + "scATAC_hemato_Buenrostro.csv" - + import wget if not os.path.isfile(data_path): data_url = "https://raw.githubusercontent.com/ShobiStassen/VIA/master/Datasets/scATAC_hemato_Buenrostro.csv" wget.download(data_url, data_path) @@ -290,7 +290,7 @@ def cell_cycle(foldername="./"): # read files as pandas objects data_path = foldername + "mcf7_38features.csv" ids_path = foldername + "mcf7_phases.csv" - + import wget if not os.path.isfile(data_path): data_url = "https://raw.githubusercontent.com/ShobiStassen/VIA/master/Datasets/mcf7_38features.csv" wget.download(data_url, data_path) @@ -325,7 +325,7 @@ def embryoid_body(foldername="./"): # read files as pandas objects data_path = foldername + "EBdata.mat" emb_path = foldername + "EB_phate_embedding.csv" - + import wget if not os.path.isfile(data_path): data_url = "https://docs.google.com/uc?id=1yz3zR1KAmghjYB_nLLUZoIlKN9Ew4RHf" gdown.download(data_url, data_path, quiet=False)