{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"code","source":"import scanpy as sc\nimport anndata as ad\nimport episcanpy\nimport pandas as pd","metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"adata_atac = pd.read_hdf(\"../input/open-problems-multimodal/train_multi_inputs.h5\")\n\nadata_atac = sc.AnnData(adata_atac)\n\n# sort peaks position, required by episcanpy\nadata_atac = adata_atac[:,sorted(adata_atac.var_names)]\n\nadata_atac.var_names_make_unique()\n\nvar_list = []\nfor i in adata_atac.var_names:\n    new_i=i.replace('-', '_').replace(':','_')\n    var_list.append(new_i)","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"adata_atac.var_names = var_list \n\nadata_new = episcanpy.tl.geneactivity(adata_atac, gtf_file = \"gencode.vM30.annotation.gtf\",annotation='HAVANA')","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"adata_new.write_h5ad('train_multi_ga.h5ad')","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"adata_atac = pd.read_hdf(\"../input/open-problems-multimodal/test_multi_inputs.h5\")\n\nadata_atac = sc.AnnData(adata_atac)\n\n# sort peaks position, required by episcanpy\nadata_atac = adata_atac[:,sorted(adata_atac.var_names)]\n\nadata_atac.var_names_make_unique()\n\nvar_list = []\nfor i in adata_atac.var_names:\n    new_i=i.replace('-', '_').replace(':','_')\n    var_list.append(new_i)","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"adata_atac.var_names = var_list \n\nadata_new = episcanpy.tl.geneactivity(adata_atac, gtf_file = \"gencode.vM30.annotation.gtf\",annotation='HAVANA')","metadata":{},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"adata_new.write_h5ad('test_multi_ga.h5ad')","metadata":{},"execution_count":null,"outputs":[]}]}