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   "source": [
    "#### convert seurat to scanpy\n",
    "\n",
    "singlecell seurat(RDS) to scanpy(h5ad) \n",
    "\n",
    "* R code\n",
    "\n",
    "```R\n",
    "library(Seurat)\n",
    "library(SeuratDisk)\n",
    "\n",
    "srt <- readRDS('subDC.rds')\n",
    "\n",
    "# convert factor to character \n",
    "i <- sapply(srt@meta.data, is.factor)\n",
    "srt@meta.data[i] <- lapply(srt@meta.data[i], as.character)\n",
    "\n",
    "DefaultAssay(srt) <- 'RNA' # set default assay\n",
    "\n",
    "\n",
    "SaveH5Seurat(srt, filename = 'srt.h5seurat', overwrite = TRUE)\n",
    "# if SaveH5Seurat get err: \n",
    "# Object too old to save, please update your Seurat object to at least v3.1.2 using UpdateSeuratObject\n",
    "# srt <- UpdateSeuratObject(srt)\n",
    "\n",
    "Convert('srt.h5seurat','srt.h5ad', assay='RNA', overwrite = TRUE)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# download test data\n",
    "```shell\n",
    "curl -o local.rds \"https://corpora-data-prod.s3.amazonaws.com/6deef5dc-d572-4990-971d-b0380850ea55/local.rds?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=ASIATLYQ5N5XTBTXPXTJ%2F20221213%2Fus-west-2%2Fs3%2Faws4_request&X-Amz-Date=20221213T024129Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Security-Token=IQoJb3JpZ2luX2VjEIb%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJIMEYCIQCbLFp40OW8T47mtmQF560aKt8j3nv1KTI2lB%2FmbuUMuQIhAMIcHizLCt0M%2BYr7Rb63hLM4Dx4jbcNaeP2m90KJDbW1KvQDCK%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEQARoMMjMxNDI2ODQ2NTc1IgxqTq9d1N0QQSHNnu0qyAMzuvesva8WIsuIpaTgLk%2BUhus3cnrycc0Q%2F%2BKF9DUYmW7MIIBu20dkqvVw9ZAeqXHoiVn7YHG21gytN4AZFqPv7aeuD%2FPM6mgUgBzUDRQHvFznNdd8%2FNTqwT0obN9ULKbyhj%2BtR1U8SG4gaAJpqayit8LfYNkg9rAk8xYEN6V%2BfSl8DywC%2BNCkaMfGa0MO3uVXv6Zw%2FZCvfKoLkQol8TOhIaB77P2w4%2F68THY7ET9Um9vIkTR44fSw%2Fs0eNt2nFe9PxcM%2B2JfrsQg%2BdRKXCztwq08Ak5YhRYDDAlcGkC%2Bg1elay0VbFftBrDQJaW9rPvIkyWp1TFzCXBP3x3ZnU0gSew2h7A05%2BTsDtAMkYDiEHGubT65fIOQ6e0z4FFFK2UmaZfqjXd3VIreh2pNY98LFQ0LiFEFWbUA8mpXzEYrvHiElFmQoPXOQ8RNCYn%2BQZAaPd6TmbqPHsrQhL9MN7JHm%2BcQkjJAB%2BIeAf4PSTHEcyr4Ja70a5BaEPJIAICxjIgAEQW%2BYk5oUuzRpjVzNFDtiKD99Ia%2F5hna%2B%2BOwEKiO6D%2F9n0e%2F1IMQ2XnFBv%2FM%2B5cHSMKEQ8wpV3FizwvI7yVRSjGgEBG3F5ykwxcvenAY6pAHJRSf5Q7vwtVMCCaKoDxD4C5XJzj6NV2V2XPnugcvg5vNaBcN2N9mxD%2B5X19FwM%2BkQ9%2FOVylXh20zIKtiDlMy9RGFoO2jNnf5mfQMXKD8Q7i8nK8F11Bw949QL69dY2fQJX5T%2Be8EeA8JPPIn3k14Hhru3iQTQmb9OVyOU8R3c9BC4qkwldkVSW8k3iMsu0OM%2BCEGxw0pCxkKBZZp1FW9BI8MFYA%3D%3D&X-Amz-Signature=66a9478d223bd6f0947a23594df48447f2628d2130ec9f0316d6c14f7ac3ce99\"\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Validating object structure\n",
      "\n",
      "Updating object slots\n",
      "\n",
      "Ensuring keys are in the proper strucutre\n",
      "\n",
      "Ensuring feature names don't have underscores or pipes\n",
      "\n",
      "Object representation is consistent with the most current Seurat version\n",
      "\n",
      "Creating h5Seurat file for version 3.1.5.9900\n",
      "\n",
      "Adding counts for RNA\n",
      "\n",
      "Adding data for RNA\n",
      "\n",
      "No variable features found for RNA\n",
      "\n",
      "Adding feature-level metadata for RNA\n",
      "\n",
      "Adding cell embeddings for pca\n",
      "\n",
      "No loadings for pca\n",
      "\n",
      "No projected loadings for pca\n",
      "\n",
      "No standard deviations for pca\n",
      "\n",
      "No JackStraw data for pca\n",
      "\n",
      "Adding cell embeddings for umap\n",
      "\n",
      "No loadings for umap\n",
      "\n",
      "No projected loadings for umap\n",
      "\n",
      "No standard deviations for umap\n",
      "\n",
      "No JackStraw data for umap\n",
      "\n",
      "Validating h5Seurat file\n",
      "\n",
      "Adding data from RNA as X\n",
      "\n",
      "Transfering meta.features to var\n",
      "\n",
      "Adding counts from RNA as raw\n",
      "\n",
      "Transfering meta.features to raw/var\n",
      "\n",
      "Transfering meta.data to obs\n",
      "\n",
      "Adding dimensional reduction information for pca\n",
      "\n",
      "Adding dimensional reduction information for umap\n",
      "\n"
     ]
    }
   ],
   "source": [
    "library(Seurat)\n",
    "library(SeuratDisk)\n",
    "srt <- readRDS('/Users/yuanzan/Downloads/local.1.rds')\n",
    "i <- sapply(srt@meta.data, is.factor)\n",
    "srt@meta.data[i] <- lapply(srt@meta.data[i], as.character)\n",
    "DefaultAssay(srt) <- 'RNA'\n",
    "\n",
    "srt <- UpdateSeuratObject(srt)\n",
    "SaveH5Seurat(srt, filename = 'kidney_tumors.h5seurat', overwrite = TRUE)\n",
    "Convert('kidney_tumors.h5seurat','kidney_tumors.h5ad', assay='RNA', overwrite = TRUE)"
   ]
  }
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