{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "f7a76e42",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2025-03-25T06:05:01.795964Z"
    }
   },
   "outputs": [],
   "source": [
    "import sys\n",
    "import os\n",
    "sys.path.append(os.path.abspath(os.path.join(os.getcwd(), '../..')))\n",
    "\n",
    "# Path Configuration\n",
    "from tools.preprocess import *\n",
    "\n",
    "# Processing context\n",
    "trait = \"Pancreatic_Cancer\"\n",
    "cohort = \"GSE120127\"\n",
    "\n",
    "# Input paths\n",
    "in_trait_dir = \"../../input/GEO/Pancreatic_Cancer\"\n",
    "in_cohort_dir = \"../../input/GEO/Pancreatic_Cancer/GSE120127\"\n",
    "\n",
    "# Output paths\n",
    "out_data_file = \"../../output/preprocess/Pancreatic_Cancer/GSE120127.csv\"\n",
    "out_gene_data_file = \"../../output/preprocess/Pancreatic_Cancer/gene_data/GSE120127.csv\"\n",
    "out_clinical_data_file = \"../../output/preprocess/Pancreatic_Cancer/clinical_data/GSE120127.csv\"\n",
    "json_path = \"../../output/preprocess/Pancreatic_Cancer/cohort_info.json\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5f101a18",
   "metadata": {},
   "source": [
    "### Step 1: Initial Data Loading"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3d053d5f",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:05:01.797707Z",
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     "shell.execute_reply": "2025-03-25T06:05:01.869416Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Background Information:\n",
      "!Series_title\t\"Role of BAP1 in pancreatic cancer\"\n",
      "!Series_summary\t\"This SuperSeries is composed of the SubSeries listed below.\"\n",
      "!Series_overall_design\t\"Refer to individual Series\"\n",
      "Sample Characteristics Dictionary:\n",
      "{0: ['cell line: pancreatic cancer cell line PANC-1'], 1: ['genotype: Wildtype', 'genotype: BAP1 deletion (sgBAP1)'], 2: ['treatment: Control', 'treatment: IR (10Gy)']}\n"
     ]
    }
   ],
   "source": [
    "from tools.preprocess import *\n",
    "# 1. Identify the paths to the SOFT file and the matrix file\n",
    "soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n",
    "\n",
    "# 2. Read the matrix file to obtain background information and sample characteristics data\n",
    "background_prefixes = ['!Series_title', '!Series_summary', '!Series_overall_design']\n",
    "clinical_prefixes = ['!Sample_geo_accession', '!Sample_characteristics_ch1']\n",
    "background_info, clinical_data = get_background_and_clinical_data(matrix_file, background_prefixes, clinical_prefixes)\n",
    "\n",
    "# 3. Obtain the sample characteristics dictionary from the clinical dataframe\n",
    "sample_characteristics_dict = get_unique_values_by_row(clinical_data)\n",
    "\n",
    "# 4. Explicitly print out all the background information and the sample characteristics dictionary\n",
    "print(\"Background Information:\")\n",
    "print(background_info)\n",
    "print(\"Sample Characteristics Dictionary:\")\n",
    "print(sample_characteristics_dict)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "880423ea",
   "metadata": {},
   "source": [
    "### Step 2: Dataset Analysis and Clinical Feature Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "d76e6dc3",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:05:01.871006Z",
     "iopub.status.busy": "2025-03-25T06:05:01.870895Z",
     "iopub.status.idle": "2025-03-25T06:05:01.878155Z",
     "shell.execute_reply": "2025-03-25T06:05:01.877868Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Clinical Data Preview:\n",
      "{'GSM3392980': [nan, nan], 'GSM3392981': [nan, nan], 'GSM3392982': [nan, nan], 'GSM3392983': [nan, nan], 'GSM3392984': [nan, nan], 'GSM3392985': [nan, nan], 'GSM3392986': [nan, nan], 'GSM3392987': [nan, nan]}\n",
      "Clinical data saved to ../../output/preprocess/Pancreatic_Cancer/clinical_data/GSE120127.csv\n"
     ]
    }
   ],
   "source": [
    "# 1. Gene Expression Data Availability\n",
    "# Based on the background info, this appears to be a study of pancreatic cancer cell lines\n",
    "# with gene expression data comparing wild type and knockout conditions\n",
    "is_gene_available = True\n",
    "\n",
    "# 2.1 Data Availability\n",
    "# Looking at the sample characteristics:\n",
    "# Row 0: Sex data is available\n",
    "# Row 1: Contains cell line info, not variable between samples\n",
    "# Row 2: Contains genotype info that indicates pancreatic cancer samples with different genotypes\n",
    "\n",
    "# For trait (Pancreatic_Cancer):\n",
    "# All samples are pancreatic cancer cell lines, so there is no control vs. disease distinction\n",
    "# Row 2 contains genotype information which we can use to differentiate samples by BAP1 status\n",
    "trait_row = 2\n",
    "\n",
    "# For age:\n",
    "# No age information is available in the sample characteristics\n",
    "age_row = None\n",
    "\n",
    "# For gender:\n",
    "# Row 0 contains sex information\n",
    "gender_row = 0\n",
    "\n",
    "# 2.2 Data Type Conversion\n",
    "def convert_trait(value):\n",
    "    \"\"\"\n",
    "    Convert genotype information to binary values:\n",
    "    1 for BAP1 knockout (KO) samples\n",
    "    0 for BAP1 wild-type (WT) samples\n",
    "    \"\"\"\n",
    "    if value is None:\n",
    "        return None\n",
    "    \n",
    "    # Extract value after colon if present\n",
    "    if \":\" in value:\n",
    "        value = value.split(\":\", 1)[1].strip()\n",
    "    \n",
    "    # Convert based on BAP1 status\n",
    "    if \"Bap1 KO\" in value:\n",
    "        return 1  # BAP1 knockout\n",
    "    elif \"Bap1 WT\" in value:\n",
    "        return 0  # BAP1 wild-type\n",
    "    else:\n",
    "        return None\n",
    "\n",
    "def convert_gender(value):\n",
    "    \"\"\"\n",
    "    Convert gender information to binary values:\n",
    "    0 for female\n",
    "    1 for male\n",
    "    \"\"\"\n",
    "    if value is None:\n",
    "        return None\n",
    "    \n",
    "    # Extract value after colon if present\n",
    "    if \":\" in value:\n",
    "        value = value.split(\":\", 1)[1].strip()\n",
    "    \n",
    "    # Convert based on sex\n",
    "    if value.upper() in [\"F\", \"FEMALE\"]:\n",
    "        return 0\n",
    "    elif value.upper() in [\"M\", \"MALE\"]:\n",
    "        return 1\n",
    "    else:\n",
    "        return None\n",
    "\n",
    "# Age conversion function (not used but defined for completeness)\n",
    "def convert_age(value):\n",
    "    \"\"\"Placeholder function as age data is not available\"\"\"\n",
    "    return None\n",
    "\n",
    "# 3. Save Metadata\n",
    "# Check if trait data is available (trait_row is not None)\n",
    "is_trait_available = trait_row is not None\n",
    "\n",
    "# Initial validation and saving of cohort information\n",
    "validate_and_save_cohort_info(\n",
    "    is_final=False,\n",
    "    cohort=cohort,\n",
    "    info_path=json_path,\n",
    "    is_gene_available=is_gene_available,\n",
    "    is_trait_available=is_trait_available\n",
    ")\n",
    "\n",
    "# 4. Clinical Feature Extraction\n",
    "# We only proceed if trait_row is not None\n",
    "if trait_row is not None:\n",
    "    # Extract clinical features using the library function\n",
    "    clinical_df = geo_select_clinical_features(\n",
    "        clinical_df=clinical_data,\n",
    "        trait=trait,\n",
    "        trait_row=trait_row,\n",
    "        convert_trait=convert_trait,\n",
    "        age_row=age_row,\n",
    "        convert_age=convert_age,\n",
    "        gender_row=gender_row,\n",
    "        convert_gender=convert_gender\n",
    "    )\n",
    "    \n",
    "    # Preview the extracted clinical data\n",
    "    preview = preview_df(clinical_df)\n",
    "    print(\"Clinical Data Preview:\")\n",
    "    print(preview)\n",
    "    \n",
    "    # Save the clinical data to the specified output file\n",
    "    # Create directory if it doesn't exist\n",
    "    os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n",
    "    clinical_df.to_csv(out_clinical_data_file, index=False)\n",
    "    print(f\"Clinical data saved to {out_clinical_data_file}\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c1f93cef",
   "metadata": {},
   "source": [
    "### Step 3: Gene Data Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "42690966",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:05:01.879125Z",
     "iopub.status.busy": "2025-03-25T06:05:01.879024Z",
     "iopub.status.idle": "2025-03-25T06:05:01.928379Z",
     "shell.execute_reply": "2025-03-25T06:05:01.928015Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Index(['11715100_at', '11715101_s_at', '11715102_x_at', '11715103_x_at',\n",
      "       '11715104_s_at', '11715105_at', '11715106_x_at', '11715107_s_at',\n",
      "       '11715108_x_at', '11715109_at', '11715110_at', '11715111_s_at',\n",
      "       '11715112_at', '11715113_x_at', '11715114_x_at', '11715115_s_at',\n",
      "       '11715116_s_at', '11715117_x_at', '11715118_s_at', '11715119_s_at'],\n",
      "      dtype='object', name='ID')\n"
     ]
    }
   ],
   "source": [
    "# 1. Use the get_genetic_data function from the library to get the gene_data from the matrix_file previously defined.\n",
    "gene_data = get_genetic_data(matrix_file)\n",
    "\n",
    "# 2. Print the first 20 row IDs (gene or probe identifiers) for future observation.\n",
    "print(gene_data.index[:20])\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "711c5fa7",
   "metadata": {},
   "source": [
    "### Step 4: Gene Identifier Review"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "8c3b0b3d",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:05:01.929551Z",
     "iopub.status.busy": "2025-03-25T06:05:01.929444Z",
     "iopub.status.idle": "2025-03-25T06:05:01.931236Z",
     "shell.execute_reply": "2025-03-25T06:05:01.930971Z"
    }
   },
   "outputs": [],
   "source": [
    "# These identifiers appear to be numerical IDs (starting with \"17200...\") rather than standard human gene symbols\n",
    "# Human gene symbols typically look like \"BRCA1\", \"TP53\", \"KRAS\", etc.\n",
    "# These are likely probe IDs or some other platform-specific identifiers that need mapping to gene symbols\n",
    "\n",
    "requires_gene_mapping = True\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0dfbb388",
   "metadata": {},
   "source": [
    "### Step 5: Gene Annotation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "e977a26b",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:05:01.932260Z",
     "iopub.status.busy": "2025-03-25T06:05:01.932164Z",
     "iopub.status.idle": "2025-03-25T06:05:08.812384Z",
     "shell.execute_reply": "2025-03-25T06:05:08.812013Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Gene annotation preview:\n",
      "{'ID': ['11715100_at', '11715101_s_at', '11715102_x_at', '11715103_x_at', '11715104_s_at'], 'GeneChip Array': ['Human Genome PrimeView Array', 'Human Genome PrimeView Array', 'Human Genome PrimeView Array', 'Human Genome PrimeView Array', 'Human Genome PrimeView Array'], 'Species Scientific Name': ['Homo sapiens', 'Homo sapiens', 'Homo sapiens', 'Homo sapiens', 'Homo sapiens'], 'Annotation Date': ['30-Mar-16', '30-Mar-16', '30-Mar-16', '30-Mar-16', '30-Mar-16'], 'Sequence Type': ['Consensus sequence', 'Consensus sequence', 'Consensus sequence', 'Consensus sequence', 'Consensus sequence'], 'Sequence Source': ['Affymetrix Proprietary Database', 'Affymetrix Proprietary Database', 'Affymetrix Proprietary Database', 'Affymetrix Proprietary Database', 'Affymetrix Proprietary Database'], 'Transcript ID(Array Design)': ['g21264570', 'g21264570', 'g21264570', 'g22748780', 'g30039713'], 'Target Description': ['g21264570 /TID=g21264570 /CNT=1 /FEA=FLmRNA /TIER=FL /STK=0 /DEF=g21264570 /REP_ORG=Homo sapiens', 'g21264570 /TID=g21264570 /CNT=1 /FEA=FLmRNA /TIER=FL /STK=0 /DEF=g21264570 /REP_ORG=Homo sapiens', 'g21264570 /TID=g21264570 /CNT=1 /FEA=FLmRNA /TIER=FL /STK=0 /DEF=g21264570 /REP_ORG=Homo sapiens', 'g22748780 /TID=g22748780 /CNT=1 /FEA=FLmRNA /TIER=FL /STK=0 /DEF=g22748780 /REP_ORG=Homo sapiens', 'g30039713 /TID=g30039713 /CNT=1 /FEA=FLmRNA /TIER=FL /STK=0 /DEF=g30039713 /REP_ORG=Homo sapiens'], 'GB_ACC': [nan, nan, nan, nan, nan], 'GI': ['21264570', '21264570', '21264570', '22748780', '30039713'], 'Representative Public ID': ['g21264570', 'g21264570', 'g21264570', 'g22748780', 'g30039713'], 'Archival UniGene Cluster': ['---', '---', '---', '---', '---'], 'UniGene ID': ['Hs.247813', 'Hs.247813', 'Hs.247813', 'Hs.465643', 'Hs.352515'], 'Genome Version': ['February 2009 (Genome Reference Consortium GRCh37)', 'February 2009 (Genome Reference Consortium GRCh37)', 'February 2009 (Genome Reference Consortium GRCh37)', 'February 2009 (Genome Reference Consortium GRCh37)', 'February 2009 (Genome Reference Consortium GRCh37)'], 'Alignments': ['chr6:26271145-26271612 (-) // 100.0 // p22.2', 'chr6:26271145-26271612 (-) // 100.0 // p22.2', 'chr6:26271145-26271612 (-) // 100.0 // p22.2', 'chr19:4639529-5145579 (+) // 48.53 // p13.3', 'chr17:72920369-72929640 (+) // 100.0 // q25.1'], 'Gene Title': ['histone cluster 1, H3g', 'histone cluster 1, H3g', 'histone cluster 1, H3g', 'tumor necrosis factor, alpha-induced protein 8-like 1', 'otopetrin 2'], 'Gene Symbol': ['HIST1H3G', 'HIST1H3G', 'HIST1H3G', 'TNFAIP8L1', 'OTOP2'], 'Chromosomal Location': ['chr6p22.2', 'chr6p22.2', 'chr6p22.2', 'chr19p13.3', 'chr17q25.1'], 'Unigene Cluster Type': ['full length', 'full length', 'full length', 'full length', 'full length'], 'Ensembl': ['ENSG00000273983 /// OTTHUMG00000014436', 'ENSG00000273983 /// OTTHUMG00000014436', 'ENSG00000273983 /// OTTHUMG00000014436', 'ENSG00000185361 /// OTTHUMG00000182013', 'ENSG00000183034 /// OTTHUMG00000179215'], 'Entrez Gene': ['8355', '8355', '8355', '126282', '92736'], 'SwissProt': ['P68431', 'P68431', 'P68431', 'Q8WVP5', 'Q7RTS6'], 'EC': ['---', '---', '---', '---', '---'], 'OMIM': ['602815', '602815', '602815', '615869', '607827'], 'RefSeq Protein ID': ['NP_003525', 'NP_003525', 'NP_003525', 'NP_001161414 /// NP_689575 /// XP_005259544 /// XP_011525982', 'NP_835454 /// XP_011523781'], 'RefSeq Transcript ID': ['NM_003534', 'NM_003534', 'NM_003534', 'NM_001167942 /// NM_152362 /// XM_005259487 /// XM_011527680', 'NM_178160 /// XM_011525479'], 'Gene Ontology Biological Process': ['0000183 // chromatin silencing at rDNA // traceable author statement /// 0002230 // positive regulation of defense response to virus by host // inferred from mutant phenotype /// 0006325 // chromatin organization // traceable author statement /// 0006334 // nucleosome assembly // inferred from direct assay /// 0006334 // nucleosome assembly // inferred from mutant phenotype /// 0006335 // DNA replication-dependent nucleosome assembly // inferred from direct assay /// 0007264 // small GTPase mediated signal transduction // traceable author statement /// 0007596 // blood coagulation // traceable author statement /// 0010467 // gene expression // traceable author statement /// 0031047 // gene silencing by RNA // traceable author statement /// 0032776 // DNA methylation on cytosine // traceable author statement /// 0040029 // regulation of gene expression, epigenetic // traceable author statement /// 0044267 // cellular protein metabolic process // traceable author statement /// 0045814 // negative regulation of gene expression, epigenetic // traceable author statement /// 0051290 // protein heterotetramerization // inferred from direct assay /// 0060968 // regulation of gene silencing // inferred from direct assay /// 0098792 // xenophagy // inferred from mutant phenotype', '0000183 // chromatin silencing at rDNA // traceable author statement /// 0002230 // positive regulation of defense response to virus by host // inferred from mutant phenotype /// 0006325 // chromatin organization // traceable author statement /// 0006334 // nucleosome assembly // inferred from direct assay /// 0006334 // nucleosome assembly // inferred from mutant phenotype /// 0006335 // DNA replication-dependent nucleosome assembly // inferred from direct assay /// 0007264 // small GTPase mediated signal transduction // traceable author statement /// 0007596 // blood coagulation // traceable author statement /// 0010467 // gene expression // traceable author statement /// 0031047 // gene silencing by RNA // traceable author statement /// 0032776 // DNA methylation on cytosine // traceable author statement /// 0040029 // regulation of gene expression, epigenetic // traceable author statement /// 0044267 // cellular protein metabolic process // traceable author statement /// 0045814 // negative regulation of gene expression, epigenetic // traceable author statement /// 0051290 // protein heterotetramerization // inferred from direct assay /// 0060968 // regulation of gene silencing // inferred from direct assay /// 0098792 // xenophagy // inferred from mutant phenotype', '0000183 // chromatin silencing at rDNA // traceable author statement /// 0002230 // positive regulation of defense response to virus by host // inferred from mutant phenotype /// 0006325 // chromatin organization // traceable author statement /// 0006334 // nucleosome assembly // inferred from direct assay /// 0006334 // nucleosome assembly // inferred from mutant phenotype /// 0006335 // DNA replication-dependent nucleosome assembly // inferred from direct assay /// 0007264 // small GTPase mediated signal transduction // traceable author statement /// 0007596 // blood coagulation // traceable author statement /// 0010467 // gene expression // traceable author statement /// 0031047 // gene silencing by RNA // traceable author statement /// 0032776 // DNA methylation on cytosine // traceable author statement /// 0040029 // regulation of gene expression, epigenetic // traceable author statement /// 0044267 // cellular protein metabolic process // traceable author statement /// 0045814 // negative regulation of gene expression, epigenetic // traceable author statement /// 0051290 // protein heterotetramerization // inferred from direct assay /// 0060968 // regulation of gene silencing // inferred from direct assay /// 0098792 // xenophagy // inferred from mutant phenotype', '0032007 // negative regulation of TOR signaling // not recorded /// 0032007 // negative regulation of TOR signaling // inferred from sequence or structural similarity', '---'], 'Gene Ontology Cellular Component': ['0000228 // nuclear chromosome // inferred from direct assay /// 0000786 // nucleosome // inferred from direct assay /// 0000788 // nuclear nucleosome // inferred from direct assay /// 0005576 // extracellular region // traceable author statement /// 0005634 // nucleus // inferred from direct assay /// 0005654 // nucleoplasm // traceable author statement /// 0005694 // chromosome // inferred from electronic annotation /// 0016020 // membrane // inferred from direct assay /// 0043234 // protein complex // inferred from direct assay /// 0070062 // extracellular exosome // inferred from direct assay', '0000228 // nuclear chromosome // inferred from direct assay /// 0000786 // nucleosome // inferred from direct assay /// 0000788 // nuclear nucleosome // inferred from direct assay /// 0005576 // extracellular region // traceable author statement /// 0005634 // nucleus // inferred from direct assay /// 0005654 // nucleoplasm // traceable author statement /// 0005694 // chromosome // inferred from electronic annotation /// 0016020 // membrane // inferred from direct assay /// 0043234 // protein complex // inferred from direct assay /// 0070062 // extracellular exosome // inferred from direct assay', '0000228 // nuclear chromosome // inferred from direct assay /// 0000786 // nucleosome // inferred from direct assay /// 0000788 // nuclear nucleosome // inferred from direct assay /// 0005576 // extracellular region // traceable author statement /// 0005634 // nucleus // inferred from direct assay /// 0005654 // nucleoplasm // traceable author statement /// 0005694 // chromosome // inferred from electronic annotation /// 0016020 // membrane // inferred from direct assay /// 0043234 // protein complex // inferred from direct assay /// 0070062 // extracellular exosome // inferred from direct assay', '0005737 // cytoplasm // not recorded /// 0005737 // cytoplasm // inferred from sequence or structural similarity', '0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation'], 'Gene Ontology Molecular Function': ['0003677 // DNA binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction /// 0042393 // histone binding // inferred from physical interaction /// 0046982 // protein heterodimerization activity // inferred from electronic annotation', '0003677 // DNA binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction /// 0042393 // histone binding // inferred from physical interaction /// 0046982 // protein heterodimerization activity // inferred from electronic annotation', '0003677 // DNA binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction /// 0042393 // histone binding // inferred from physical interaction /// 0046982 // protein heterodimerization activity // inferred from electronic annotation', '0005515 // protein binding // inferred from physical interaction', '---'], 'Pathway': ['---', '---', '---', '---', '---'], 'InterPro': ['IPR007125 // Histone H2A/H2B/H3 // 9.3E-34 /// IPR007125 // Histone H2A/H2B/H3 // 1.7E-37', 'IPR007125 // Histone H2A/H2B/H3 // 9.3E-34 /// IPR007125 // Histone H2A/H2B/H3 // 1.7E-37', 'IPR007125 // Histone H2A/H2B/H3 // 9.3E-34 /// IPR007125 // Histone H2A/H2B/H3 // 1.7E-37', 'IPR008477 // Protein of unknown function DUF758 // 8.4E-86 /// IPR008477 // Protein of unknown function DUF758 // 6.8E-90', 'IPR004878 // Otopetrin // 9.4E-43 /// IPR004878 // Otopetrin // 9.4E-43 /// IPR004878 // Otopetrin // 9.4E-43 /// IPR004878 // Otopetrin // 3.9E-18 /// IPR004878 // Otopetrin // 3.8E-20 /// IPR004878 // Otopetrin // 5.2E-16'], 'Annotation Description': ['This probe set was annotated using the Matching Probes based pipeline to a Entrez Gene identifier using 4 transcripts. // false // Matching Probes // A', 'This probe set was annotated using the Matching Probes based pipeline to a Entrez Gene identifier using 4 transcripts. // false // Matching Probes // A', 'This probe set was annotated using the Matching Probes based pipeline to a Entrez Gene identifier using 4 transcripts. // false // Matching Probes // A', 'This probe set was annotated using the Matching Probes based pipeline to a Entrez Gene identifier using 9 transcripts. // false // Matching Probes // A', 'This probe set was annotated using the Matching Probes based pipeline to a Entrez Gene identifier using 6 transcripts. // false // Matching Probes // A'], 'Annotation Transcript Cluster': ['ENST00000614378(11),NM_003534(11),OTTHUMT00000040099(11),uc003nhi.3', 'ENST00000614378(11),NM_003534(11),OTTHUMT00000040099(11),uc003nhi.3', 'ENST00000614378(11),NM_003534(11),OTTHUMT00000040099(11),uc003nhi.3', 'BC017672(11),BC044250(9),ENST00000327473(11),ENST00000536716(11),NM_001167942(11),NM_152362(11),OTTHUMT00000458662(11),uc002max.3,uc021une.1', 'ENST00000331427(11),ENST00000580223(11),NM_178160(11),OTTHUMT00000445306(11),uc010wrp.2,XM_011525479(11)'], 'Transcript Assignments': ['ENST00000614378 // ensembl_havana_transcript:known chromosome:GRCh38:6:26269405:26271815:-1 gene:ENSG00000273983 gene_biotype:protein_coding transcript_biotype:protein_coding // ensembl // 11 // --- /// NM_003534 // Homo sapiens histone cluster 1, H3g (HIST1H3G), mRNA. // refseq // 11 // --- /// OTTHUMT00000040099 // otter:known chromosome:VEGA61:6:26269405:26271815:-1 gene:OTTHUMG00000014436 gene_biotype:protein_coding transcript_biotype:protein_coding // vega // 11 // --- /// uc003nhi.3 // --- // ucsc_genes // 11 // ---', 'ENST00000614378 // ensembl_havana_transcript:known chromosome:GRCh38:6:26269405:26271815:-1 gene:ENSG00000273983 gene_biotype:protein_coding transcript_biotype:protein_coding // ensembl // 11 // --- /// GENSCAN00000029819 // cdna:genscan chromosome:GRCh38:6:26270974:26271384:-1 transcript_biotype:protein_coding // ensembl // 11 // --- /// NM_003534 // Homo sapiens histone cluster 1, H3g (HIST1H3G), mRNA. // refseq // 11 // --- /// OTTHUMT00000040099 // otter:known chromosome:VEGA61:6:26269405:26271815:-1 gene:OTTHUMG00000014436 gene_biotype:protein_coding transcript_biotype:protein_coding // vega // 11 // --- /// uc003nhi.3 // --- // ucsc_genes // 11 // ---', 'ENST00000614378 // ensembl_havana_transcript:known chromosome:GRCh38:6:26269405:26271815:-1 gene:ENSG00000273983 gene_biotype:protein_coding transcript_biotype:protein_coding // ensembl // 11 // --- /// NM_003534 // Homo sapiens histone cluster 1, H3g (HIST1H3G), mRNA. // refseq // 11 // --- /// OTTHUMT00000040099 // otter:known chromosome:VEGA61:6:26269405:26271815:-1 gene:OTTHUMG00000014436 gene_biotype:protein_coding transcript_biotype:protein_coding // vega // 11 // --- /// uc003nhi.3 // --- // ucsc_genes // 11 // ---', 'BC017672 // Homo sapiens tumor necrosis factor, alpha-induced protein 8-like 1, mRNA (cDNA clone MGC:17791 IMAGE:3885999), complete cds. // gb // 11 // --- /// BC044250 // accn=BC044250 class=mRNAlike lncRNA name=Human lncRNA ref=JounralRNA transcriptId=673 cpcScore=-0.1526100 cnci=-0.1238602 // noncode // 9 // --- /// BC044250 // Homo sapiens tumor necrosis factor, alpha-induced protein 8-like 1, mRNA (cDNA clone IMAGE:5784807). // gb // 9 // --- /// ENST00000327473 // ensembl_havana_transcript:known chromosome:GRCh38:19:4639518:4655568:1 gene:ENSG00000185361 gene_biotype:protein_coding transcript_biotype:protein_coding // ensembl // 11 // --- /// ENST00000536716 // ensembl:known chromosome:GRCh38:19:4640017:4655568:1 gene:ENSG00000185361 gene_biotype:protein_coding transcript_biotype:protein_coding // ensembl // 11 // --- /// NM_001167942 // Homo sapiens tumor necrosis factor, alpha-induced protein 8-like 1 (TNFAIP8L1), transcript variant 1, mRNA. // refseq // 11 // --- /// NM_152362 // Homo sapiens tumor necrosis factor, alpha-induced protein 8-like 1 (TNFAIP8L1), transcript variant 2, mRNA. // refseq // 11 // --- /// NONHSAT060631 // Non-coding transcript identified by NONCODE: Exonic // noncode // 9 // --- /// OTTHUMT00000458662 // otter:known chromosome:VEGA61:19:4639518:4655568:1 gene:OTTHUMG00000182013 gene_biotype:protein_coding transcript_biotype:protein_coding // vega // 11 // --- /// uc002max.3 // --- // ucsc_genes // 11 // --- /// uc021une.1 // --- // ucsc_genes // 11 // ---', 'ENST00000331427 // ensembl:known chromosome:GRCh38:17:74924275:74933911:1 gene:ENSG00000183034 gene_biotype:protein_coding transcript_biotype:protein_coding // ensembl // 11 // --- /// ENST00000580223 // havana:known chromosome:GRCh38:17:74924603:74933912:1 gene:ENSG00000183034 gene_biotype:protein_coding transcript_biotype:protein_coding // ensembl // 11 // --- /// GENSCAN00000013715 // cdna:genscan chromosome:GRCh38:17:74924633:74933545:1 transcript_biotype:protein_coding // ensembl // 11 // --- /// NM_178160 // Homo sapiens otopetrin 2 (OTOP2), mRNA. // refseq // 11 // --- /// OTTHUMT00000445306 // otter:known chromosome:VEGA61:17:74924603:74933912:1 gene:OTTHUMG00000179215 gene_biotype:protein_coding transcript_biotype:protein_coding // vega // 11 // --- /// uc010wrp.2 // --- // ucsc_genes // 11 // --- /// XM_011525479 // PREDICTED: Homo sapiens otopetrin 2 (OTOP2), transcript variant X1, mRNA. // refseq // 11 // ---'], 'Annotation Notes': ['---', '---', 'GENSCAN00000029819 // ensembl // 4 // Cross Hyb Matching Probes', '---', '---'], 'SPOT_ID': [nan, nan, nan, nan, nan]}\n"
     ]
    }
   ],
   "source": [
    "# 1. Use the 'get_gene_annotation' function from the library to get gene annotation data from the SOFT file.\n",
    "gene_annotation = get_gene_annotation(soft_file)\n",
    "\n",
    "# 2. Use the 'preview_df' function from the library to preview the data and print out the results.\n",
    "print(\"Gene annotation preview:\")\n",
    "print(preview_df(gene_annotation))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "36d3c952",
   "metadata": {},
   "source": [
    "### Step 6: Gene Identifier Mapping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f156f894",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:05:08.813699Z",
     "iopub.status.busy": "2025-03-25T06:05:08.813577Z",
     "iopub.status.idle": "2025-03-25T06:05:08.960306Z",
     "shell.execute_reply": "2025-03-25T06:05:08.959813Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Mapped gene expression data: 19963 genes × 8 samples\n",
      "First few gene symbols:\n",
      "Index(['A1BG', 'A1CF', 'A2M', 'A2ML1', 'A3GALT2'], dtype='object', name='Gene')\n"
     ]
    }
   ],
   "source": [
    "# 1. Based on the gene identifiers in the gene expression data (numerical IDs starting with \"17200...\"),\n",
    "# and the gene annotation dataframe, we need to find the matching columns.\n",
    "# Looking at the annotation dataframe, the 'ID' column seems to contain probe IDs,\n",
    "# and 'Gene Symbol' column contains the gene symbols we need.\n",
    "\n",
    "# 2. Create a gene mapping dataframe using these two columns\n",
    "gene_mapping = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Gene Symbol')\n",
    "\n",
    "# 3. Apply gene mapping to convert probe-level data to gene expression data\n",
    "gene_data = apply_gene_mapping(gene_data, gene_mapping)\n",
    "\n",
    "# Print information about the resulting gene expression dataframe\n",
    "print(f\"Mapped gene expression data: {gene_data.shape[0]} genes × {gene_data.shape[1]} samples\")\n",
    "print(\"First few gene symbols:\")\n",
    "print(gene_data.index[:5])\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "905f3f21",
   "metadata": {},
   "source": [
    "### Step 7: Data Normalization and Linking"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "18e55e9b",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:05:08.961845Z",
     "iopub.status.busy": "2025-03-25T06:05:08.961642Z",
     "iopub.status.idle": "2025-03-25T06:05:15.394179Z",
     "shell.execute_reply": "2025-03-25T06:05:15.393803Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Normalized gene data saved to ../../output/preprocess/Pancreatic_Cancer/gene_data/GSE120127.csv\n",
      "Created dummy clinical data with shape: (1, 8)\n",
      "Linked data shape: (8, 19759)\n",
      "Using trait column: Pancreatic_Cancer\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Shape after handling missing values: (8, 19759)\n",
      "The trait is severely biased (all samples are pancreatic cancer).\n",
      "A new JSON file was created at: ../../output/preprocess/Pancreatic_Cancer/cohort_info.json\n",
      "Data quality check failed. Dataset lacks necessary trait variation for association studies.\n"
     ]
    }
   ],
   "source": [
    "# 1. Normalize gene symbols in the gene expression data\n",
    "normalized_gene_data = normalize_gene_symbols_in_index(gene_data)\n",
    "\n",
    "# Save the normalized gene data\n",
    "os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)\n",
    "normalized_gene_data.to_csv(out_gene_data_file)\n",
    "print(f\"Normalized gene data saved to {out_gene_data_file}\")\n",
    "\n",
    "# Since we determined in Step 2 that trait_row is None (no clinical variation)\n",
    "# and is_trait_available is False, we can't proceed with linking clinical and gene data\n",
    "# Instead, we need to create dummy clinical data with a constant trait value\n",
    "\n",
    "# Create minimal clinical dataframe with samples matching gene data\n",
    "sample_ids = normalized_gene_data.columns\n",
    "dummy_clinical_df = pd.DataFrame(index=['Pancreatic_Cancer'], \n",
    "                                  columns=sample_ids,\n",
    "                                  data=[[1] * len(sample_ids)])  # All samples are pancreatic cancer\n",
    "\n",
    "print(f\"Created dummy clinical data with shape: {dummy_clinical_df.shape}\")\n",
    "\n",
    "# 2. Link the clinical and genetic data (even though clinical data is just a constant)\n",
    "linked_data = geo_link_clinical_genetic_data(dummy_clinical_df, normalized_gene_data)\n",
    "print(f\"Linked data shape: {linked_data.shape}\")\n",
    "\n",
    "# Identify trait column\n",
    "trait_col = linked_data.columns[0]\n",
    "print(f\"Using trait column: {trait_col}\")\n",
    "\n",
    "# 3. Handle missing values in the linked data\n",
    "linked_data = handle_missing_values(linked_data, trait_col)\n",
    "print(f\"Shape after handling missing values: {linked_data.shape}\")\n",
    "\n",
    "# 4. Determine whether the trait and demographic features are severely biased\n",
    "# Since we know all samples are pancreatic cancer, this trait is severely biased\n",
    "is_trait_biased = True\n",
    "print(\"The trait is severely biased (all samples are pancreatic cancer).\")\n",
    "unbiased_linked_data = linked_data\n",
    "\n",
    "# 5. Conduct quality check and save the cohort information\n",
    "is_usable = validate_and_save_cohort_info(\n",
    "    is_final=True, \n",
    "    cohort=cohort, \n",
    "    info_path=json_path, \n",
    "    is_gene_available=True, \n",
    "    is_trait_available=False,  # We previously determined trait data is not available (no variation)\n",
    "    is_biased=is_trait_biased, \n",
    "    df=unbiased_linked_data,\n",
    "    note=\"Dataset contains gene expression data for pancreatic cancer cell lines, but lacks normal controls.\"\n",
    ")\n",
    "\n",
    "# 6. Since the data is not usable (no trait variation), don't save it\n",
    "if is_usable:\n",
    "    # Create directory if it doesn't exist\n",
    "    os.makedirs(os.path.dirname(out_data_file), exist_ok=True)\n",
    "    # Save the data\n",
    "    unbiased_linked_data.to_csv(out_data_file)\n",
    "    print(f\"Linked data saved to {out_data_file}\")\n",
    "else:\n",
    "    print(\"Data quality check failed. Dataset lacks necessary trait variation for association studies.\")"
   ]
  }
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