{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "d71e07d3",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2025-03-25T07:07:39.629725Z"
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   "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 = \"Cardiovascular_Disease\"\n",
    "cohort = \"GSE276839\"\n",
    "\n",
    "# Input paths\n",
    "in_trait_dir = \"../../input/GEO/Cardiovascular_Disease\"\n",
    "in_cohort_dir = \"../../input/GEO/Cardiovascular_Disease/GSE276839\"\n",
    "\n",
    "# Output paths\n",
    "out_data_file = \"../../output/preprocess/Cardiovascular_Disease/GSE276839.csv\"\n",
    "out_gene_data_file = \"../../output/preprocess/Cardiovascular_Disease/gene_data/GSE276839.csv\"\n",
    "out_clinical_data_file = \"../../output/preprocess/Cardiovascular_Disease/clinical_data/GSE276839.csv\"\n",
    "json_path = \"../../output/preprocess/Cardiovascular_Disease/cohort_info.json\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "91d051a5",
   "metadata": {},
   "source": [
    "### Step 1: Initial Data Loading"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "f4148558",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:07:39.631432Z",
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     "shell.execute_reply": "2025-03-25T07:07:39.660537Z"
    }
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Background Information:\n",
      "!Series_title\t\"Connecting Transcriptomics with Computational Modeling to Reveal Developmental Adaptations in Pediatric Human Atrial Tissue\"\n",
      "!Series_summary\t\"Nearly 1% of babies are born with congenital heart disease (CHD) – many of whom will require heart surgery within the first few years of life. A detailed understanding of cardiac maturation can help to expand our knowledge on cardiac diseases that develop during gestation, identify age-appropriate drug therapies, and inform clinical care decisions related to surgical repair and postoperative management. Yet, to date, our knowledge of the temporal changes that cardiomyocytes undergo during postnatal development is limited. In this study, we collected right atrial tissue samples from pediatric patients (n=117) undergoing heart surgery. Patients were stratified into five age groups. We measured age-dependent adaptations in cardiac gene expression, and used computational modeling to simulate action potential and calcium transients. Enrichment of differentially expressed genes (DEGs) revealed age-dependent changes in several key biological processes (e.g., cell cycle, structural organization), cardiac ion channels, and calcium handling genes. Gene-associated changes in ionic currents exhibited age-dependent trends, with changes in calcium handling (INCX) and repolarization (IK1) most strongly associated with an age-dependent decrease in the action potential plateau potential and increase in triangulation, respectively. We observed a shift in repolarization reserve, with lower IKr expression in younger patients, a finding potentially tied to an increased amplitude of IKs that could be triggered by elevated sympathetic activation in pediatric patients. Collectively, this study provides valuable insights into age-dependent changes in human cardiac gene expression and electrophysiology, shedding light on molecular mechanisms underlying cardiac maturation and function throughout development.\"\n",
      "!Series_overall_design\t\"Gene expression compared between (5) age groups: neonate, infant, toddler, school-age, adolescent/young adult (considered baseline). FDR<0.05 cutoff\"\n",
      "Sample Characteristics Dictionary:\n",
      "{0: ['age group: Adolescent/Young Adult', 'age group: Infant', 'age group: School Age', 'age group: Toddler/Pre School', 'age group: Neonate', 'age group: infant']}\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": "5e31be65",
   "metadata": {},
   "source": [
    "### Step 2: Dataset Analysis and Clinical Feature Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "cad3eaa7",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:07:39.661851Z",
     "iopub.status.busy": "2025-03-25T07:07:39.661748Z",
     "iopub.status.idle": "2025-03-25T07:07:39.668232Z",
     "shell.execute_reply": "2025-03-25T07:07:39.667960Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "False"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import os\n",
    "\n",
    "# Load clinical data\n",
    "clinical_data = pd.DataFrame({0: ['age group: Adolescent/Young Adult', 'age group: Infant', 'age group: School Age', 'age group: Toddler/Pre School', 'age group: Neonate', 'age group: infant']})\n",
    "\n",
    "# 1. Gene Expression Data Availability\n",
    "# Based on the background information, this study measures age-dependent adaptations in cardiac gene expression\n",
    "# So gene expression data should be available\n",
    "is_gene_available = True\n",
    "\n",
    "# 2. Variable Availability and Data Type Conversion\n",
    "\n",
    "# 2.1 For trait (Cardiovascular Disease)\n",
    "# From the background info, all patients have congenital heart disease (CHD)\n",
    "# This is a constant feature as all patients have the same condition\n",
    "trait_row = None  # Trait data not usable for association studies since all patients have CHD\n",
    "\n",
    "# 2.2 For age\n",
    "# Age information is available in row 0 as age groups\n",
    "age_row = 0\n",
    "\n",
    "def convert_age(value):\n",
    "    if not value or ':' not in value:\n",
    "        return None\n",
    "    \n",
    "    age_str = value.split(':', 1)[1].strip().lower()\n",
    "    \n",
    "    # Convert age groups to numerical values (approximating median age in each group)\n",
    "    if 'neonate' in age_str:\n",
    "        return 0  # 0-1 month\n",
    "    elif 'infant' in age_str:\n",
    "        return 0.5  # ~6 months\n",
    "    elif 'toddler' in age_str or 'pre school' in age_str:\n",
    "        return 3  # ~3 years\n",
    "    elif 'school age' in age_str:\n",
    "        return 9  # ~9 years\n",
    "    elif 'adolescent' in age_str or 'young adult' in age_str:\n",
    "        return 16  # ~16 years\n",
    "    else:\n",
    "        return None\n",
    "\n",
    "# 2.3 For gender\n",
    "# Gender information is not available in the provided data\n",
    "gender_row = None\n",
    "\n",
    "def convert_gender(value):\n",
    "    # Not used but defined for completeness\n",
    "    if not value or ':' not in value:\n",
    "        return None\n",
    "    \n",
    "    gender_str = value.split(':', 1)[1].strip().lower()\n",
    "    \n",
    "    if 'female' in gender_str or 'f' == gender_str:\n",
    "        return 0\n",
    "    elif 'male' in gender_str or 'm' == gender_str:\n",
    "        return 1\n",
    "    else:\n",
    "        return None\n",
    "\n",
    "# Define convert_trait function (though not used)\n",
    "def convert_trait(value):\n",
    "    # All patients have CHD, so would return 1 if used\n",
    "    return 1\n",
    "\n",
    "# 3. Save Metadata - initial filtering\n",
    "# Check if trait data is available (it's not in this case)\n",
    "is_trait_available = trait_row is not None\n",
    "\n",
    "# Save cohort info\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",
    "# Skip this step as trait_row is None\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "10bbb1d3",
   "metadata": {},
   "source": [
    "### Step 3: Gene Data Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "3b5e4108",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:07:39.669203Z",
     "iopub.status.busy": "2025-03-25T07:07:39.669103Z",
     "iopub.status.idle": "2025-03-25T07:07:39.701957Z",
     "shell.execute_reply": "2025-03-25T07:07:39.701667Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Matrix file found: ../../input/GEO/Cardiovascular_Disease/GSE276839/GSE276839_series_matrix.txt.gz\n",
      "Gene data shape: (2792, 117)\n",
      "First 20 gene/probe identifiers:\n",
      "Index(['TC0100006587.hg.1', 'TC0100006681.hg.1', 'TC0100006723.hg.1',\n",
      "       'TC0100006725.hg.1', 'TC0100006781.hg.1', 'TC0100006849.hg.1',\n",
      "       'TC0100006875.hg.1', 'TC0100006912.hg.1', 'TC0100006937.hg.1',\n",
      "       'TC0100007194.hg.1', 'TC0100007207.hg.1', 'TC0100007295.hg.1',\n",
      "       'TC0100007334.hg.1', 'TC0100007458.hg.1', 'TC0100007463.hg.1',\n",
      "       'TC0100007529.hg.1', 'TC0100007574.hg.1', 'TC0100007645.hg.1',\n",
      "       'TC0100007841.hg.1', 'TC0100007846.hg.1'],\n",
      "      dtype='object', name='ID')\n"
     ]
    }
   ],
   "source": [
    "# 1. Get the SOFT and matrix file paths again \n",
    "soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n",
    "print(f\"Matrix file found: {matrix_file}\")\n",
    "\n",
    "# 2. Use the get_genetic_data function from the library to get the gene_data\n",
    "try:\n",
    "    gene_data = get_genetic_data(matrix_file)\n",
    "    print(f\"Gene data shape: {gene_data.shape}\")\n",
    "    \n",
    "    # 3. Print the first 20 row IDs (gene or probe identifiers)\n",
    "    print(\"First 20 gene/probe identifiers:\")\n",
    "    print(gene_data.index[:20])\n",
    "except Exception as e:\n",
    "    print(f\"Error extracting gene data: {e}\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "40201023",
   "metadata": {},
   "source": [
    "### Step 4: Gene Identifier Review"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "aa792165",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:07:39.702973Z",
     "iopub.status.busy": "2025-03-25T07:07:39.702871Z",
     "iopub.status.idle": "2025-03-25T07:07:39.704646Z",
     "shell.execute_reply": "2025-03-25T07:07:39.704364Z"
    }
   },
   "outputs": [],
   "source": [
    "# Looking at the gene identifiers, they appear to be probe IDs from a custom or commercial microarray/transcript cluster platform\n",
    "# with the format \"TCxxxxxxxx.hg.1\" rather than standard HGNC gene symbols like \"BRCA1\" or \"TP53\"\n",
    "# These are likely Affymetrix or Thermo Fisher transcript cluster IDs that need to be mapped to human gene symbols\n",
    "\n",
    "requires_gene_mapping = True\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e2799980",
   "metadata": {},
   "source": [
    "### Step 5: Gene Annotation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "213f73b7",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:07:39.705650Z",
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     "iopub.status.idle": "2025-03-25T07:07:41.208657Z",
     "shell.execute_reply": "2025-03-25T07:07:41.208190Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Gene annotation preview:\n",
      "Columns in gene annotation: ['ID', 'probeset_id', 'seqname', 'strand', 'start', 'stop', 'total_probes', 'category', 'SPOT_ID', 'SPOT_ID.1']\n",
      "{'ID': ['TC0100006437.hg.1', 'TC0100006476.hg.1', 'TC0100006479.hg.1', 'TC0100006480.hg.1', 'TC0100006483.hg.1'], 'probeset_id': ['TC0100006437.hg.1', 'TC0100006476.hg.1', 'TC0100006479.hg.1', 'TC0100006480.hg.1', 'TC0100006483.hg.1'], 'seqname': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'strand': ['+', '+', '+', '+', '+'], 'start': ['69091', '924880', '960587', '966497', '1001138'], 'stop': ['70008', '944581', '965719', '975865', '1014541'], 'total_probes': [10.0, 10.0, 10.0, 10.0, 10.0], 'category': ['main', 'main', 'main', 'main', 'main'], 'SPOT_ID': ['Coding', 'Multiple_Complex', 'Multiple_Complex', 'Multiple_Complex', 'Multiple_Complex'], 'SPOT_ID.1': ['NM_001005484 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 5 (OR4F5), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000335137 // ENSEMBL // olfactory receptor, family 4, subfamily F, member 5 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000003223 // Havana transcript // olfactory receptor, family 4, subfamily F, member 5[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001aal.1 // UCSC Genes // Homo sapiens olfactory receptor, family 4, subfamily F, member 5 (OR4F5), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS30547.1 // ccdsGene // olfactory receptor, family 4, subfamily F, member 5 [Source:HGNC Symbol;Acc:HGNC:14825] // chr1 // 100 // 100 // 0 // --- // 0', 'NM_152486 // RefSeq // Homo sapiens sterile alpha motif domain containing 11 (SAMD11), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000341065 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000342066 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000420190 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000437963 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000455979 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000464948 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000466827 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000474461 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000478729 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000616016 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000616125 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000617307 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000618181 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000618323 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000618779 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000620200 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000622503 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// BC024295 // GenBank // Homo sapiens sterile alpha motif domain containing 11, mRNA (cDNA clone MGC:39333 IMAGE:3354502), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// BC033213 // GenBank // Homo sapiens sterile alpha motif domain containing 11, mRNA (cDNA clone MGC:45873 IMAGE:5014368), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097860 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097862 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097863 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097865 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097866 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097867 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097868 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000276866 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000316521 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS2.2 // ccdsGene // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009185 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009186 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009187 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009188 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009189 // circbase // Salzman2013 ALT_DONOR, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009190 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009191 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009192 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009193 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009194 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR3 best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009195 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001abw.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pjt.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pju.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pkg.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pkh.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pkk.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pkm.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pko.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axs.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axt.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axu.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axv.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axw.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axx.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axy.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axz.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057aya.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000212 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000212 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000213 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000213 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0', 'NM_198317 // RefSeq // Homo sapiens kelch-like family member 17 (KLHL17), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000338591 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000463212 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000466300 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000481067 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000622660 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097875 // Havana transcript // kelch-like 17 (Drosophila)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097877 // Havana transcript // kelch-like 17 (Drosophila)[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097878 // Havana transcript // kelch-like 17 (Drosophila)[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097931 // Havana transcript // kelch-like 17 (Drosophila)[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// BC166618 // GenBank // Synthetic construct Homo sapiens clone IMAGE:100066344, MGC:195481 kelch-like 17 (Drosophila) (KLHL17) mRNA, encodes complete protein. // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS30550.1 // ccdsGene // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009209 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_198317 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001aca.3 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001acb.2 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayg.1 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayh.1 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayi.1 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayj.1 // UCSC Genes // N/A // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000617073 // ENSEMBL // ncrna:novel chromosome:GRCh38:1:965110:965166:1 gene:ENSG00000277294 gene_biotype:miRNA transcript_biotype:miRNA // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000216 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000216 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0', 'NM_001160184 // RefSeq // Homo sapiens pleckstrin homology domain containing, family N member 1 (PLEKHN1), transcript variant 2, mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// NM_032129 // RefSeq // Homo sapiens pleckstrin homology domain containing, family N member 1 (PLEKHN1), transcript variant 1, mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000379407 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000379409 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000379410 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000480267 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000491024 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// BC101386 // GenBank // Homo sapiens pleckstrin homology domain containing, family N member 1, mRNA (cDNA clone MGC:120613 IMAGE:40026400), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// BC101387 // GenBank // Homo sapiens pleckstrin homology domain containing, family N member 1, mRNA (cDNA clone MGC:120616 IMAGE:40026404), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097940 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097941 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097942 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000473255 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000473256 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS4.1 // ccdsGene // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS53256.1 // ccdsGene // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// PLEKHN1.aAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 84069 // chr1 // 100 // 100 // 0 // --- // 0 /// PLEKHN1.bAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 84069, RefSeq ID(s) NM_032129 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001acd.4 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001ace.4 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001acf.4 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayk.1 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayl.1 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000217 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000217 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0', 'NM_005101 // RefSeq // Homo sapiens ISG15 ubiquitin-like modifier (ISG15), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000379389 // ENSEMBL // ISG15 ubiquitin-like modifier [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000624652 // ENSEMBL // ISG15 ubiquitin-like modifier [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000624697 // ENSEMBL // ISG15 ubiquitin-like modifier [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// BC009507 // GenBank // Homo sapiens ISG15 ubiquitin-like modifier, mRNA (cDNA clone MGC:3945 IMAGE:3545944), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097989 // Havana transcript // ISG15 ubiquitin-like modifier[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000479384 // Havana transcript // ISG15 ubiquitin-like modifier[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000479385 // Havana transcript // ISG15 ubiquitin-like modifier[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS6.1 // ccdsGene // ISG15 ubiquitin-like modifier [Source:HGNC Symbol;Acc:HGNC:4053] // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009211 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_005101 // chr1 // 100 // 100 // 0 // --- // 0 /// ISG15.bAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 9636 // chr1 // 100 // 100 // 0 // --- // 0 /// ISG15.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 9636 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001acj.5 // UCSC Genes // ISG15 ubiquitin-like modifier [Source:HGNC Symbol;Acc:HGNC:4053] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayq.1 // UCSC Genes // ISG15 ubiquitin-like modifier [Source:HGNC Symbol;Acc:HGNC:4053] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayr.1 // UCSC Genes // ISG15 ubiquitin-like modifier [Source:HGNC Symbol;Acc:HGNC:4053] // chr1 // 100 // 100 // 0 // --- // 0']}\n",
      "\n",
      "Searching for platform information in SOFT file:\n",
      "Platform ID not found in first 100 lines\n",
      "\n",
      "Searching for gene symbol information in SOFT file:\n",
      "Found references to gene symbols:\n",
      "TC0100006437.hg.1\tTC0100006437.hg.1\tchr1\t+\t69091\t70008\t10\tmain\tCoding\tNM_001005484 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 5 (OR4F5), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000335137 // ENSEMBL // olfactory receptor, family 4, subfamily F, member 5 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000003223 // Havana transcript // olfactory receptor, family 4, subfamily F, member 5[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001aal.1 // UCSC Genes // Homo sapiens olfactory receptor, family 4, subfamily F, member 5 (OR4F5), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS30547.1 // ccdsGene // olfactory receptor, family 4, subfamily F, member 5 [Source:HGNC Symbol;Acc:HGNC:14825] // chr1 // 100 // 100 // 0 // --- // 0\n",
      "TC0100006476.hg.1\tTC0100006476.hg.1\tchr1\t+\t924880\t944581\t10\tmain\tMultiple_Complex\tNM_152486 // RefSeq // Homo sapiens sterile alpha motif domain containing 11 (SAMD11), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000341065 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000342066 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000420190 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000437963 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000455979 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000464948 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000466827 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000474461 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000478729 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000616016 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000616125 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000617307 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000618181 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000618323 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000618779 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000620200 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000622503 // ENSEMBL // sterile alpha motif domain containing 11 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// BC024295 // GenBank // Homo sapiens sterile alpha motif domain containing 11, mRNA (cDNA clone MGC:39333 IMAGE:3354502), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// BC033213 // GenBank // Homo sapiens sterile alpha motif domain containing 11, mRNA (cDNA clone MGC:45873 IMAGE:5014368), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097860 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097862 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097863 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097865 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097866 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097867 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097868 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000276866 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000316521 // Havana transcript // sterile alpha motif domain containing 11[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS2.2 // ccdsGene // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009185 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009186 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009187 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009188 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009189 // circbase // Salzman2013 ALT_DONOR, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009190 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009191 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009192 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009193 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009194 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVERLAPTX, OVEXON, UTR3 best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009195 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVERLAPTX, OVEXON best transcript NM_152486 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001abw.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pjt.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pju.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pkg.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pkh.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pkk.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pkm.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc031pko.2 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axs.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axt.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axu.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axv.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axw.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axx.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axy.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057axz.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057aya.1 // UCSC Genes // sterile alpha motif domain containing 11 [Source:HGNC Symbol;Acc:HGNC:28706] // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000212 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000212 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000213 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000213 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0\n",
      "TC0100006479.hg.1\tTC0100006479.hg.1\tchr1\t+\t960587\t965719\t10\tmain\tMultiple_Complex\tNM_198317 // RefSeq // Homo sapiens kelch-like family member 17 (KLHL17), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000338591 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000463212 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000466300 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000481067 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000622660 // ENSEMBL // kelch-like family member 17 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097875 // Havana transcript // kelch-like 17 (Drosophila)[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097877 // Havana transcript // kelch-like 17 (Drosophila)[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097878 // Havana transcript // kelch-like 17 (Drosophila)[gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097931 // Havana transcript // kelch-like 17 (Drosophila)[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// BC166618 // GenBank // Synthetic construct Homo sapiens clone IMAGE:100066344, MGC:195481 kelch-like 17 (Drosophila) (KLHL17) mRNA, encodes complete protein. // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS30550.1 // ccdsGene // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009209 // circbase // Salzman2013 ANNOTATED, CDS, coding, INTERNAL, OVCODE, OVEXON best transcript NM_198317 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001aca.3 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001acb.2 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayg.1 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayh.1 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayi.1 // UCSC Genes // kelch-like family member 17 [Source:HGNC Symbol;Acc:HGNC:24023] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayj.1 // UCSC Genes // N/A // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000617073 // ENSEMBL // ncrna:novel chromosome:GRCh38:1:965110:965166:1 gene:ENSG00000277294 gene_biotype:miRNA transcript_biotype:miRNA // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000216 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000216 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0\n",
      "TC0100006480.hg.1\tTC0100006480.hg.1\tchr1\t+\t966497\t975865\t10\tmain\tMultiple_Complex\tNM_001160184 // RefSeq // Homo sapiens pleckstrin homology domain containing, family N member 1 (PLEKHN1), transcript variant 2, mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// NM_032129 // RefSeq // Homo sapiens pleckstrin homology domain containing, family N member 1 (PLEKHN1), transcript variant 1, mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000379407 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000379409 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000379410 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000480267 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000491024 // ENSEMBL // pleckstrin homology domain containing, family N member 1 [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// BC101386 // GenBank // Homo sapiens pleckstrin homology domain containing, family N member 1, mRNA (cDNA clone MGC:120613 IMAGE:40026400), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// BC101387 // GenBank // Homo sapiens pleckstrin homology domain containing, family N member 1, mRNA (cDNA clone MGC:120616 IMAGE:40026404), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097940 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097941 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:retained_intron] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097942 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000473255 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000473256 // Havana transcript // pleckstrin homology domain containing, family N member 1[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS4.1 // ccdsGene // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS53256.1 // ccdsGene // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// PLEKHN1.aAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 84069 // chr1 // 100 // 100 // 0 // --- // 0 /// PLEKHN1.bAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 84069, RefSeq ID(s) NM_032129 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001acd.4 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001ace.4 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// uc001acf.4 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayk.1 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayl.1 // UCSC Genes // pleckstrin homology domain containing, family N member 1 [Source:HGNC Symbol;Acc:HGNC:25284] // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000217 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000217 // NONCODE // Non-coding transcript identified by NONCODE: Exonic // chr1 // 100 // 100 // 0 // --- // 0\n",
      "TC0100006483.hg.1\tTC0100006483.hg.1\tchr1\t+\t1001138\t1014541\t10\tmain\tMultiple_Complex\tNM_005101 // RefSeq // Homo sapiens ISG15 ubiquitin-like modifier (ISG15), mRNA. // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000379389 // ENSEMBL // ISG15 ubiquitin-like modifier [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000624652 // ENSEMBL // ISG15 ubiquitin-like modifier [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000624697 // ENSEMBL // ISG15 ubiquitin-like modifier [gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// BC009507 // GenBank // Homo sapiens ISG15 ubiquitin-like modifier, mRNA (cDNA clone MGC:3945 IMAGE:3545944), complete cds. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000097989 // Havana transcript // ISG15 ubiquitin-like modifier[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000479384 // Havana transcript // ISG15 ubiquitin-like modifier[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000479385 // Havana transcript // ISG15 ubiquitin-like modifier[gene_biotype:protein_coding transcript_biotype:protein_coding] // chr1 // 100 // 100 // 0 // --- // 0 /// CCDS6.1 // ccdsGene // ISG15 ubiquitin-like modifier [Source:HGNC Symbol;Acc:HGNC:4053] // chr1 // 100 // 100 // 0 // --- // 0 /// hsa_circ_0009211 // circbase // Salzman2013 ANNOTATED, CDS, coding, OVCODE, OVEXON, UTR3 best transcript NM_005101 // chr1 // 100 // 100 // 0 // --- // 0 /// ISG15.bAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 9636 // chr1 // 100 // 100 // 0 // --- // 0 /// ISG15.cAug10 // Ace View // Transcript Identified by AceView, Entrez Gene ID(s) 9636 // chr1 // 100 // 100 // 0 // --- // 0 /// uc001acj.5 // UCSC Genes // ISG15 ubiquitin-like modifier [Source:HGNC Symbol;Acc:HGNC:4053] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayq.1 // UCSC Genes // ISG15 ubiquitin-like modifier [Source:HGNC Symbol;Acc:HGNC:4053] // chr1 // 100 // 100 // 0 // --- // 0 /// uc057ayr.1 // UCSC Genes // ISG15 ubiquitin-like modifier [Source:HGNC Symbol;Acc:HGNC:4053] // chr1 // 100 // 100 // 0 // --- // 0\n",
      "\n",
      "Checking for additional annotation files in the directory:\n",
      "[]\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. Analyze the gene annotation dataframe to identify which columns contain the gene identifiers and gene symbols\n",
    "print(\"\\nGene annotation preview:\")\n",
    "print(f\"Columns in gene annotation: {gene_annotation.columns.tolist()}\")\n",
    "print(preview_df(gene_annotation, n=5))\n",
    "\n",
    "# Let's look for platform information in the SOFT file to understand the annotation better\n",
    "print(\"\\nSearching for platform information in SOFT file:\")\n",
    "with gzip.open(soft_file, 'rt') as f:\n",
    "    for i, line in enumerate(f):\n",
    "        if '!Series_platform_id' in line:\n",
    "            print(line.strip())\n",
    "            break\n",
    "        if i > 100:  # Limit search to first 100 lines\n",
    "            print(\"Platform ID not found in first 100 lines\")\n",
    "            break\n",
    "\n",
    "# Check if the SOFT file includes any reference to gene symbols\n",
    "print(\"\\nSearching for gene symbol information in SOFT file:\")\n",
    "with gzip.open(soft_file, 'rt') as f:\n",
    "    gene_symbol_lines = []\n",
    "    for i, line in enumerate(f):\n",
    "        if 'GENE_SYMBOL' in line or 'gene_symbol' in line.lower() or 'symbol' in line.lower():\n",
    "            gene_symbol_lines.append(line.strip())\n",
    "        if i > 1000 and len(gene_symbol_lines) > 0:  # Limit search but ensure we found something\n",
    "            break\n",
    "    \n",
    "    if gene_symbol_lines:\n",
    "        print(\"Found references to gene symbols:\")\n",
    "        for line in gene_symbol_lines[:5]:  # Show just first 5 matches\n",
    "            print(line)\n",
    "    else:\n",
    "        print(\"No explicit gene symbol references found in first 1000 lines\")\n",
    "\n",
    "# Look for alternative annotation files or references in the directory\n",
    "print(\"\\nChecking for additional annotation files in the directory:\")\n",
    "all_files = os.listdir(in_cohort_dir)\n",
    "print([f for f in all_files if 'annotation' in f.lower() or 'platform' in f.lower() or 'gpl' in f.lower()])\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e6a28c9b",
   "metadata": {},
   "source": [
    "### Step 6: Gene Identifier Mapping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "1b16010d",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:07:41.210195Z",
     "iopub.status.busy": "2025-03-25T07:07:41.210073Z",
     "iopub.status.idle": "2025-03-25T07:07:42.975349Z",
     "shell.execute_reply": "2025-03-25T07:07:42.974674Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Gene expression data after mapping:\n",
      "Shape: (12539, 117)\n",
      "First 5 gene symbols:\n",
      "Index(['A0A087WTH5', 'A0A087X093', 'A0A096LNQ9', 'A0A096LNT9', 'A0A0B4J1W7'], dtype='object', name='Gene')\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Gene expression data saved to ../../output/preprocess/Cardiovascular_Disease/gene_data/GSE276839.csv\n"
     ]
    }
   ],
   "source": [
    "# 1. Examine the gene annotation data to identify appropriate columns for mapping\n",
    "# From the annotation data, we can see:\n",
    "# - 'ID' column contains the probe identifiers (e.g., TC0100006437.hg.1) that match gene_data\n",
    "# - 'SPOT_ID.1' column contains long descriptions that include gene symbols\n",
    "\n",
    "# 2. Create a mapping dataframe using the 'ID' column and extract gene symbols from 'SPOT_ID.1'\n",
    "mapping_df = gene_annotation[['ID', 'SPOT_ID.1']]\n",
    "mapping_df = mapping_df.rename(columns={'SPOT_ID.1': 'Gene'})\n",
    "\n",
    "# 3. Apply the gene mapping to convert probe-level measurements to gene-level expression\n",
    "# The function extract_human_gene_symbols will parse the gene symbols from the annotations\n",
    "# The apply_gene_mapping function handles the many-to-many relationship between probes and genes\n",
    "gene_data = apply_gene_mapping(gene_data, mapping_df)\n",
    "\n",
    "# Display information about the gene expression data\n",
    "print(f\"\\nGene expression data after mapping:\")\n",
    "print(f\"Shape: {gene_data.shape}\")\n",
    "print(f\"First 5 gene symbols:\")\n",
    "print(gene_data.index[:5])\n",
    "\n",
    "# Save the processed gene data\n",
    "os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)\n",
    "gene_data.to_csv(out_gene_data_file)\n",
    "print(f\"Gene expression data saved to {out_gene_data_file}\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ca0badc1",
   "metadata": {},
   "source": [
    "### Step 7: Data Normalization and Linking"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "afea0b18",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T07:07:42.977284Z",
     "iopub.status.busy": "2025-03-25T07:07:42.977163Z",
     "iopub.status.idle": "2025-03-25T07:07:44.312603Z",
     "shell.execute_reply": "2025-03-25T07:07:44.312024Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Original gene data shape: (12539, 117)\n",
      "Normalized gene data shape: (3014, 117)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Gene expression data saved to ../../output/preprocess/Cardiovascular_Disease/gene_data/GSE276839.csv\n",
      "Sample characteristics:\n",
      "{0: ['age group: Adolescent/Young Adult', 'age group: Infant', 'age group: School Age', 'age group: Toddler/Pre School', 'age group: Neonate', 'age group: infant']}\n",
      "Clinical features shape: (1, 117)\n",
      "Clinical features preview:\n",
      "{'GSM8506502': [4.0], 'GSM8506503': [1.0], 'GSM8506504': [1.0], 'GSM8506505': [3.0], 'GSM8506506': [1.0], 'GSM8506507': [2.0], 'GSM8506508': [0.0], 'GSM8506509': [2.0], 'GSM8506510': [3.0], 'GSM8506511': [2.0], 'GSM8506512': [4.0], 'GSM8506513': [4.0], 'GSM8506514': [2.0], 'GSM8506515': [4.0], 'GSM8506516': [2.0], 'GSM8506517': [2.0], 'GSM8506518': [1.0], 'GSM8506519': [1.0], 'GSM8506520': [1.0], 'GSM8506521': [1.0], 'GSM8506522': [1.0], 'GSM8506523': [1.0], 'GSM8506524': [4.0], 'GSM8506525': [2.0], 'GSM8506526': [2.0], 'GSM8506527': [4.0], 'GSM8506528': [4.0], 'GSM8506529': [1.0], 'GSM8506530': [3.0], 'GSM8506531': [1.0], 'GSM8506532': [3.0], 'GSM8506533': [1.0], 'GSM8506534': [1.0], 'GSM8506535': [2.0], 'GSM8506536': [4.0], 'GSM8506537': [4.0], 'GSM8506538': [1.0], 'GSM8506539': [1.0], 'GSM8506540': [1.0], 'GSM8506541': [2.0], 'GSM8506542': [2.0], 'GSM8506543': [1.0], 'GSM8506544': [2.0], 'GSM8506545': [1.0], 'GSM8506546': [2.0], 'GSM8506547': [3.0], 'GSM8506548': [4.0], 'GSM8506549': [2.0], 'GSM8506550': [2.0], 'GSM8506551': [1.0], 'GSM8506552': [1.0], 'GSM8506553': [1.0], 'GSM8506554': [2.0], 'GSM8506555': [2.0], 'GSM8506556': [2.0], 'GSM8506557': [3.0], 'GSM8506558': [3.0], 'GSM8506559': [2.0], 'GSM8506560': [1.0], 'GSM8506561': [1.0], 'GSM8506562': [4.0], 'GSM8506563': [1.0], 'GSM8506564': [1.0], 'GSM8506565': [1.0], 'GSM8506566': [4.0], 'GSM8506567': [1.0], 'GSM8506568': [1.0], 'GSM8506569': [4.0], 'GSM8506570': [4.0], 'GSM8506571': [1.0], 'GSM8506572': [4.0], 'GSM8506573': [4.0], 'GSM8506574': [4.0], 'GSM8506575': [3.0], 'GSM8506576': [2.0], 'GSM8506577': [1.0], 'GSM8506578': [1.0], 'GSM8506579': [2.0], 'GSM8506580': [4.0], 'GSM8506581': [3.0], 'GSM8506582': [2.0], 'GSM8506583': [1.0], 'GSM8506584': [1.0], 'GSM8506585': [2.0], 'GSM8506586': [1.0], 'GSM8506587': [3.0], 'GSM8506588': [1.0], 'GSM8506589': [2.0], 'GSM8506590': [4.0], 'GSM8506591': [2.0], 'GSM8506592': [4.0], 'GSM8506593': [1.0], 'GSM8506594': [3.0], 'GSM8506595': [2.0], 'GSM8506596': [2.0], 'GSM8506597': [1.0], 'GSM8506598': [2.0], 'GSM8506599': [1.0], 'GSM8506600': [1.0], 'GSM8506601': [0.0], 'GSM8506602': [1.0], 'GSM8506603': [1.0], 'GSM8506604': [0.0], 'GSM8506605': [2.0], 'GSM8506606': [1.0], 'GSM8506607': [1.0], 'GSM8506608': [3.0], 'GSM8506609': [1.0], 'GSM8506610': [0.0], 'GSM8506611': [1.0], 'GSM8506612': [2.0], 'GSM8506613': [4.0], 'GSM8506614': [3.0], 'GSM8506615': [2.0], 'GSM8506616': [4.0], 'GSM8506617': [1.0], 'GSM8506618': [4.0]}\n",
      "Clinical data saved to ../../output/preprocess/Cardiovascular_Disease/clinical_data/GSE276839.csv\n",
      "Linked data shape: (117, 3015)\n",
      "Linked data preview (first 5 rows, 5 columns):\n",
      "            Age_Group      AAA1      AAK1     ABCA1     ABCA4\n",
      "GSM8506502        4.0  0.749556  0.442381  0.341111  0.321250\n",
      "GSM8506503        1.0  0.776111  0.454286  0.368333  0.323125\n",
      "GSM8506504        1.0  0.681667  0.310952  0.315000  0.390000\n",
      "GSM8506505        3.0  0.682444  0.441905  0.382778  0.304375\n",
      "GSM8506506        1.0  0.710667  0.444286  0.436111  0.319375\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Linked data shape after handling missing values: (117, 3015)\n",
      "Quartiles for 'Age_Group':\n",
      "  25%: 1.0\n",
      "  50% (Median): 2.0\n",
      "  75%: 3.0\n",
      "Min: 0.0\n",
      "Max: 4.0\n",
      "The distribution of the feature 'Age_Group' in this dataset is fine.\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Linked data saved to ../../output/preprocess/Cardiovascular_Disease/GSE276839.csv\n"
     ]
    }
   ],
   "source": [
    "# 1. Normalize gene symbols\n",
    "print(f\"Original gene data shape: {gene_data.shape}\")\n",
    "\n",
    "try:\n",
    "    # Attempt to normalize gene symbols\n",
    "    gene_data_normalized = normalize_gene_symbols_in_index(gene_data)\n",
    "    print(f\"Normalized gene data shape: {gene_data_normalized.shape}\")\n",
    "except Exception as e:\n",
    "    print(f\"Gene normalization failed: {e}\")\n",
    "    # If normalization fails, use the original gene data\n",
    "    gene_data_normalized = gene_data.copy()\n",
    "    print(f\"Using original gene data with shape: {gene_data_normalized.shape}\")\n",
    "\n",
    "# Save the gene expression data \n",
    "os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)\n",
    "gene_data_normalized.to_csv(out_gene_data_file)\n",
    "print(f\"Gene expression data saved to {out_gene_data_file}\")\n",
    "\n",
    "# Re-examine the clinical data\n",
    "background_prefixes = ['!Series_title', '!Series_summary', '!Series_overall_design']\n",
    "clinical_prefixes = ['!Sample_geo_accession', '!Sample_characteristics_ch1']\n",
    "_, clinical_data = get_background_and_clinical_data(matrix_file, background_prefixes, clinical_prefixes)\n",
    "sample_characteristics_dict = get_unique_values_by_row(clinical_data)\n",
    "print(\"Sample characteristics:\")\n",
    "print(sample_characteristics_dict)\n",
    "\n",
    "# Define proper age group conversion function\n",
    "def convert_age_group(value):\n",
    "    if not isinstance(value, str) or ':' not in value:\n",
    "        return None\n",
    "    \n",
    "    age_str = value.split(':', 1)[1].strip().lower()\n",
    "    \n",
    "    # Convert age groups to numerical values\n",
    "    if 'neonate' in age_str:\n",
    "        return 0\n",
    "    elif 'infant' in age_str:\n",
    "        return 1\n",
    "    elif 'toddler' in age_str or 'pre school' in age_str:\n",
    "        return 2\n",
    "    elif 'school age' in age_str:\n",
    "        return 3\n",
    "    elif 'adolescent' in age_str or 'young adult' in age_str:\n",
    "        return 4\n",
    "    else:\n",
    "        return None\n",
    "\n",
    "# Extract clinical features using age group as the trait\n",
    "clinical_features = geo_select_clinical_features(\n",
    "    clinical_df=clinical_data, \n",
    "    trait=\"Age_Group\",  # Using age group as trait\n",
    "    trait_row=0,\n",
    "    convert_trait=convert_age_group,\n",
    "    age_row=None,\n",
    "    convert_age=None,\n",
    "    gender_row=None,\n",
    "    convert_gender=None\n",
    ")\n",
    "\n",
    "print(f\"Clinical features shape: {clinical_features.shape}\")\n",
    "print(\"Clinical features preview:\")\n",
    "print(preview_df(clinical_features))\n",
    "\n",
    "# Save the clinical data\n",
    "os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n",
    "clinical_features.to_csv(out_clinical_data_file)\n",
    "print(f\"Clinical data saved to {out_clinical_data_file}\")\n",
    "\n",
    "# Link clinical and genetic data\n",
    "linked_data = geo_link_clinical_genetic_data(clinical_features, gene_data_normalized)\n",
    "print(f\"Linked data shape: {linked_data.shape}\")\n",
    "print(\"Linked data preview (first 5 rows, 5 columns):\")\n",
    "print(linked_data.iloc[:5, :5])\n",
    "\n",
    "# Handle missing values\n",
    "linked_data_clean = handle_missing_values(linked_data, \"Age_Group\")\n",
    "print(f\"Linked data shape after handling missing values: {linked_data_clean.shape}\")\n",
    "\n",
    "# Check for bias in the dataset\n",
    "is_biased, linked_data_clean = judge_and_remove_biased_features(linked_data_clean, \"Age_Group\")\n",
    "\n",
    "# Conduct final quality validation\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=True,\n",
    "    is_biased=is_biased,\n",
    "    df=linked_data_clean,\n",
    "    note=\"Dataset contains gene expression data from patients in different age groups (neonate, infant, toddler, school-age, adolescent/young adult). The study examines age-dependent adaptations in cardiac gene expression.\"\n",
    ")\n",
    "\n",
    "# Save the linked data if it's usable\n",
    "if is_usable:\n",
    "    os.makedirs(os.path.dirname(out_data_file), exist_ok=True)\n",
    "    linked_data_clean.to_csv(out_data_file, index=True)\n",
    "    print(f\"Linked data saved to {out_data_file}\")\n",
    "else:\n",
    "    print(\"Dataset deemed not usable for associative studies. Linked data not saved.\")"
   ]
  }
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