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{
"cells": [
{
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"metadata": {
"execution": {
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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 = \"Asthma\"\n",
"cohort = \"GSE182797\"\n",
"\n",
"# Input paths\n",
"in_trait_dir = \"../../input/GEO/Asthma\"\n",
"in_cohort_dir = \"../../input/GEO/Asthma/GSE182797\"\n",
"\n",
"# Output paths\n",
"out_data_file = \"../../output/preprocess/Asthma/GSE182797.csv\"\n",
"out_gene_data_file = \"../../output/preprocess/Asthma/gene_data/GSE182797.csv\"\n",
"out_clinical_data_file = \"../../output/preprocess/Asthma/clinical_data/GSE182797.csv\"\n",
"json_path = \"../../output/preprocess/Asthma/cohort_info.json\"\n"
]
},
{
"cell_type": "markdown",
"id": "5cc52335",
"metadata": {},
"source": [
"### Step 1: Initial Data Loading"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "f0fbe750",
"metadata": {
"execution": {
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Background Information:\n",
"!Series_title\t\"Transcriptomic profiling of adult-onset asthma related to damp and moldy buildings and idiopathic environmental intolerance [nasal biopsy]\"\n",
"!Series_summary\t\"The objective of the study was to characterize distinct endotypes of asthma related to damp and moldy buildings and to evaluate the potential molecular similarities with idiopathic environmental intolerance (IEI). The nasal biopsy transcriptome of 88 study subjects was profiled using samples obtained at baseline.\"\n",
"!Series_overall_design\t\"Nasal biopsy samples were collected from female adult-onset asthma patients (n=45), IEI patients (n=14) and healthy subjects (n=21) yielding 80 study subjects. Biopsies were homogenized and total RNA extracted for microarray analyses.\"\n",
"Sample Characteristics Dictionary:\n",
"{0: ['diagnosis: healthy', 'diagnosis: adult-onset asthma', 'diagnosis: IEI'], 1: ['gender: Female'], 2: ['age: 38.33', 'age: 38.08', 'age: 48.83', 'age: 33.42', 'age: 46.08', 'age: 45.58', 'age: 28', 'age: 30.83', 'age: 39.25', 'age: 60.17', 'age: 52.75', 'age: 25.75', 'age: 60.67', 'age: 64.67', 'age: 54.83', 'age: 57.67', 'age: 47', 'age: 47.5', 'age: 24.25', 'age: 47.67', 'age: 47.58', 'age: 18.42', 'age: 41.33', 'age: 24.5', 'age: 47.08', 'age: 41.17', 'age: 47.17', 'age: 59.83', 'age: 42.58', 'age: 56.67'], 3: ['tissue: Nasal biopsy'], 4: ['subject: 605', 'subject: 611', 'subject: 621', 'subject: 35', 'subject: 11', 'subject: 1', 'subject: 601', 'subject: 54', 'subject: 68_A', 'subject: 55', 'subject: 44', 'subject: 603_A', 'subject: 63', 'subject: 39', 'subject: 13', 'subject: 3', 'subject: 619', 'subject: 58', 'subject: 79', 'subject: 77', 'subject: 41', 'subject: 624', 'subject: 37_A', 'subject: 61', 'subject: 31', 'subject: 25', 'subject: 617', 'subject: 65', 'subject: 81', 'subject: 82']}\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": "9aee2a39",
"metadata": {},
"source": [
"### Step 2: Dataset Analysis and Clinical Feature Extraction"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "eb57f7f9",
"metadata": {
"execution": {
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Identified variables and conversion functions for future clinical data processing:\n",
"trait_row = 0, convert_trait function defined\n",
"age_row = 2, convert_age function defined\n",
"gender_row = None, convert_gender function defined\n"
]
}
],
"source": [
"import pandas as pd\n",
"import os\n",
"import json\n",
"from typing import Optional, Callable, Dict, Any\n",
"\n",
"# 1. Gene Expression Data Availability\n",
"# Based on Series_title and Sample Characteristics, this appears to be transcriptomic profiling data\n",
"# This is likely to contain gene expression data, not just miRNA or methylation\n",
"is_gene_available = True\n",
"\n",
"# 2. Variable Availability and Data Type Conversion\n",
"# 2.1 Data Availability\n",
"\n",
"# For trait (asthma):\n",
"# Key 0 contains diagnosis information - healthy, adult-onset asthma, or IEI\n",
"trait_row = 0\n",
"\n",
"# For age:\n",
"# Key 2 contains age information with multiple unique values\n",
"age_row = 2\n",
"\n",
"# For gender:\n",
"# Key 1 shows only \"gender: Female\" - this is a constant feature with only one value\n",
"# Since all subjects are female, this is not useful for association analysis\n",
"gender_row = None # Only one gender value (all Female)\n",
"\n",
"# 2.2 Data Type Conversion Functions\n",
"\n",
"def convert_trait(value):\n",
" \"\"\"Convert diagnosis value to binary trait (Asthma: 1, Not Asthma: 0)\"\"\"\n",
" if value is None:\n",
" return None\n",
" if ':' in value:\n",
" value = value.split(': ')[1].strip().lower()\n",
" \n",
" if value == 'adult-onset asthma':\n",
" return 1 # Has asthma\n",
" elif value == 'healthy' or value == 'iei': # IEI (Idiopathic Environmental Intolerance) is not asthma\n",
" return 0 # Does not have asthma\n",
" else:\n",
" return None # Unknown\n",
"\n",
"def convert_age(value):\n",
" \"\"\"Convert age value to continuous numeric value\"\"\"\n",
" if value is None:\n",
" return None\n",
" if ':' in value:\n",
" value = value.split(': ')[1].strip()\n",
" \n",
" try:\n",
" return float(value)\n",
" except (ValueError, TypeError):\n",
" return None\n",
"\n",
"def convert_gender(value):\n",
" \"\"\"Convert gender value to binary (Female: 0, Male: 1)\"\"\"\n",
" if value is None:\n",
" return None\n",
" if ':' in value:\n",
" value = value.split(': ')[1].strip().lower()\n",
" \n",
" if value == 'female':\n",
" return 0\n",
" elif value == 'male':\n",
" return 1\n",
" else:\n",
" return None\n",
"\n",
"# 3. Save Metadata - Initial filtering\n",
"is_trait_available = trait_row is not None\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",
"# Note: Skipping clinical feature extraction as we don't have the properly structured clinical data yet.\n",
"# The relevant variables (trait_row, age_row, gender_row) and conversion functions \n",
"# (convert_trait, convert_age, convert_gender) have been identified for future steps.\n",
"print(\"Identified variables and conversion functions for future clinical data processing:\")\n",
"print(f\"trait_row = {trait_row}, convert_trait function defined\")\n",
"print(f\"age_row = {age_row}, convert_age function defined\")\n",
"print(f\"gender_row = {gender_row}, convert_gender function defined\")\n"
]
},
{
"cell_type": "markdown",
"id": "cb950a3d",
"metadata": {},
"source": [
"### Step 3: Gene Data Extraction"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "9f4ed3dd",
"metadata": {
"execution": {
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"shell.execute_reply": "2025-03-25T06:40:21.880217Z"
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},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Matrix file found: ../../input/GEO/Asthma/GSE182797/GSE182797_series_matrix.txt.gz\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Gene data shape: (37616, 80)\n",
"First 20 gene/probe identifiers:\n",
"Index(['A_19_P00315452', 'A_19_P00315492', 'A_19_P00315493', 'A_19_P00315502',\n",
" 'A_19_P00315506', 'A_19_P00315518', 'A_19_P00315529', 'A_19_P00315551',\n",
" 'A_19_P00315581', 'A_19_P00315584', 'A_19_P00315593', 'A_19_P00315603',\n",
" 'A_19_P00315627', 'A_19_P00315631', 'A_19_P00315641', 'A_19_P00315647',\n",
" 'A_19_P00315649', 'A_19_P00315668', 'A_19_P00315691', 'A_19_P00315705'],\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": "0bb6c895",
"metadata": {},
"source": [
"### Step 4: Gene Identifier Review"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "90fd6c71",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T06:40:21.881985Z",
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},
"outputs": [],
"source": [
"# Based on the gene identifiers observed in the data, these appear to be Agilent microarray \n",
"# probe IDs (starting with A_19_P), not standard human gene symbols.\n",
"# These identifiers will need to be mapped to official gene symbols for meaningful analysis.\n",
"\n",
"requires_gene_mapping = True\n"
]
},
{
"cell_type": "markdown",
"id": "69df257a",
"metadata": {},
"source": [
"### Step 5: Gene Annotation"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "5e5e0868",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T06:40:21.885047Z",
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"shell.execute_reply": "2025-03-25T06:40:26.734983Z"
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Gene annotation preview:\n",
"{'ID': ['GE_BrightCorner', 'DarkCorner', 'A_21_P0014386', 'A_33_P3396872', 'A_33_P3267760'], 'CONTROL_TYPE': ['pos', 'pos', 'FALSE', 'FALSE', 'FALSE'], 'REFSEQ': [nan, nan, nan, 'NM_001105533', nan], 'GB_ACC': [nan, nan, nan, 'NM_001105533', nan], 'LOCUSLINK_ID': [nan, nan, nan, 79974.0, 54880.0], 'GENE_SYMBOL': [nan, nan, nan, 'CPED1', 'BCOR'], 'GENE_NAME': [nan, nan, nan, 'cadherin-like and PC-esterase domain containing 1', 'BCL6 corepressor'], 'UNIGENE_ID': [nan, nan, nan, 'Hs.189652', nan], 'ENSEMBL_ID': [nan, nan, nan, nan, 'ENST00000378463'], 'ACCESSION_STRING': [nan, nan, nan, 'ref|NM_001105533|gb|AK025639|gb|BC030538|tc|THC2601673', 'ens|ENST00000378463'], 'CHROMOSOMAL_LOCATION': [nan, nan, 'unmapped', 'chr7:120901888-120901947', 'chrX:39909128-39909069'], 'CYTOBAND': [nan, nan, nan, 'hs|7q31.31', 'hs|Xp11.4'], 'DESCRIPTION': [nan, nan, nan, 'Homo sapiens cadherin-like and PC-esterase domain containing 1 (CPED1), transcript variant 2, mRNA [NM_001105533]', 'BCL6 corepressor [Source:HGNC Symbol;Acc:HGNC:20893] [ENST00000378463]'], 'GO_ID': [nan, nan, nan, 'GO:0005783(endoplasmic reticulum)', 'GO:0000122(negative regulation of transcription from RNA polymerase II promoter)|GO:0000415(negative regulation of histone H3-K36 methylation)|GO:0003714(transcription corepressor activity)|GO:0004842(ubiquitin-protein ligase activity)|GO:0005515(protein binding)|GO:0005634(nucleus)|GO:0006351(transcription, DNA-dependent)|GO:0007507(heart development)|GO:0008134(transcription factor binding)|GO:0030502(negative regulation of bone mineralization)|GO:0031072(heat shock protein binding)|GO:0031519(PcG protein complex)|GO:0035518(histone H2A monoubiquitination)|GO:0042476(odontogenesis)|GO:0042826(histone deacetylase binding)|GO:0044212(transcription regulatory region DNA binding)|GO:0045892(negative regulation of transcription, DNA-dependent)|GO:0051572(negative regulation of histone H3-K4 methylation)|GO:0060021(palate development)|GO:0065001(specification of axis polarity)|GO:0070171(negative regulation of tooth mineralization)'], 'SEQUENCE': [nan, nan, 'AATACATGTTTTGGTAAACACTCGGTCAGAGCACCCTCTTTCTGTGGAATCAGACTGGCA', 'GCTTATCTCACCTAATACAGGGACTATGCAACCAAGAAACTGGAAATAAAAACAAAGATA', 'CATCAAAGCTACGAGAGATCCTACACACCCAGATTTAAAAAATAATAAAAACTTAAGGGC'], 'SPOT_ID': ['GE_BrightCorner', 'DarkCorner', 'A_21_P0014386', 'A_33_P3396872', 'A_33_P3267760']}\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": "daced846",
"metadata": {},
"source": [
"### Step 6: Gene Identifier Mapping"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "ca7c8025",
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"execution": {
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Total probes with gene symbol mappings: 48862\n",
"First 5 gene mapping records:\n",
" ID Gene\n",
"3 A_33_P3396872 CPED1\n",
"4 A_33_P3267760 BCOR\n",
"5 A_32_P194264 CHAC2\n",
"6 A_23_P153745 IFI30\n",
"10 A_21_P0014180 GPR146\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Gene expression data shape after mapping: (21476, 80)\n",
"First 10 gene symbols after mapping:\n",
"Index(['A1BG', 'A1BG-AS1', 'A1CF-3', 'A2M', 'A2M-1', 'A2M-AS1', 'A2ML1',\n",
" 'A2MP1', 'A4GALT', 'AAAS'],\n",
" dtype='object', name='Gene')\n"
]
}
],
"source": [
"# 1. Identify which columns in the gene annotation data correspond to:\n",
"# - Probe identifiers (same format as in gene expression data)\n",
"# - Gene symbols\n",
"\n",
"# The gene expression data uses identifiers starting with \"A_19_P\" format\n",
"# In the gene annotation data, the \"ID\" column holds these probe identifiers \n",
"# The \"GENE_SYMBOL\" column holds the gene symbols\n",
"\n",
"# 2. Create the gene mapping dataframe by extracting these two columns\n",
"gene_mapping = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='GENE_SYMBOL')\n",
"\n",
"# Check how many probe IDs have gene symbol mappings\n",
"print(f\"Total probes with gene symbol mappings: {len(gene_mapping)}\")\n",
"print(\"First 5 gene mapping records:\")\n",
"print(gene_mapping.head())\n",
"\n",
"# 3. Convert probe-level measurements to gene-level expression using the mapping\n",
"# This handles the many-to-many mapping between probes and genes\n",
"gene_data = apply_gene_mapping(gene_data, gene_mapping)\n",
"\n",
"print(f\"Gene expression data shape after mapping: {gene_data.shape}\")\n",
"print(\"First 10 gene symbols after mapping:\")\n",
"print(gene_data.index[:10])\n"
]
},
{
"cell_type": "markdown",
"id": "51914551",
"metadata": {},
"source": [
"### Step 7: Data Normalization and Linking"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "e1153410",
"metadata": {
"execution": {
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"shell.execute_reply": "2025-03-25T06:40:37.251699Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Normalized gene data saved to ../../output/preprocess/Asthma/gene_data/GSE182797.csv\n",
"Clinical data saved to ../../output/preprocess/Asthma/clinical_data/GSE182797.csv\n",
"Linked data shape: (80, 17832)\n",
"Linked data preview (first 5 rows, 5 columns):\n",
" Asthma Age Gender A1BG A1BG-AS1\n",
"GSM5537157 0.0 38.33 0.0 7.77916 5.86818\n",
"GSM5537158 0.0 38.08 0.0 7.59209 5.59018\n",
"GSM5537159 0.0 48.83 0.0 7.45290 5.83891\n",
"GSM5537160 1.0 33.42 0.0 7.30202 5.70201\n",
"GSM5537161 1.0 46.08 0.0 7.39065 5.76369\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Data shape after handling missing values: (66, 17832)\n",
"For the feature 'Asthma', the least common label is '0.0' with 21 occurrences. This represents 31.82% of the dataset.\n",
"The distribution of the feature 'Asthma' in this dataset is fine.\n",
"\n",
"Quartiles for 'Age':\n",
" 25%: 39.582499999999996\n",
" 50% (Median): 47.08\n",
" 75%: 53.3725\n",
"Min: 18.42\n",
"Max: 64.67\n",
"The distribution of the feature 'Age' in this dataset is fine.\n",
"\n",
"For the feature 'Gender', the least common label is '0.0' with 66 occurrences. This represents 100.00% of the dataset.\n",
"The distribution of the feature 'Gender' in this dataset is severely biased.\n",
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"A new JSON file was created at: ../../output/preprocess/Asthma/cohort_info.json\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Linked data saved to ../../output/preprocess/Asthma/GSE182797.csv\n"
]
}
],
"source": [
"# 1. Normalize gene symbols in the gene expression data\n",
"gene_data = normalize_gene_symbols_in_index(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\"Normalized gene data saved to {out_gene_data_file}\")\n",
"\n",
"# Define the correct convert_trait function as established in Step 2\n",
"def convert_trait(value: str) -> Optional[int]:\n",
" \"\"\"Convert trait values to binary (0 for control, 1 for Asthma).\"\"\"\n",
" if pd.isna(value):\n",
" return None\n",
" \n",
" # Extract value after colon\n",
" if \":\" in value:\n",
" value = value.split(\":\", 1)[1].strip()\n",
" \n",
" # Convert to binary\n",
" if \"adult-onset asthma\" in value.lower():\n",
" return 1 # Asthma\n",
" elif \"healthy\" in value.lower():\n",
" return 0 # Control\n",
" else:\n",
" return None # IEI or other conditions\n",
"\n",
"def convert_age(value: str) -> Optional[float]:\n",
" \"\"\"Convert age values to float.\"\"\"\n",
" if pd.isna(value):\n",
" return None\n",
" \n",
" # Extract value after colon\n",
" if \":\" in value:\n",
" value = value.split(\":\", 1)[1].strip()\n",
" \n",
" try:\n",
" return float(value)\n",
" except ValueError:\n",
" return None\n",
"\n",
"def convert_gender(value: str) -> Optional[int]:\n",
" \"\"\"Convert gender values to binary (0 for female, 1 for male).\"\"\"\n",
" if pd.isna(value):\n",
" return None\n",
" \n",
" # Extract value after colon\n",
" if \":\" in value:\n",
" value = value.split(\":\", 1)[1].strip().lower()\n",
" \n",
" if \"female\" in value:\n",
" return 0\n",
" elif \"male\" in value:\n",
" return 1\n",
" else:\n",
" return None\n",
"\n",
"# Re-extract clinical features using the appropriate conversion functions\n",
"selected_clinical_df = geo_select_clinical_features(\n",
" clinical_df=clinical_data,\n",
" trait=trait,\n",
" trait_row=0, # Correct trait row from Step 2\n",
" convert_trait=convert_trait,\n",
" age_row=2, # Age row from Step 2\n",
" convert_age=convert_age,\n",
" gender_row=1, # Gender row from Step 2\n",
" convert_gender=convert_gender\n",
")\n",
"\n",
"# Save the processed clinical data\n",
"os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n",
"selected_clinical_df.to_csv(out_clinical_data_file)\n",
"print(f\"Clinical data saved to {out_clinical_data_file}\")\n",
"\n",
"# 2. Link clinical and genetic data\n",
"linked_data = geo_link_clinical_genetic_data(selected_clinical_df, gene_data)\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] if not linked_data.empty else \"Linked data is empty\")\n",
"\n",
"# 3. Handle missing values\n",
"linked_data = handle_missing_values(linked_data, trait)\n",
"print(f\"Data shape after handling missing values: {linked_data.shape}\")\n",
"\n",
"# 4. Check for bias in features\n",
"is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)\n",
"\n",
"# 5. Validate and save 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=True,\n",
" is_biased=is_biased,\n",
" df=linked_data,\n",
" note=\"Dataset contains gene expression data from adult patients with asthma related to damp/moldy buildings and controls.\"\n",
")\n",
"\n",
"# 6. Save the linked data if usable\n",
"if is_usable:\n",
" os.makedirs(os.path.dirname(out_data_file), exist_ok=True)\n",
" linked_data.to_csv(out_data_file)\n",
" print(f\"Linked data saved to {out_data_file}\")\n",
"else:\n",
" print(\"Dataset is not usable for analysis. No linked data file saved.\")"
]
}
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