README.md

UTUC_Classifier

This repository provides a Python package for molecular subtyping prediction of UTUC samples.
Before running predictions, you must check that your input gene names and order are exactly the same as those in the demo files: demo_data/RNA_exp.txt and demo_data/mut_data.txt.

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Installation

1. Clone the repository and enter the directory:

   git clone https://github.com/Hoho1996/UTUC_Classifier.git
   cd UTUC_Classifier

2. Install dependencies and the package:

   pip install .

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Input Data Format

• File format: Tab-separated (.txt or .tsv)
• Rows: Gene names (features)
• Columns: Sample IDs
• Cells: Value for each gene in each sample (mutation: 0/1, expression: TPM)

Example:

	Sample1	Sample2	Sample3
TP53	1	0	1
FGFR3	0	1	0
...	...	...	...

• Gene names (row order) must be exactly the same as in the demo files.
• Sample IDs (column order) should be consistent across data types.
• Files must include headers and row names.
• Fill missing values with 0 or appropriate values.

Demo files for reference:

• demo_data/mut_data.txt
• demo_data/RNA_exp.txt

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Gene Name Consistency Check

Before prediction, check that your input file gene names and order match the demo files. Example code:

import pandas as pd

# Read demo and input files
demo_mutation_data = pd.read_csv("demo_data/mut_data.txt", sep="\t", index_col=0)
your_mutation_data = pd.read_csv("your_mut_data.txt", sep="\t", index_col=0)

if (demo_mutation_data.index == your_mutation_data.index).all():
    print("Gene names and order are consistent. Ready for prediction.")
else:
    raise ValueError("Gene names/order in your input file do not match the demo file. Please check before running!")

Repeat for RNA expression data:

demo_rna_data = pd.read_csv("demo_data/RNA_exp.txt", sep="\t", index_col=0)
your_rna_data = pd.read_csv("your_RNA_exp.txt", sep="\t", index_col=0)

if (demo_rna_data.index == your_rna_data.index).all():
    print("Gene names and order are consistent. Ready for prediction.")
else:
    raise ValueError("Gene names/order in your RNA file do not match the demo file. Please check before running!")

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Prediction Workflow

from utuc_classifier import predict_group

# Check gene name consistency (see above)
result = predict_group("your_mut_data.txt", "your_RNA_exp.txt")
print(result)
result.to_csv("prediction_result.txt", sep="\t", index=False)

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Result Description

• Sample_ID: Sample identifier
• Predicted_Group: Predicted group label (SNF1, SNF2, SNF3)

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FAQ

For questions, please contact the project maintainer.