Sequence Extractor

The app analyzes DNA sequence data and presents it in two different views.

Available at: https://sequence-extractor.streamlit.app/

Here's how it works:

Input Files

1. RS Totales File:

   • Contains RS IDs (e.g., "rs123") and their associated data
   • Required columns: 'dbSNP ID', 'Reference Allele', 'Codigo reference allele', 'Variant Allele', 'Codigo variant allele'
   • Each RS ID appears in one row

2. Variant Tables:

   • Contains genotype data for each individual, showing genetic variations at each RS ID
   • Each file corresponds to one individual
   • Shows which RS IDs were found and their variant frequency

Output Tables

The app provides two different ways to view the results:

1. Codes Table (Two rows per individual)

• Rows: Two rows per individual - one for each allele in the pair
• Columns: One for each RS ID (from the RS Totales file)
• Cells: Contain the genetic code numbers for that position
• Color Coding: Uses colors to distinguish reference (blue text) from variant (red text)

2. Nucleotides Table (One row per individual)

• Rows: One row per individual
• Columns: One for each RS ID (from the RS Totales file)
• Cells: Contain the concatenated nucleotide pairs (e.g., "GC")
• Format: Shows the actual nucleotides (A, C, G, T) rather than codes

Rules for Cell Values

For the Codes Table:

1. RS ID not found in the individual's data:

   • Display the reference code in both rows (blue text)
   • Example: If reference code is "101", both rows show "101"

2. RS ID found with frequency = 1 (homozygous for variant):

   • Display the variant code in both rows (red text, blue background)
   • Example: If variant code is "102", both rows show "102"

3. RS ID found with frequency = 0.5 (heterozygous):

   • Display reference code in first row, variant code in second row (orange background)
   • Example: First row shows "101" (blue), second row shows "102" (red)

For the Nucleotides Table:

1. RS ID not found in the individual's data:

   • Display the reference allele twice (e.g., "GG")

2. RS ID found with frequency = 1 (homozygous for variant):

   • Display the variant allele twice (e.g., "TT")

3. RS ID found with frequency = 0.5 (heterozygous):

   • Display reference + variant allele (e.g., "GT")

Color Coding (Codes Table)

The Codes Table uses colors to make patterns easier to identify:

• Blue text: Reference code
• Red text: Variant code
• Blue background: Homozygous variant (frequency = 1)
• Orange background: Heterozygous variant (frequency = 0.5)
• No background: Reference genotype (RS not found in variant file)

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Development

Developed as a streamlit application for processing Excel files.

Requirements

• Python 3.13 or higher

Setup with UV

Declare new dependencies:

uv add streamlit pandas openpyxl
uv add --dev pytest

Usage

Run the application:

uv run -m streamlit run main.py

Development

Run tests (none for now):

pytest