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fastqc_db's Introduction

This is a small project to read fastqc_files into a database and display the results. Two options makes a sqlite3 database of results, and one just displays the results without making a database (No DB).

The full version creates a DB with the following schema:

CREATE TABLE fastqc_archive (id INTEGER PRIMARY KEY, file_name TEXT UNIQUE, version TEXT);
CREATE TABLE basic_statistics (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE per_base_sequence_quality (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE per_tile_sequence_quality (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE per_sequence_quality_scores (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE per_base_sequence_content (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE per_sequence_gc_content (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE per_base_n_content (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE sequence_length_distribution (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE sequence_duplication_levels (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE overrepresented_sequences (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE adapter_content (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);
CREATE TABLE kmer_content (id INTEGER PRIMARY KEY, result TEXT, raw_data TEXT, graph BLOB);

The results db creates a DB with the schema:

CREATE TABLE basic (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    filename TEXT,
    filetype TEXT,
    encoding TEXT,
    total_sequences TEXT,
    filtered_sequences TEXT,
    sequence_length TEXT,
    percent_gc TEXT
);

CREATE TABLE module_stats (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    overall TEXT,
    per_base_sequence_quality TEXT,
    per_tile_sequence_quality TEXT,
    per_sequence_quality_scores TEXT,
    per_base_sequence_content TEXT,
    per_sequence_gc_content TEXT,
    per_base_n_content TEXT,
    sequence_length_distribution TEXT,
    sequence_duplication_levels TEXT,
    overrepresented_sequences TEXT,
    adapter_content TEXT,
    kmer_content TEXT
);

The full database also generates a simple Flask application that reads all zipped files in a direcory and parses them into a table for display. As such, this application requires Flask to be installed (either on the system, or using a virtualenv). Once the application is running, people on your local network can see it by visiting [your IP address]:5000 on your favorite browser

Usage:

python3 Full\ DB/fastqc_db.py <input_root> <database_name.db>

The results DB searches a directory for fastqc_data.txt files and reads them into a database

Usage:

python3 Results\ DB/fastqc_results_db.py <input_root> <database_name.db>

Usage:

python3 No\ DB/fastqc_report.py <input_root>

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