RNASQLite is a tool for managing RNA-Seq data with SQLite. This package allows you to process RNA-Seq counts files, insert count files into a database, and retrieve sample information from the database.
First, navigate to the directory containing setup.py and install the package:
pip install .Alternatively, if the package is available on PyPI, you can install it directly:
pip install RNASQLite
Create Database Create a new database.
RNASQLite -create
Process and Split RNAseq Counts File Process the given RNAseq counts file and save the count files for each sample in the counts directory. This step uses the gene info file (gene_info.csv) to add gene information.
RNASQLite -split path/to/your/rna_seq_counts_file.csv
Insert Count Files into Database Read the count files from the counts directory and insert them into the database.
RNASQLite -load
Fetch All Samples from Database Retrieve all sample information from the database.
RNASQLite -fetch
Fetch Samples by Column and Value Fetch samples from the database by specifying a column name and a value. This command extracts count data for samples matching the specified condition and saves the result as a CSV file.
RNASQLite -column COLUMN VALUE
Example:
RNASQLite -column GSE_number GSE201396
In this example, the command fetches all samples from the database where the GSE_number column matches GSE201396. The count data for these samples are then combined into a single CSV file. The file is named based on the column and value provided, e.g., filtered_GSE_number_GSE201396.csv.
RNASQLite/cli.py: Handles the command line interface.
RNASQLite/db_utils.py: Contains utility functions related to the database.
RNASQLite/process_file.py: Processes the given gene_info.csv and RNAseq counts file to generate count files.
gene_info.csv: CSV file containing gene information.
setup.py: Contains package metadata and dependencies.
README.md: This file, which includes the description and usage of the RNASQLite package.