igvf-data-collect

Here are some scripts to collect analysis-sets and per-sample information from the IGVF portal.

Overview

This repository contains tools to extract sequencing data information from the IGVF portal and download the associated FASTQ files.

Scripts

1. analysis_to_sample.py

Extracts data from the IGVF portal for a given analysis set ID and generates two TSV files:

• An analysis sets file mapping IDs to measurement/auxiliary sets (tsv)
• A per-sample file containing sequencing details (paths, checksums, modalities, etc.) (tsv)

Usage

python analysis_to_sample.py -i ANALYSIS_SET_ID --access-key ACCESS_KEY --secret-key SECRET_KEY -per-sample-output per_sample_file.tsv -analysis-set-output analysis_sets.tsv

2. download_fastq.py

Downloads all FASTQ files listed in the per-sample file generated from the previous step.

Usage

python download_fastq.py --sample per-sample_file.tsv --access-key ACCESS_KEY --secret-key SECRET_KEY

This will create a directory fastq_files and download all FASTQ files into this directory.