validate_files

Validates BAM, bigWig, and BED files for deepTools analysis. Checks for file existence, proper indexing, and basic format requirements.

Skills
Scientific
0

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
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Install (Claude Code)

mkdir -p .claude/skills/validate-files && curl -fsSL https://doutorai.pt/data/lib/skills__validate-files.md -o .claude/skills/validate-files/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

#!/usr/bin/env python3
"""
deepTools File Validation Script

Validates BAM, bigWig, and BED files for deepTools analysis.
Checks for file existence, proper indexing, and basic format requirements.
"""

import os
import sys
import argparse
from pathlib import Path


def check_file_exists(filepath):
    """Check if file exists and is readable."""
    if not os.path.exists(filepath):
        return False, f"File not found: {filepath}"
    if not os.access(filepath, os.R_OK):
        return False, f"File not readable: {filepath}"
    return True, f"✓ File exists: {filepath}"


def check_bam_index(

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