Sequence And Format IO

Version Compatibility

Reference examples assume recent stable releases of the preferred tools, especially biopython and the other tools listed below.

Before using code or command patterns, verify installed versions match the environment:

• Python: python -c "import <module>; print(<module>.__version__)"
• CLI: <tool> --version
• If signatures differ, inspect the installed help or API and adapt the pattern instead of retrying unchanged.

Overview

Workflow for foundational sequence parsing, conversion, compression handling, and interval-aware file validation.

When To Use This Skill

• use when the task is file parsing, sequence manipulation, or format conversion
• use when FASTA, FASTQ, BED, GTF, BAM, or related files need validation or transformation
• use when a downstream omics workflow is blocked on messy input files

Quick Route

• If the input is raw or minimally processed data, start with validation and QC before any modeling.
• If the input is already processed, skip directly to the first workflow step that matches the user goal.
• If the user asks for a biological conclusion, always produce at least one QC or confidence artifact alongside the final result.

Progressive Disclosure

• Read references/technical_reference.md when you need deeper tool-selection rules, environment adaptation notes, or extra validation guidance.
• Keep SKILL.md as the main execution path and load the reference file only when the task or failure mode needs the extra detail.

Default Rules

• Prefer Python-first workflows unless the task explicitly requires something else.
• Keep intermediate and final outputs separated.
• Record software versions, reference builds, and key parameters when they affect interpretation.
• Favor reproducible tables and figures over one-off interactive-only outputs.

Expected Inputs

• sequence or annotation files
• format specifications
• optional metadata

Expected Outputs

• validated or converted files
• summary statistics
• format sanity-check reports

Preferred Tools

• biopython
• pysam
• pandas
• basic shell utilities

Starter Pattern

Preferred starting point: biopython
Inputs: sequence or annotation files, format specifications, optional metadata
Outputs: validated or converted files, summary statistics, format sanity-check reports

Workflow

1. Identify file semantics

Do not assume a file is clean just because the extension looks right.

2. Validate core structure

Check headers, coordinates, indexing, compression, and identifier consistency.

3. Convert safely

Preserve metadata and line ordering where downstream tools depend on it.

4. Summarize content

Produce quick counts and sanity-check metrics after transformation.

5. Hand off clean artifacts

Save validated outputs with explicit naming and build context.

Output Artifacts

• Recommended output layout:
• results/ for final tables and serialized objects
• figures/ for plots and static visual exports
• qc/ for checks that justify downstream interpretation
• Minimum expected outputs for this skill:
• validated or converted files
• summary statistics
• format sanity-check reports

Quality Review

• Confirm identifiers and metadata join correctly before modeling or summarizing.
• Generate at least one QC artifact before final biological interpretation.
• Keep raw or minimally processed inputs separate from transformed outputs.
• Check coordinate systems, compression, and index consistency after every conversion.
• Run a lightweight sanity check before handing files to downstream tools.

Anti-Patterns

• silently converting between 0-based and 1-based coordinate systems
• rewriting compressed indexed files without regenerating indexes
• dropping metadata columns during format conversion

Related Skills

• Alignment And Mapping
• Read QC
• Database Access
• Reporting And Figure Export

Optional Supplements

• pysam
• biopython