pysam-genomic-files
CommunityManipulate genomic files with Python.
Authorjaechang-hits
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill simplifies the complex task of reading, writing, and querying standard genomic file formats like BAM, VCF, and FASTA, enabling efficient bioinformatics analysis directly within your Python environment.
Core Features & Use Cases
- Alignment File Handling: Read, filter, and write SAM, BAM, and CRAM alignment files.
- Variant File Processing: Parse, filter, and analyze VCF and BCF variant files.
- Sequence Access: Efficiently retrieve sequences from indexed FASTA files.
- Coverage & Pileup: Calculate per-base coverage and detailed read pileups.
- CLI Integration: Seamlessly call samtools and bcftools commands from Python.
Quick Start
Use the pysam-genomic-files skill to read the first 10 reads from the 'sample.bam' file in the region chr1:10000-20000.
Dependency Matrix
Required Modules
None requiredComponents
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: pysam-genomic-files Download link: https://github.com/jaechang-hits/SciAgent-Skills/archive/main.zip#pysam-genomic-files Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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