biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

1.31x

Quality

82%

Does it follow best practices?

Impact

95%

1.31x

Average score across 3 eval scenarios

Securityby

Passed

No findings from the security scan

Evaluation results

98%

54%

DNA Sequence Quality Filtering Pipeline

Sequence file processing and statistics

Criteria

Baseline

With context

uv install command

100%

Explicit imports

100%

Lowercase format string

100%

Iterator-based parsing

100%

gc_fraction usage

100%

Context manager or handle close

100%

75%

Length filter applied

100%

GC filter applied

100%

SeqIO.write for output

100%

Statistics report

100%

molecular_weight with seq_type

100%

No to_dict on large file

100%

Enzyme Family Sequence Similarity Analysis

Protein pairwise alignment

Criteria

Baseline

With context

uv install command

100%

PairwiseAligner used

100%

No pairwise2

100%

BLOSUM62 matrix loaded

100%

Gap penalties set

100%

Explicit imports

100%

Alignment score extracted

100%

Alignment printed or saved

100%

Results file produced

100%

Global mode for similar-length sequences

100%

Context manager or file close

100%

88%

Insulin Gene Sequence Collection from NCBI

NCBI Entrez database access and batch download

Criteria

Baseline

With context

uv install command

100%

Entrez.email set

100%

Handles closed

100%

70%

Explicit imports

100%

Batch pagination used

30%

Local caching

100%

Error handling

100%

75%

esearch used

100%

efetch with correct rettype

100%

SeqIO parse of fetched data

100%

Output report produced

100%

Entrez.read for XML

100%

Repository: wu-yc/LabClaw
Path: skills/bio/biopython/SKILL.md
Commit: df37802

Evaluated: 5 months ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

DNA Sequence Quality Filtering Pipeline Enzyme Family Sequence Similarity Analysis Insulin Gene Sequence Collection from NCBI

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