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BI
bio-read-sequences
Maintainer FreedomIntelligence · Last updated April 1, 2026
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random access to large files, or high-performance parsing.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-sequences
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: SeqIO.parse() or SeqIO.read() (BioPython).
- R: readDNAStringSet() or readAAStringSet() (Biostrings).
- Read biological sequence data from files using Biopython's Bio.SeqIO module.
- Read sequences from a file" → Parse file into a collection of SeqRecord objects with IDs, sequences, and annotations accessible. Python: SeqIO.parse() or SeqIO.read() (BioPython) R: readDNAStringSet() or readAAStringSet() (Biostrings).
- records = SeqIO.index_db('index.sqlite', 'large.fasta', 'fasta') seq = records['sequence_id'].seq records.close().
Source Doc
Excerpt From SKILL.md
SeqIO.parse() - Multiple Records
Use for files with one or more sequences. Returns an iterator of SeqRecord objects.
Important: Always specify the format explicitly as the second argument.
SeqIO.read() - Single Record
Use when file contains exactly one sequence. Raises error if zero or multiple records.
SeqIO.to_dict() - Load All Into Memory
Use for random access by record ID. Loads entire file into memory.
Use cases
- Use when parsing sequence files, iterating multi-sequence files, random access to large files, or high-performance parsing.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- write-sequences - Write parsed sequences to new files
- filter-sequences - Filter sequences by criteria after reading
- format-conversion - Convert between formats
- compressed-files - Read gzip/bzip2/BGZF compressed sequence files
- sequence-manipulation/seq-objects - Work with parsed SeqRecord objects
- database-access - Fetch sequences from NCBI instead of local files
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