bio-read-sequences
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show biopython` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Read Sequences 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) ## Required Import #### Core import ```python from Bio import SeqIO ``` ## Core Functions ### SeqIO.parse() - Multiple Records Use for files with one or more sequences. Returns an iterator of SeqRecord objects. ```python for record in SeqIO.parse('sequences.fasta', 'fasta'): print(record.id, len(record.seq)) ``` **Important:** Always specify the format explicitly as the second argument. ### SeqIO.read() - Single Record Use when file contains exactly one seq
- Version Compatibility
- Required Import
- Core Functions
- SeqIO.parse() - Multiple Records
- SeqIO.read() - Single Record
- SeqIO.todict() - Load All Into Memory
- SeqIO.index() - Large File Random Access
- SeqIO.indexdb() - SQLite-Backed Indexing
- High-Performance Parsing
- SimpleFastaParser
- FastqGeneralIterator
- Common Formats
- Specialized Formats
- Reading ABI Trace Files
What does the bio-read-sequences skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-sequences --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.