This source did not publish a separate summary. Review SKILL.md before using the skill.
SKILL.md
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
from Bio import SeqIO
Core Functions
SeqIO.parse() - Multiple Records
Use for files with one or more sequences. Returns an iterator of SeqRecord objects.
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 sequence. Raises error if zero or multiple records.
record = SeqIO.read('single.fasta', 'fasta')
SeqIO.to_dict() - Load All Into Memory
Use for random access by record ID. Loads entire file into memory.
records = SeqIO.to_dict(SeqIO.parse('sequences.fasta', 'fasta'))
seq = records['sequence_id'].seq
SeqIO.index() - Large File Random Access
Use for large files when random access is needed without loading everything into memory.
records = SeqIO.index('large.fasta', 'fasta')
seq = records['sequence_id'].seq
records.close()
SeqIO.index_db() - SQLite-Backed Indexing
Use for very large files or multiple files. Creates persistent SQLite index.
# Create index (first time - parses file)
records = SeqIO.index_db('index.sqlite', 'large.fasta', 'fasta')
seq = records['sequence_id'].seq
records.close()
# Reuse existing index (instant load)
records = SeqIO.index_db('index.sqlite')
# Index multiple files together
records = SeqIO.index_db('combined.sqlite', ['file1.fasta', 'file2.fasta'], 'fasta')
Advantages over index():
Persistent index survives program restarts
Can index multiple files as one database
Lower memory for extremely large files
SQLite file can be shared across processes
High-Performance Parsing
For maximum throughput on large files, use low-level parsers (3-6x faster than SeqIO.parse):
SimpleFastaParser
Goal: Parse large FASTA files at maximum speed without SeqRecord overhead.
Approach: Use low-level tuple-based parser returning (title, sequence) strings.
Reference (BioPython 1.83+):
from Bio.SeqIO.FastaIO import SimpleFastaParser
with open('large.fasta') as handle:
for title, sequence in SimpleFastaParser(handle):
if len(sequence) > 1000:
print(title.split()[0]) # First word is usually ID
Returns (title, sequence) tuples as strings (no SeqRecord overhead).
FastqGeneralIterator
Goal: Parse large FASTQ files at maximum speed.
Approach: Use low-level tuple-based parser returning (title, sequence, quality_string) strings.
Reference (BioPython 1.83+):
from Bio.SeqIO.QualityIO import FastqGeneralIterator
with open('reads.fastq') as handle:
for title, sequence, quality in FastqGeneralIterator(handle):
avg_qual = sum(ord(c) - 33 for c in quality) / len(quality)
for record in SeqIO.parse('reads.sff', 'sff'):
print(record.id, len(record.seq))
# With trimming applied
for record in SeqIO.parse('reads.sff', 'sff-trim'):
print(record.id, len(record.seq))
Reading PDB Sequences
# Get sequences from SEQRES records
for record in SeqIO.parse('structure.pdb', 'pdb-seqres'):
print(f'Chain {record.id}: {record.seq}')
# Get sequences from ATOM coordinates
for record in SeqIO.parse('structure.pdb', 'pdb-atom'):
print(f'Chain {record.id}: {record.seq}')
Alignment Formats (Read-Only)
Format
String
Notes
PHYLIP
'phylip'
Interleaved phylip
PHYLIP Sequential
'phylip-sequential'
Sequential phylip
PHYLIP Relaxed
'phylip-relaxed'
Longer names allowed
Clustal
'clustal'
ClustalW output
Stockholm
'stockholm'
Rfam/Pfam alignments
NEXUS
'nexus'
PAUP/MrBayes format
MAF
'maf'
Multiple Alignment Format
SeqRecord Object Attributes
After parsing, each record has these key attributes:
record.id # Sequence identifier (string)
record.name # Sequence name (string)
record.description # Full description line (string)
record.seq # Sequence data (Seq object)
record.features # List of SeqFeature objects (GenBank/EMBL)
record.annotations # Dictionary of annotations
record.letter_annotations # Per-letter annotations (quality scores)
record.dbxrefs # Database cross-references
Code Patterns
Collect All Sequences Into a List
records = list(SeqIO.parse('sequences.fasta', 'fasta'))
Count Records Without Loading All
count = sum(1 for _ in SeqIO.parse('sequences.fasta', 'fasta'))
Fast Count (FASTA only)
from Bio.SeqIO.FastaIO import SimpleFastaParser
with open('sequences.fasta') as f:
count = sum(1 for _ in SimpleFastaParser(f))
Get Sequence IDs Only
ids = [record.id for record in SeqIO.parse('sequences.fasta', 'fasta')]
Read GenBank with Features
for record in SeqIO.parse('sequence.gb', 'genbank'):
for feature in record.features:
if feature.type == 'CDS':
print(feature.qualifiers.get('product', ['Unknown'])[0])
cds_seq = feature.extract(record.seq) # Get feature sequence
Access FASTQ Quality Scores
for record in SeqIO.parse('reads.fastq', 'fastq'):
qualities = record.letter_annotations['phred_quality']
avg_quality = sum(qualities) / len(qualities)
Read From File Handle
with open('sequences.fasta', 'r') as handle:
for record in SeqIO.parse(handle, 'fasta'):
print(record.id)
Custom ID Function for Indexing
def get_accession(identifier):
return identifier.split('.')[0] # Remove version
records = SeqIO.index('sequences.fasta', 'fasta', key_function=get_accession)
Common Errors
Error
Cause
Solution
ValueError: More than one record
Used read() on multi-record file
Use parse() instead
ValueError: No records found
Used read() on empty file
Check file exists and has content
ValueError: unknown format
Typo in format string
Check format string spelling
UnicodeDecodeError
Binary file or wrong encoding
Open with encoding='latin-1' or check file
sqlite3.OperationalError
index_db file locked
Close other connections first
Decision Tree
Need to read sequences?
├── Single record in file?
│ └── Use SeqIO.read()
├── Multiple records?
│ ├── Need all in memory at once?
│ │ └── Use list(SeqIO.parse()) or SeqIO.to_dict()
│ ├── Process one at a time (memory efficient)?
│ │ └── Use SeqIO.parse() iterator
│ ├── Large file, need random access by ID?
│ │ ├── Single session? → Use SeqIO.index()
│ │ └── Persistent/multi-file? → Use SeqIO.index_db()
│ └── Maximum throughput needed?
│ └── Use SimpleFastaParser or FastqGeneralIterator
├── Sanger sequencing trace?
│ └── Use 'abi' or 'abi-trim' format
├── 454/Ion Torrent data?
│ └── Use 'sff' or 'sff-trim' format
└── Protein from structure?
└── Use 'pdb-seqres' or 'pdb-atom' format
Related Skills
write-sequences - Write parsed sequences to new files
filter-sequences - Filter sequences by criteria after reading
