Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between streaming, in-memory, and on-disk-indexed access. Use when parsing sequence files, iterating multi-record files, randomly accessing records by ID in large files, or maximizing parse throughput.
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Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between streaming, in-memory, and on-disk-indexed access. Use when parsing sequence files, iterating multi-record files, randomly accessing records by ID in large files, or maximizing parse throughput.
tool_type
python
primary_tool
Bio.SeqIO
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 a file into SeqRecord objects exposing id, sequence, and annotations.
Stream by default. SeqIO.parse() yields one record at a time and never holds the whole file in RAM, so it scales to any size. Reach for an in-memory or indexed structure only when the access pattern demands it: load all records () only for small files needing random access; build an index ( / ) for random access into large files. Never a huge file or it - that defeats streaming and can exhaust memory.
to_dict
index
index_db
list()
to_dict()
Which Function to Use
Method
Returns
Memory model
Random access
Persists
Multi-file
parse(handle, format)
generator of SeqRecord
one record at a time
no
no
no
read(handle, format)
one SeqRecord
one record
n/a
no
no
to_dict(records)
real dict
ALL records in RAM
yes
no
feed combined iterators
index(filename, format)
dict-like (read-only)
byte offsets only, re-parses on access
yes
no
no
index_db(idx_file, files, format)
dict-like (read-only)
on-disk SQLite index
yes
yes
yes
Decision rule: parse for streaming; read for a known single-record file; to_dict when the file is small and random access by ID is needed; index for random access into one large file; index_db for files larger than RAM, many files indexed together, or an index reused across runs.
Behavioral traps these methods hide:
parse() is a one-pass generator. It is NOT subscriptable (parse(...)[3] raises TypeError), and it EXHAUSTS SILENTLY: a second for loop over the same generator object yields nothing with no error. Re-call parse() for each pass, or list() it once if the file is small.
read() fails LOUDLY: zero records raise ValueError: No records found in handle; more than one raises ValueError: More than one record found in handle. Use it as an assertion that the file holds exactly one sequence.
to_dict(), index(), and index_db() all raise ValueError on a DUPLICATE id (Duplicate key '...'). Supply a key_function to derive unique keys when ids collide.
index() needs a FILENAME, not a handle (it must seek). It stores only byte offsets and re-parses the record from disk on every access, so it returns a fresh object each time and mutations do not persist. It is read-only (__setitem__ raises NotImplementedError).
index_db() stores the offset index in an on-disk SQLite file. It PERSISTS across sessions (reopen later with just the index filename), and scales beyond RAM and across multiple files (pass a list of filenames). This is the right answer for data larger than memory.
The alphabet= argument still appears in some signatures for back-compatibility but is a no-op since BioPython 1.78; leave it None.
Required Import
from Bio import SeqIO
Reading Records
SeqIO.parse() - Stream Multiple Records
Returns a one-pass iterator of SeqRecord objects. Always pass the format explicitly as the second argument.
for record in SeqIO.parse('sequences.fasta', 'fasta'):
print(record.id, len(record.seq))
SeqIO.read() - Exactly One Record
Use when the file must contain a single sequence; raises on zero or multiple records.
record = SeqIO.read('single.fasta', 'fasta')
Random Access
SeqIO.to_dict() - Small Files
Loads every record into a dictionary keyed by id. Fast random access, but holds all records in RAM.
records = SeqIO.to_dict(SeqIO.parse('sequences.fasta', 'fasta'))
seq = records['sequence_id'].seq
SeqIO.index() - One Large File
Goal: Random access by id into a large file without loading every record into memory.
Approach: Build an in-memory map of byte offsets keyed by id; each lookup re-parses one record from disk.
Reference (BioPython 1.83+):
records = SeqIO.index('large.fasta', 'fasta')
seq = records['sequence_id'].seq
records.close()
A key_function maps the id STRING to a custom key (note: to_dict's key_function receives the whole record instead):
defget_accession(identifier):
return identifier.split('.')[0] # drop the version suffix
records = SeqIO.index('sequences.fasta', 'fasta', key_function=get_accession)
SeqIO.index_db() - Huge / Multiple Files
Goal: Random access into data larger than RAM, or across many files, with the index reusable across runs.
Approach: Persist the offset index in an on-disk SQLite database; reopen it later without re-parsing.
Reference (BioPython 1.83+):
# First call parses the file(s) and builds the SQLite index
records = SeqIO.index_db('index.sqlite', 'large.fasta', 'fasta')
seq = records['sequence_id'].seq
records.close()
# Later sessions reopen instantly with just the index filename
records = SeqIO.index_db('index.sqlite')
# Index multiple files as one database
records = SeqIO.index_db('combined.sqlite', ['file1.fasta', 'file2.fasta'], 'fasta')
High-Performance Parsing
For maximum throughput on large files, low-level parsers (SimpleFastaParser, FastqGeneralIterator) yield raw tuples and skip SeqRecord construction, so they run substantially faster than SeqIO.parse.
SimpleFastaParser
Goal: Parse large FASTA files at maximum speed without SeqRecord overhead.
Approach: Iterate (title, sequence) string tuples directly from the handle.
Reference (BioPython 1.83+):
from Bio.SeqIO.FastaIO import SimpleFastaParser
withopen('large.fasta') as handle:
for title, sequence in SimpleFastaParser(handle):
iflen(sequence) > 1000:
seq_id = title.split()[0] # first whitespace token is the id
from Bio.SeqIO.QualityIO import FastqGeneralIterator
withopen('reads.fastq') as handle:
for title, sequence, quality in FastqGeneralIterator(handle):
avg_qual = sum(ord(c) - 33for c in quality) / len(quality) # Phred+33
SeqRecord Attributes
After parsing, each record exposes:
record.id# first whitespace token of the header (string)
record.name # same first token (for FASTA, name == id)
record.description # the ENTIRE header after '>', including the id token
record.seq # sequence data (Seq object; case-preserving)
record.features # list of SeqFeature objects (GenBank/EMBL)
record.annotations # dict of annotations (organism, molecule_type, ...)
record.letter_annotations # per-letter dict (e.g. 'phred_quality' list)
record.dbxrefs # database cross-references
id vs name vs description - the first-space split
A FASTA header >FIRST rest of the line parses to: id = FIRST (the first whitespace token), name = FIRST (same token), description = FIRST rest of the line (the WHOLE header after >, including the id). So >seq1 some desc gives id seq1, name seq1, description seq1 some desc. The id is therefore the leading word of the description, not a separate field - relevant when writing records back out.
Common Formats
Format
String
Typical Extension
Notes
FASTA
'fasta'
.fasta, .fa, .fna, .faa
Most common
FASTA 2-line
'fasta-2line'
.fasta
One line per sequence (no wrapping)
FASTQ
'fastq'
.fastq, .fq
Alias of fastq-sanger (Phred+33)
FASTQ Solexa
'fastq-solexa'
.fastq
Old Solexa (Solexa+64, scores -5..62)
FASTQ Illumina
'fastq-illumina'
.fastq
Illumina 1.3-1.7 (Phred+64)
GenBank
'genbank' or 'gb'
.gb, .gbk
With features/annotations
EMBL
'embl'
.embl
European format with features
Swiss-Prot
'swiss'
.dat
UniProt format
FASTQ quality encoding cannot be auto-detected reliably: the same quality line can be valid Phred+33 and Phred+64. Picking the wrong string can silently shift every score by 31. Confirm the encoding before parsing; see fastq-quality for the full encoding decision.
for record in SeqIO.parse('reads.sff', 'sff'):
print(record.id, len(record.seq))
Reading PDB Sequences
for record in SeqIO.parse('structure.pdb', 'pdb-seqres'):
print(record.id, record.seq)
Alignment Formats (Read-Only)
Format
String
Notes
PHYLIP
'phylip'
Interleaved; 'phylip-relaxed' allows longer names
Clustal
'clustal'
ClustalW output
Stockholm
'stockholm'
Rfam/Pfam alignments
NEXUS
'nexus'
PAUP/MrBayes format
MAF
'maf'
Multiple Alignment Format
Code Patterns
Count Records Without Loading All
count = sum(1for _ 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':
product = feature.qualifiers.get('product', ['Unknown'])[0]
cds_seq = feature.extract(record.seq) # spliced 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 a File Handle
withopen('sequences.fasta') as handle:
for record in SeqIO.parse(handle, 'fasta'):
print(record.id)
Common Errors
Symptom
Cause
Fix
Second loop over a parser yields nothing, no error
parse() generator exhausted after the first pass
Re-call parse() per pass, or list() once for small files
TypeError: 'generator' object is not subscriptable
Indexed/sliced a parse() result
Wrap in list(), or use to_dict/index for keyed access
ValueError: More than one record found in handle
read() on a multi-record file
Use parse()
ValueError: No records found in handle
read() on an empty/zero-record file
Check the file and format string; use parse() if multi-record
ValueError: Duplicate key '...'
to_dict/index/index_db hit a repeated id
Pass a key_function that derives unique keys
Random access by id silently slow / re-reads disk
index() re-parses each access; mutations don't persist
Expected; cache needed records, or use to_dict for small files
MemoryError / process killed on a huge file
list() or to_dict() loaded everything into RAM
Stream with parse(); use index_db() for random access
ValueError: unknown format
Misspelled format string
Use a lowercase string from the format tables
ValueError/AssertionError naming the LOCUS line
GenBank parser reads fixed LOCUS columns (molecule type ~44-54, topology ~55-63); ICE/SnapGene/Ensembl/assembler LOCUS lines violate the spec
Biologically valid content can still fail the strict column parse; fix the LOCUS columns or re-export from a spec-compliant writer
FASTQ scores all off by ~31 with no error
Wrong FASTQ variant string (Phred+33 vs +64 overlap)
Confirm encoding; see fastq-quality
AttributeError referencing .alphabet
Code assumes pre-1.78 alphabet API
Drop alphabet usage; molecule type lives in annotations['molecule_type']
Related Skills
write-sequences - Write parsed sequences to new files
filter-sequences - Filter sequences by criteria after reading
format-conversion - Convert between formats (GenBank->FASTA silently drops annotations)
compressed-files - Read gzip/bzip2/BGZF compressed files; only BGZF supports indexed random access
fastq-quality - FASTQ encoding (Phred vs Solexa) and offset selection
sequence-manipulation/seq-objects - Work with parsed SeqRecord and Seq objects
database-access/entrez-fetch - Fetch sequences from NCBI instead of local files
alignment-files/sam-bam-basics - For SAM/BAM/CRAM alignment files, use samtools/pysam
