Biopython – Sequence File Formats

Bio.SeqIO module of Biopython provides a wide range of simple uniform interfaces to input and output the desired file formats. This file formats can only deal with the sequences as a SeqRecord object. Lowercase strings are used while specifying the file format. The same formats are also supported by the Bio.AlignIO module. The list of the file formats is given below :

File Format	Description
abi	It is sequencing trace format for Applied Biosystem, reads the Sanger capillary sequence including PHRED quality scores for base calls. Each file contains only one sequence so no point of indexing the file.
abi-trim	Same as the abi format but has a quality trimming with Mott’s algorithm.
ace	Reads the overlapping or contiguous sequences from the ACE assembly file.
cif-atom	Used to figure out the partial protein sequence by structure based on atomic coordinates
cif-seqres	Determines the complete protein sequence by reading a macromolecular Crystallographic Information File(also known as mmCIF) as defined by the _pdbx_poly_seq_scheme record.
embl	EMBL(Protein and DNA seq file format) flat file format, uses Bio.GenBank internally.
fasta	A generic sequence file format, each record starts with a line starting with > character followed by other sequence lines.
fasta-2line	Strict interpretation of FASTA file format by no line wrapping(i.e. using two line per record).
fastq	A FASTA variant with Sanger used to store PHRED sequence quality values with an ASCII of offset 33.
fastq-sanger	Alias for FASTA having consistency with BioPerl and EMBOSS
fastq-solexa	Original Solexa/Illumnia interpretation of FASTA format which is used to encode solexa quality scores with ASCII having offset of 64.
fastq-illumina	Solexa/Illumnia 1.3 to 1.7 version of FASTA format used to encode PHRED quality scores with ASCII of offset 64.
gck	Local format used by Gene Construction Kit.
genbank	GenBank or GenPept flat file format.
gb	Alias for genbank, having consistency with NCBI Entrez Utilities.
ig	IntelliGenetics file format, appears to be same as the MASE alignment format.
imgt	EMBL variant format from IMGT, where feature tables are intentionally allowed for longer feature types.
nib	UCSC nib file format for nucleotide uses 4-bits(1-nibble) to represent one nucleotide(2 nucleotides require i byte).
nexus	NEXUS multiple alignment format, also called PAUP format.
pdb-seqres	Reads PDB(Protein Data Bank) file and determines complete data sequence by header.
pdb-atom	Determines partial protein sequence by structure based on atomic coordinates section of file.
phd	These files are output of PHRED, used by PHRAP and CONSED for input.
pir	FASTA variant created by NBRF(National Biomedical Research Foundation) for Protein Information Resource database(PIR), presently art of UniProt.
seqxml	Simple XML file format.
sff	Standard Flow gram Format binary files created by Roche 454 and IonTorrent/IonProton sequencing machines.
sff-trim	Standard Flow gram Format (SFF) applies trimming to listed files.
snapgene	Local format used by SnapGene.
swiss	Plain text Swiss-Pro also called UniProt format.
tab	Simple two column tab separated sequence file, each line stores record identifier and sequence.
qual	FASTA variant having PHRED quality values from sequencing DNA.
uniprot-xml	UniProt XML format replacement of SwissProt plain text format.
xdna	DNA Strider’s and SerialCloner’s local format, used by Christian Marck.

Below implementation explains about how to parse two of the most popular sequence file formats, i.e. FASTA and GenBank.

FASTA:

It is the most basic file format to store sequence data. Originally FASTA was a software package created during early evolution of Bioinformatics for sequence alignment of proteins and DNA, mostly used for searching similarities. Below is a simple example of parsing FASTA file format:

Example:

To get the input file used click here.

Python3

# Import libraries
from Bio.SeqIO import parse

# file path/location
file = open('is_orchid.fasta')

# Parsing the FASTA file
for record in parse(file, "fasta"):
    print(record.id)

Output:

GeneBank:

Richer sequence format for genes which includes various annotations. Parsing the GenBank format is as simple as changing the format option in Biopython parse method. Below is a simple example of parsing GenBank file format:

Example:

To get the input file used click here.

Python3

# Import libraries
from Bio import SeqIO
from Bio.SeqIO import parse

# Parsing Sequence
seq_record = next(parse(open('is_orchid.gbk'), 'genbank'))

# Sequence ID
print("\nSequence ID :", seq_record.id)

# Sequence Name
print("\nSequence Name :", seq_record.name)

# Sequence
print("\nSequence  :", seq_record.seq)

# Sequence Description
print("\nSequence ID :", seq_record.description)

# Sequence Annotations
print("\nSequence Annotations :", seq_record.annotations)

Output: