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A lightweight Python package to read and write sequence records in FASTA format.
The design was inspired by the utility of BioPython’s SeqIO, which supports many sequence formats. This repo focuses only on FASTA records. It is faster than BioPython, can handle compressed FASTA files (gzip, bzip2, zip), and has no Python package dependencies.
Python >= 3.8
You can install fastapy from PyPI:
pip install fastapy
or directly from GitHub:
pip install "git+https://github.com/aziele/fastapy.git"You can also use fastapy without installation since it doesn't have any dependencies. Simply clone or download this repository and you're ready to use it.
git clone https://github.com/aziele/fastapy.git cd fastapy python >>> import fastapy >>> fastapy.__doc__ 'A lightweight Python module to read and write FASTA sequence records'
Typical usage is to read a FASTA file and loop over the sequences record(s).
import fastapy for record in fastapy.parse('tests/test.fasta'): print(record.id, len(record), record.seq[:10], record.desc)
Output:
NP_002433.1 362 METDAPQPGL RNA-binding protein Musashi homolog 1 [Homo sapiens]
ENO94161.1 79 MKLLISGLGP RRM domain-containing RNA-binding protein
sequence 292 MKLSKIALMM
This module contains the Record class representing a FASTA sequence record and the parse() function to read FASTA records from a file.
Record is an object that contains information on a FASTA sequence record, including id, description, and the sequence itself.
import fastapy record = fastapy.Record( id='NP_950171.2', seq='MEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFASICRKRQE', desc='APITD1-CORT protein isoform 2 [Homo sapiens]' ) print(record.id) # NP_950171.2 print(record.desc) # APITD1-CORT protein isoform 2 [Homo sapiens] print(record.seq) # MEEEAE.. print(record.description) # >NP_950171.2 G APITD1-CORT protein isoform 2 [Homo sapiens] print(len(record)) # 77 print('EEEA' in record) # True
By default, the sequence line is wrapped to 70 characters. You can provide the line length. Use zero (or None) for no wrapping.
print(record) # >NP_950171.2 APITD1-CORT protein isoform 2 [Homo sapiens] # MEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFAS # ICRKRQE print(record.format(wrap=30)) # >NP_001382951.1 G protein subunit gamma 5 [Homo sapiens] # MEEEAETEEQQRFSYQQRLKAAVHYTVGCL # CEEVALDKEMQFSKQTIAAISELTFRQCEN # FAKDLEMFASICRKRQE print(record.format(wrap=None)) # >NP_950171.2 APITD1-CORT protein isoform 2 [Homo sapiens] # MEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFASICRKRQE
The parse() function is a generator to read FASTA records as Record objects one by one from a file (plain FASTA or compressed using gzip or bzip2). Because only one record is created at a time, very little memory is required.
import fastapy for record in fastapy.parse('tests/test.fasta.gz'): print(record.id)
For some tasks you may need to have a reusable access to the records. For this purpose, you can use the built-in Python list() function to turn the iterator into a list:
import fastapy records = list(fastapy.parse('tests/test.fasta.gz')) print(records[0].id) # First record print(records[-1].id) # Last record
Another common task is to index your records by sequence identifier. Use to_dict() to turn a Record iterator (or list) into a dictionary.
import fastapy records = fastapy.to_dict(fasta.parse('tests/test.fasta.gz')) print(records['NP_002433.1']) # Use any record id
The read() function reads only the first FASTA record from a file. It does not read any subsequent records in the file.
import fastapy seq_record = fastapy.read('tests/test.fasta') print(seq_record.id) # NP_002433.1
You can run tests to ensure that the module works as expected.
python -m unittest discover