pyfastatools 2.3.0

Simple FASTA file tools to parse, edit, subset, split, and perform stats on FASTA files

FASTA file parsing written in C++ with Python bindings

Installation

pip install pyfastatools

Usage

The pyfastatools.Parser object is the primary API that parses FASTA files and yields pyfastatools.Record objects.

If you have a FASTA file called proteins.faa that looks like this:

>seq_1
MSKFKKIPL
>seq_2
MQSSSKTCN
>seq_3
MEDNMITIY

Then you can parse this file in python like this:

from pyfastatools import Parser

for record in Parser("proteins.faa"):
    print(record.header.name, record.seq)

which will print:

>>> 'seq_1 MSKFKKIPL'
>>> 'seq_2 MQSSSKTCN'
>>> 'seq_3 MEDNMITIY'

API

This library has a very simple API that can be displayed in a few lines:

Parser

This is the main class that will satisfy 99% of user needs. While parsing FASTA files, it produces Record objects. Only the name of a FASTA file is needed:

pyfastatools.Parser("my_fasta.fasta")

The parser will attempt to auto-detect the RecordType of the file by checking the input file extension and the first 5 sequences.

However, the record type can optionally be specified:

pyfastatools.Parser("my_fasta.fasta", pyfastatools.RecordType.PROTEIN)

The parser can be iterated over to yield one Record at a time:

parser = pyfastatools.Parser("my_fasta.fasta")
for record in parser:
    ...

Methods

There are also other convenience methods:

• all - Read all records into a list-like object.
• take - Take up to n records into a list-like object.
• filter - Keep/exclude sequences based on the sequence name.
• remove_stops - Yield sequences without a * stop codon character if the sequences are proteins.
• clean_header - Yield sequences while cleaning the header to not have a description.
• headers - Yield Header objects only without parsing the sequence itself.
• all_headers - Return all headers into a list-like object.

Properties

• num_records - Returns the number of sequences in the FASTA file. This is cached after the first time it is called. Note: This can also be computed using len(parser)
• format - Returns the RecordType enum that corresponds to the FASTA file's record type
• extension - Returns the file extension based on the format

Record

A single FASTA record. It has the following fields:

• header - A Header object that has the fields name and desc
• seq - A str storing the entire sequence

Methods

• empty - Checks if the Header and sequence are empty
• clear - Sets the Header and sequence to empty strings
• to_string - Returns the record as a string representation identical to what was parsed from the file
• clean_header - Sets the Header description to an empty string
• remove_stops - Removes * stop codon characters from the sequence if they are present