fasta_parser

A python library that implements a fasta / multi-fasta parser with some useful features.

Contacts

Michele Berselli, [email protected]

Importing the library

To use the library simply import fasta_parser into your code.

Usage

The library implements the objects FastaHandler and FastaSequence.

FastaHandler

The FastaHandler is an object that stores the fasta sequences as FastaSequence objects.

Initialize the object

Initialize the object with handler = fasta_parser.FastaHandler().

Parse input fasta file

Different methods can be used to parse the fasta file:

• parse( inputfile ) method parses inputfile and saves the fasta sequences as string of characters.

  handler.parse('inputfile.fas')

• parse_binary( inputfile ) method parses inputfile and saves the fasta sequences with a binary encoding to reduce memory usage (two bits per base). Requires sequences containing only canonical bases A, C, G, T.

  handler.parse_binary('inputfile.fas')

• parse_generator( inputfile ) method parses inpufile and creates a generator of the sequences, each iteration returns a tuple in the form (header, sequence).

  IT = handler.parse_generator('inputfile.fas')

Access sequences stored in the object

To access the stored sequences differrent methods can be used:

• iter_sequences( ) method creates a generator of the stored sequences, each iteration returns a FastaSequence object.

  IT = handler.iter_sequences()

• get_sequences( ) method returns the list of the stored sequences as a list of FastaSequence objects.

  handler.get_sequences()

• write_sequences( fo, [max_char_per_line] ) method writes the sequences in fasta format to buffer (fo) using a maximum (max_char_per_line) number of characters per line.

  handler.write_sequences(fo, [max])

FastaSequence

The FastaSequence is an object that stores the information for a fasta sequence. Contains the header of the sequence and the sequence itself. The sequence can be stored as a string of charachters or as a bitarray that represents the binary encoding for the sequence (two bits per character).

Initialize the object

Initialize the object with sequence = fasta_parser.FastaHandler.FastaSequence(header, sequence).

Access information stored in the object

• get_header( ) method returns the header for the sequence (without >).

  sequence.get_header()

• get_sequence( ) method returns the sequence as a string of characters.

  sequence.get_sequence()

• get_bitarray( ) metod returns the sequence as binary encoded in a bitarray object. Requires that the sequence is stored as a bitarray.

  sequence.get_bitarray()

• write_sequence( fo, [max_char_per_line] ) method writes the sequence in fasta format to buffer (fo) using a maximum (max_char_per_line) number of characters per line.

  sequence.write_sequence(fo, [max])

Libraries

bitarray library is required