Source code for

# -*- coding: utf-8 -*-
import numpy as np

[docs]def write_fasta(path, sequences, names, mode='w', width=80): """Write nucleotide sequences stored as numpy arrays to a FASTA file. Parameters ---------- path : string File path. sequences : sequence of arrays One or more ndarrays of dtype 'S1' containing the sequences. names : sequence of strings Names of the sequences. mode : string, optional Use 'a' to append to an existing file. width : int, optional Maximum line width. """ # check inputs if isinstance(sequences, np.ndarray): # single sequence sequences = [sequences] names = [names] if len(sequences) != len(names): raise ValueError('must provide the same number of sequences and names') for sequence in sequences: if sequence.dtype != np.dtype('S1'): raise ValueError('expected S1 dtype, found %r' % sequence.dtype) # force binary mode mode = 'ab' if 'a' in mode else 'wb' # write to file with open(path, mode=mode) as fasta: for name, sequence in zip(names, sequences): # force bytes if isinstance(name, str): name = name.encode('ascii') header = b'>' + name + b'\n' fasta.write(header) for i in range(0, sequence.size, width): line = sequence[i:i+width].tostring() + b'\n' fasta.write(line)