A library to load fasta format text

load_fasta.py

# coding=utf-8
"""
"""
__author__ = 'Alisue <lambdalisue@hashnote.net>'
def load_fasta(iterator):
    """
    Load fasta file and return sequence list

    >>> fasta = '''
    ... >avGFP
    ... M-SKGEE----LFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT-GKLPVPWPTLVTTF
    ... SYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDG
    ... NILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQ
    ... SALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK
    ...
    ... >ECFP
    ... MVSKGEE----LFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT-GKLPVPWPTLVTTL
    ... TWGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDG
    ... NILGHKLEYNYISHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQ
    ... SALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK'''
    >>> sequences = load_fasta(fasta)
    >>> sorted(sequences.keys())
    ['ECFP', 'avGFP']
    >>> sequences['ECFP']
    'MVSKGEE----LFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT-GKLPVPWPTLVTTLTWGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYISHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK'
    >>> sequences['avGFP']
    'M-SKGEE----LFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT-GKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK'
    """
    if not isinstance(iterator, basestring):
        iterator = "\n".join(iterator)
    sequence_blocks = [x.strip() for x in iterator.split(">") if x.strip()]
    name = None
    sequences = {}
    for sequence_block in sequence_blocks:
        sequence_block = sequence_block.splitlines()
        name = sequence_block[0].strip()
        sequence = [x.strip() for x in sequence_block[1:] if x.strip()]
        sequence = "".join(sequence)
        sequences[name] = sequence
    return sequences


if __name__ == '__main__':
    import doctest; doctest.testmod()