#!/usr/bin/env python


"""Read GenBank flat files.

Currently only reads sequence data and not annotations.

"""

from ..seq import Alphabet, Seq, SeqList
from ..utils import isblank

names = ('genbank',)
extensions = ('gb', 'genbank', 'gbk')


def read(fin, alphabet=None):
    """Read and parse a file of genbank records.

    Args:
    fin -- A stream or file to read
    alphabet -- The expected alphabet of the data, if given

    Returns:
    SeqList -- A list of sequences

    Raises:
    ValueError -- If the file is unparsable
    """
    seqs = [s for s in iterseq(fin, alphabet)]
    return SeqList(seqs)


def iterseq(fin, alphabet=None):
    """ Iterate over genbank records

    Args:
    fin -- A stream or file to read
    alphabet -- The expected alphabet of the data, if given

    Yeilds:
    Seq -- One alphabetic sequence at a time.

    Raises:
    ValueError -- If the file is unparsable
    """
    alphabet = Alphabet(alphabet)

    header, block, data = range(3)
    state = header
    seq = []
    for L, line in enumerate(fin):
        if isblank(line):
            continue
        if state == header:
            if not line.startswith('LOCUS'):
                raise ValueError(
                   "Cannot find start of record at line %d" % L)
            state = block
        elif state == block:
            if line.startswith('ORIGIN') or line.startswith('//'):
                state = data
        elif state == data:
            if line.startswith('//'):
                yield Seq(''.join(seq), alphabet)
                seq = []
                state = block
            else:
                seq.extend(line.split()[1:])