#!/usr/bin/env python

__author__ = "Matthew Wakefield"
__copyright__ = "Copyright 2007-2020, The Cogent Project"
__credits__ = ["Matthew Wakefield", "Peter Maxwell", "Gavin Huttley"]
__license__ = "BSD-3"
__version__ = "2020.12.21a"
__maintainer__ = "Matthew Wakefield"
__email__ = "wakefield@wehi.edu.au"
__status__ = "Production"

import warnings


def MsfParser(f):
    """Read sequences from a msf format file"""
    alignmentdict = {}
    # parse optional header
    # parse optional text information
    # file header and sequence header are seperated by a line ending in '..'
    line = f.readline().strip()
    for line in f:
        line = line.strip()
        if line.endswith(".."):
            break
    # parse sequence info
    seqinfo = {}
    for line in f:
        line = line.strip()
        if line.startswith("//"):
            break
        line = line.split()
        if line and line[0] == "Name:":
            seqinfo[line[1]] = int(line[3])
    # parse sequences
    sequences = {}
    for line in f:
        line = line.strip().split()
        if line and line[0] in sequences:
            sequences[line[0]] += "".join(line[1:])
        elif line and line[0] in seqinfo:
            sequences[line[0]] = "".join(line[1:])
    # consistency check
    if len(sequences) != len(seqinfo):
        warnings.warn(
            "Number of loaded seqs[%s] not same as "
            "expected[%s]." % (len(sequences), len(seqinfo))
        )
    for name in sequences:
        if len(sequences[name]) != seqinfo[name]:
            warnings.warn(
                "Length of loaded seqs [%s] is [%s] not "
                "[%s] as expected." % (name, len(sequences[name]), seqinfo[name])
            )

    # yield sequences
    for name in sequences:
        yield (name, sequences[name])
