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AbiIO.py
# Copyright 2011 by Wibowo Arindrarto (w.arindrarto@gmail.com)
# Revisions copyright 2011 by Peter Cock.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.

"""Bio.SeqIO parser for the ABI format.

ABI is the format used by Applied Biosystem's sequencing machines to store
sequencing results. 

For more details on the format specification, visit:
http://www.appliedbiosystem.com/support/software_community/ABIF_File_Format.pdf

"""

__docformat__ = "epytext en"

import datetime
import struct

from os.path import basename
from sys import version_info

from Bio import Alphabet
from Bio.Alphabet.IUPAC import ambiguous_dna, unambiguous_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio._py3k import _bytes_to_string, _as_bytes

# dictionary for determining which tags goes into SeqRecord annotation
# each key is tag_name + tag_number
# if a tag entry needs to be added, just add its key and its key
# for the annotations dictionary as the value
_EXTRACT = {
            'TUBE1': 'sample_well',
            'DySN1': 'dye',
            'GTyp1': 'polymer',
            'MODL1': 'machine_model',
           }
# dictionary for tags that require preprocessing before use in creating
# seqrecords
_SPCTAGS = [
            'PBAS2',    # base-called sequence
            'PCON2',    # quality values of base-called sequence
            'SMPL1',    # sample id inputted before sequencing run
            'RUND1',    # run start date
            'RUND2',    # run finish date
            'RUNT1',    # run start time
            'RUNT2',    # run finish time
           ]
# dictionary for data unpacking format
_BYTEFMT = {
            1: 'b',     # byte
            2: 's',     # char
            3: 'H',     # word
            4: 'h',     # short
            5: 'i',     # long
            6: '2i',    # rational, legacy unsupported
            7: 'f',     # float
            8: 'd',     # double
            10: 'h2B',  # date
            11: '4B',   # time
            12: '2i2b', # thumb
            13: 'B',    # bool
            14: '2h',   # point, legacy unsupported
            15: '4h',   # rect, legacy unsupported
            16: '2i',   # vPoint, legacy unsupported
            17: '4i',   # vRect, legacy unsupported
            18: 's',    # pString
            19: 's',    # cString
            20: '2i',   # tag, legacy unsupported
           }
# header data structure (exluding 4 byte ABIF marker)
_HEADFMT = '>H4sI2H3I'
# directory data structure
_DIRFMT = '>4sI2H4I'

def AbiIterator(handle, alphabet=None, trim=False):
    """Iterator for the Abi file format.
    """
    # raise exception is alphabet is not dna
    if alphabet is not None:
        if isinstance(Alphabet._get_base_alphabet(alphabet),
                      Alphabet.ProteinAlphabet):
            raise ValueError("Invalid alphabet, ABI files do not hold proteins.")
        if isinstance(Alphabet._get_base_alphabet(alphabet),
                      Alphabet.RNAAlphabet):
            raise ValueError("Invalid alphabet, ABI files do not hold RNA.")

    # raise exception if handle mode is not 'rb'
    if hasattr(handle, 'mode'):
        if set('rb') != set(handle.mode.lower()):
            raise ValueError("ABI files has to be opened in 'rb' mode.") 

    # check if input file is a valid Abi file
    handle.seek(0)
    marker = handle.read(4)
    if not marker:
        # handle empty file gracefully
        raise StopIteration
    if marker != _as_bytes('ABIF'):
        raise IOError('File should start ABIF, not %r' % marker)

    # dirty hack for handling time information
    times = {'RUND1': '', 'RUND2': '', 'RUNT1': '', 'RUNT2': '', }

    # initialize annotations
    annot = dict(zip(_EXTRACT.values(), [None] * len(_EXTRACT)))

    # parse header and extract data from directories
    header = struct.unpack(_HEADFMT, \
             handle.read(struct.calcsize(_HEADFMT)))

    for tag_name, tag_number, tag_data in _abi_parse_header(header, handle):
        # stop iteration if all desired tags have been extracted
        # 4 tags from _EXTRACT + 2 time tags from _SPCTAGS - 3,
        # and seq, qual, id
        # todo

        key = tag_name + str(tag_number)

        # PBAS2 is base-called sequence
        if key == 'PBAS2': 
            seq = tag_data
            ambigs = 'KYWMRS'
            if alphabet is None:
                if set(seq).intersection(ambigs):
                    alphabet = ambiguous_dna
                else:
                    alphabet = unambiguous_dna
        # PCON2 is quality values of base-called sequence
        elif key == 'PCON2':
            qual = [ord(val) for val in tag_data]
        # SMPL1 is sample id entered before sequencing run
        elif key == 'SMPL1':
            sample_id = tag_data
        elif key in times:
            times[key] = tag_data
        else:
            # extract sequence annotation as defined in _EXTRACT          
            if key in _EXTRACT:
                annot[_EXTRACT[key]] = tag_data

    # set time annotations
    annot['run_start'] = '%s %s' % (times['RUND1'], times['RUNT1'])
    annot['run_finish'] = '%s %s' % (times['RUND2'], times['RUNT2'])
    
    # use the file name as SeqRecord.name if available
    try:
        file_name = basename(handle.name).replace('.ab1','')
    except:
        file_name = ""

    record = SeqRecord(Seq(seq, alphabet),
                       id=sample_id, name=file_name,
                       description='',
                       annotations=annot,
                       letter_annotations={'phred_quality': qual})
                      
    if not trim:
        yield record
    else:
        yield _abi_trim(record)

def _AbiTrimIterator(handle):
    """Iterator for the Abi file format that yields trimmed SeqRecord objects.
    """
    return AbiIterator(handle, trim=True)

def _abi_parse_header(header, handle):
    """Generator that returns directory contents.
    """
    # header structure (after ABIF marker):
    # file version, tag name, tag number,
    # element type code, element size, number of elements
    # data size, data offset, handle (not file handle)
    head_elem_size = header[4]
    head_elem_num = header[5]
    head_offset = header[7]
    index = 0

    while index < head_elem_num:
        start = head_offset + index * head_elem_size
        # add directory offset to tuple
        # to handle directories with data size <= 4 bytes
        handle.seek(start)
        dir_entry = struct.unpack(_DIRFMT, \
                    handle.read(struct.calcsize(_DIRFMT))) + (start,)
        index += 1
        # only parse desired dirs
        key = _bytes_to_string(dir_entry[0])
        key += str(dir_entry[1])
        if key in (list(_EXTRACT.keys()) + _SPCTAGS):
            tag_name = _bytes_to_string(dir_entry[0])
            tag_number = dir_entry[1]
            elem_code = dir_entry[2]
            elem_num = dir_entry[4]
            data_size = dir_entry[5]
            data_offset = dir_entry[6]
            tag_offset = dir_entry[8]
            # if data size <= 4 bytes, data is stored inside tag
            # so offset needs to be changed
            if data_size <= 4:
                data_offset = tag_offset + 20
            handle.seek(data_offset)
            data = handle.read(data_size)
            yield tag_name, tag_number, \
                  _parse_tag_data(elem_code, elem_num, data)


def _abi_trim(seq_record):
    """Trims the sequence using Richard Mott's modified trimming algorithm.

    seq_record - SeqRecord object to be trimmed.

    Trimmed bases are determined from their segment score, which is a
    cumulative sum of each base's score. Base scores are calculated from
    their quality values.

    More about the trimming algorithm:
    http://www.phrap.org/phredphrap/phred.html
    http://www.clcbio.com/manual/genomics/Quality_abif_trimming.html
    """

    start = False   # flag for starting position of trimmed sequence
    segment = 20    # minimum sequence length
    trim_start = 0  # init start index
    cutoff = 0.05   # default cutoff value for calculating base score

    if len(seq_record) <= segment:
        return seq_record
    else:
        # calculate base score
        score_list = [cutoff - (10 ** (qual/-10.0)) for qual in
                      seq_record.letter_annotations['phred_quality']]

        # calculate cummulative score
        # if cummulative value < 0, set it to 0
        # first value is set to 0, because of the assumption that
        # the first base will always be trimmed out
        cummul_score = [0]
        for i in range(1, len(score_list)):
            score = cummul_score[-1] + score_list[i]
            if score < 0:
                cummul_score.append(0)
            else:
                cummul_score.append(score)
                if not start:
                    # trim_start = value when cummulative score is first > 0
                    trim_start = i
                    start = True
        
        # trim_finish = index of highest cummulative score,
        # marking the end of sequence segment with highest cummulative score
        trim_finish = cummul_score.index(max(cummul_score))
                         
        return seq_record[trim_start:trim_finish]

def _parse_tag_data(elem_code, elem_num, raw_data):
    """Returns single data value.
    
    elem_code - What kind of data
    elem_num - How many data points
    raw_data - abi file object from which the tags would be unpacked
    """
    if elem_code in _BYTEFMT:
        # because '>1s' unpack differently from '>s'
        if elem_num == 1:
            num = ''
        else:
            num = str(elem_num)
        fmt = '>' + num + _BYTEFMT[elem_code]

        assert len(raw_data) == struct.calcsize(fmt)
        data = struct.unpack(fmt, raw_data)

        # no need to use tuple if len(data) == 1
        # also if data is date / time
        if elem_code not in [10, 11] and len(data) == 1:
            data = data[0]

        # account for different data types
        if elem_code == 2:
            return _bytes_to_string(data)
        elif elem_code == 10:
            return str(datetime.date(*data))
        elif elem_code == 11:
            return str(datetime.time(*data[:3]))
        elif elem_code == 13:
            return bool(data)
        elif elem_code == 18:
            return _bytes_to_string(data[1:])
        elif self.elem_code == 19:
            return _bytes_to_string(data[:-1])
        else:
            return data
    else:
        return None

if __name__ == '__main__':
    pass

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