<gh_stars>10-100
#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Copyright (C) 2015-2016 by <NAME>
# gaik (dot) tamazian (at) gmail (dot) com

import logging
import pyfaidx
import random
import string
from bioformats.blast import BlastTab
from chromosomer.exception import MapError
from chromosomer.exception import AlignmentToMapError
from bioformats.fasta import RandomSequence
from bioformats.fasta import Writer
from collections import defaultdict
from itertools import izip
from collections import namedtuple
from operator import attrgetter

logging.basicConfig()
logger = logging.getLogger(__name__)


class Map(object):
    """
    The class implements routines related to creation, reading and
    writing a fragment map that describes how genome fragments are
    situated on reference genome chromosomes.
    """

    numeric_values = (1, 2, 3, 6, 7)
    
    record_names = ('fr_name', 'fr_length', 'fr_start', 'fr_end',
                    'fr_strand', 'ref_chr', 'ref_start', 'ref_end')

    Record = namedtuple('Record', record_names)

    def __init__(self):
        """
        Initializes a Map object.
        """
        self.__fragments = defaultdict(list)
        self.__block_adding = False

    def add_record(self, new_record):
        """
        Given a new fragment record, add it to the fragment map.

        :param new_record: a record to be added to the map
        :type new_record: Map.Record
        """
        self.__fragments[new_record.ref_chr].append(new_record)

    def read(self, filename):
        """
        Read a fragment map from the specified file. The file records
        are added to the records in the map.

        :param filename: a name of a file to read a fragment map from
        :type: str
        """
        lineno = 0
        i = 0
        with open(filename) as input_map_file:
            for line in input_map_file:
                lineno += 1
                line_parts = line.split('\t', 8)
                if len(line_parts) < 8:
                    logger.error('line %d: the incorrect number of '
                                 'columns', lineno)
                    raise MapError
                for i in self.numeric_values:
                    try:
                        line_parts[i] = int(line_parts[i])
                    except ValueError:
                        logger.error('line %d: the incorrect numeric '
                                     'value %s', lineno, line_parts[i])
                        raise MapError
                new_record = Map.Record(*line_parts)
                self.add_record(new_record)
                i += 1
        logger.debug('map of %d fragments was successfully read from '
                     '%s', i, filename)

    @property
    def records(self):
        return self.__fragments

    def chromosomes(self):
        """
        Return an iterator to the chromosomes the fragment map
        describes.

        :return: an iterator to iterate through the fragment map
            chromosomes
        """
        sorted_chromosomes = sorted(self.__fragments.keys())
        for i in sorted_chromosomes:
            yield i

    def fragments(self, chromosome):
        """
        Return an iterator to fragments of the specified chromosome
        describes by the map. If the chromosome is absent, None is
        returned.

        :param chromosome: a chromosome which fragments are to be
            iterated
        :type chromosome: str
        :return: an iterator to iterate through the chromosome's
            fragments
        """
        if chromosome not in self.__fragments:
            logging.error('%s missing in the fragment map', chromosome)
            raise MapError

        sorted_fragments = sorted(self.__fragments[chromosome],
                                  key=attrgetter('ref_start'))

        for i in sorted_fragments:
            yield i

    def write(self, filename):
        """
        Write the fragment map to the specified file.

        :param filename: a name of a file to write the fragment map to
        :type filename: str
        """
        template = '\t'.join(['{}'] * len(self.record_names)) + '\n'
        i = 0
        with open(filename, 'w') as output_map_file:
            for chromosome in self.chromosomes():
                for fragment in self.fragments(chromosome):
                    new_line = template.format(*fragment)
                    output_map_file.write(new_line)
                    i += 1
        logger.debug('the map of %d fragments successfully written '
                     'to %s', i, filename)

    def assemble(self, fragment_filename, output_filename,
                 save_soft_mask=False):
        """
        Assemble chromosome sequences from fragments.

        :param fragment_filename: a name of a FASTA file of fragment
            sequences
        :param output_filename: a name of the output FASTA file of
            the assembled chromosomes
        :param save_soft_mask: save soft-masking in sequences being
            assembled or not
        :type fragment_filename: str
        :type output_filename: str
        :type save_soft_mask: bool
        """
        logger.debug('assembling chromosomes...')
        logger.debug('FASTA of fragments: %s', fragment_filename)
        logger.debug('FASTA of chromosomes: %s', output_filename)
        logger.debug('saving soft mask: %r', save_soft_mask)
        num_fragments = 0
        num_chromosomes = 0

        fragment_fasta = pyfaidx.Fasta(fragment_filename)
        complement = string.maketrans('ATCGatcgNnXx', 'TAGCtagcNnXx')
        with Writer(output_filename) as chromosome_writer:
            for chromosome in self.chromosomes():
                seq = []
                for record in self.fragments(chromosome):
                    if record.fr_name == 'GAP':
                        record_seq = 'N' * (record.fr_end -
                                            record.fr_start)
                    else:
                        if record.fr_name not in fragment_fasta:
                            logger.error('the fragment %s sequence '
                                         'missing', record.fr_name)
                            raise MapError
                        record_seq = fragment_fasta[record.fr_name][
                            record.fr_start:record.fr_end].seq
                        # convert the sequence to non-unicode
                        record_seq = str(record_seq)
                        if not save_soft_mask:
                            record_seq = record_seq.upper()
                        # if the fragment orientation is reverse, then
                        # the reverse complement of the fragment
                        # sequence is written
                        if record.fr_strand == '-':
                            record_seq = record_seq[::-1].translate(
                                complement)
                    seq.append(record_seq)
                    num_fragments += 1
                chromosome_writer.write(chromosome, ''.join(seq))
                num_chromosomes += 1

        logger.debug('%d fragments assembled to %d chromosomes',
                     num_fragments, num_chromosomes)

    def shrink_gaps(self, gap_size):
        """
        Shrink gaps inserted into the map to the specified size.

        :param gap_size: a required gap size
        :type gap_size: int
        """
        logger.debug('shrinking gaps to %d bp', gap_size)
        total_shift = 0

        # process each chromosome separately
        for chrom in self.__fragments.keys():
            if len(self.__fragments[chrom]) > 1:
                shifts = []
                # iterate through gaps
                for i in self.__fragments[chrom]:
                    if i.fr_name == 'GAP':
                        len_diff = i.fr_length - gap_size
                        shifts.append(len_diff)
                        total_shift += len_diff
                    else:
                        shifts.append(0)
                # calculate absolute shifts for chromosome fragments
                accumulated_shift = 0
                for i in xrange(len(shifts)):
                    accumulated_shift += shifts[i]
                    shifts[i] = accumulated_shift
                for i in xrange(len(self.__fragments[chrom])):
                    fragment = list(self.__fragments[chrom][i])
                    if fragment[0] == 'GAP':
                        # change gap length and end position
                        fragment[1] = gap_size
                        fragment[3] = gap_size
                        fragment[6] -= shifts[i-1]
                        fragment[7] = fragment[6] + gap_size
                    else:
                        fragment[6] -= shifts[i]
                        fragment[7] -= shifts[i]
                    self.__fragments[chrom][i] = Map.Record(*fragment)

        logger.debug('in total, gaps shrinked by %d bp', total_shift)

    def summary(self):
        """
        Return a summary on the fragment map.

        :return: a dictionary of tuples each describing one assembled
            chromosome
        :rtype: dict
        """
        summary = {}
        for chromosome in self.chromosomes():
            gaps = 0
            chr_fragments = list(self.fragments(chromosome))
            for fragment in chr_fragments:
                if fragment.fr_name == 'GAP':
                    gaps += fragment.fr_length
            chr_length = chr_fragments[-1].ref_end
            fr_num = len(chr_fragments)
            summary[chromosome] = (fr_num, gaps, chr_length)
        return summary

    def convert2bed(self, bed_filename):
        """
        Given a name of the output BED3 file, write the fragment map
        to it in the BED format.

        :param bed_filename: a name of the output BED file of the
            fragment map
        :type bed_filename: str
        """
        template = '\t'.join(['{}'] * (len(Map.record_names) + 1)) + \
                   '\n'
        with open(bed_filename, 'w') as bed_file:
            for chromosome in sorted(self.chromosomes()):
                for fragment in self.fragments(chromosome):
                    bed_file.write(template.format(
                        fragment.ref_chr,
                        fragment.ref_start,
                        fragment.ref_end,
                        fragment.fr_name,
                        1000,
                        fragment.fr_strand,
                        fragment.fr_start,
                        fragment.fr_end,
                        fragment.fr_length
                    ))


class AlignmentToMap(object):
    """
    The class implements routines to create a fragment map from a set
    of alignments between fragments to be assembled and reference
    chromosomes.
    """

    Anchor = namedtuple('Anchor', ('fragment', 'fr_start', 'fr_end',
                                   'fr_strand', 'ref_chr',
                                   'ref_start', 'ref_end'))

    def __init__(self, gap_size, fragment_lengths,
                 min_fragment_length=None, centromeres=None):
        """
        Create a converter object to create fragment maps from
        alignmets between reference chromosomes and fragments to be
        assembled.

        :param gap_size: a size of a gap between fragments
        :param fragment_lengths: a dictionary of fragment lengths
            which keys are their names and values are their lengths
        :param min_fragment_length: the minimal length of a fragment
            to be included in the map
        :param centromeres: a dictionary of reference chromosome
            centromere locations
        :type gap_size: int
        :type fragment_lengths: dict
        :type min_fragment_length: int
        :type centromeres: dict
        """
        self.__gap_size = gap_size
        self.__fragment_lengths = fragment_lengths
        self.__min_fragment_length = min_fragment_length
        self.__centromeres = centromeres

        self.__anchors = {}
        self.__unlocalized = []
        self.__unplaced = []
        self.__fragment_map = Map()

    def blast(self, blast_alignments, bitscore_ratio_threshold):
        """
        Create a fragment map from BLAST blast_alignments between
        fragments and reference chromosomes.

        :param blast_alignments: BLAST blast_alignments
        :param bitscore_ratio_threshold: the minimal ratio of two
            greatest fragment alignment bit scores to consider the
            fragment placed to a reference
        :type blast_alignments: BlastTab
        :type bitscore_ratio_threshold: float
        :return: a tuple containing the fragment map constructed from
            the provided BLAST alignments, the list of unlocalized
            fragments and a list of unplaced fragments
        :rtype: tuple
        """
        self.__anchors = {}
        self.__unlocalized = []
        self.__unplaced = []

        temp_anchors = defaultdict(list)

        for alignment in blast_alignments.alignments():
            if self.__min_fragment_length is not None:
                # check if the fragment length is equal or greater
                # than the threshold value
                try:
                    if self.__fragment_lengths[alignment.query] < \
                            self.__min_fragment_length:
                        # skip the alignment
                        continue
                except KeyError:
                    logger.error('the fragment %s length is missing',
                                 alignment.query)
                    raise AlignmentToMapError

            # consider the centromeres if required
            if self.__centromeres is not None and alignment.subject \
                    in self.__centromeres:
                # the chromosome a fragment was aligned to has a
                # centromere, so we determine which arm the alignment
                # refers to and modify the chromosome name by adding
                # '_1' or '_2' to it
                if min(alignment.s_start, alignment.s_end) < \
                        self.__centromeres[alignment.subject].start:
                    arm_prefix = '_1'
                else:
                    arm_prefix = '_2'
                new_alignment = list(alignment)
                new_alignment[1] += arm_prefix
                alignment = BlastTab.Alignment(*new_alignment)

            temp_anchors[alignment.query].append(alignment)
            # check if there is more than 2 alignments for the
            # fragment; if there is, then leave two fragments with
            # the greatest bit-score values
            if len(temp_anchors[alignment.query]) > 2:
                temp_anchors[alignment.query] = sorted(
                    temp_anchors[alignment.query],
                    key=attrgetter('bit_score'),
                    reverse=True
                )
                temp_anchors[alignment.query] = temp_anchors[
                    alignment.query][0:2]

        for fragment, alignments in temp_anchors.iteritems():
            if len(alignments) > 1:
                # check if the ratio of the alignment bit scores is
                # greater than the required threshold to consider a
                # fragment places
                if alignments[0].bit_score/alignments[1].bit_score > \
                        bitscore_ratio_threshold:
                    self.__anchors[fragment] = \
                        AlignmentToMap.Anchor(
                            fragment=alignments[0].query,
                            fr_start=alignments[0].q_start - 1,
                            fr_end=alignments[0].q_end,
                            fr_strand='+' if alignments[0].s_start <
                            alignments[0].s_end else '-',
                            ref_chr=alignments[0].subject,
                            ref_start=min(alignments[0].s_start,
                                          alignments[0].s_end) - 1,
                            ref_end=max(alignments[0].s_start,
                                        alignments[0].s_end)
                        )
                elif alignments[0].subject == alignments[1].subject:
                    # the fragment is considered unlocalized
                    self.__unlocalized.append(
                        (fragment, alignments[0].subject))
                else:
                    # the fragment is considered unplaced
                    self.__unplaced.append(fragment)
            else:
                # there is a single alignment, use it as an anchor
                self.__anchors[fragment] = \
                    AlignmentToMap.Anchor(
                        fragment=alignments[0].query,
                        fr_start=alignments[0].q_start - 1,
                        fr_end=alignments[0].q_end,
                        fr_strand='+' if alignments[0].s_start <
                        alignments[0].s_end else '-',
                        ref_chr=alignments[0].subject,
                        ref_start=min(alignments[0].s_start,
                                      alignments[0].s_end) - 1,
                        ref_end=max(alignments[0].s_start,
                                    alignments[0].s_end)
                    )

        # get total lengths of mapped, unlocalized and unplaced
        # fragments
        total_mapped = total_unlocalized = total_unplaced = 0
        for i in self.__anchors.itervalues():
            total_mapped += self.__fragment_lengths[i.fragment]
        for i in self.__unlocalized:
            total_unlocalized += self.__fragment_lengths[i[0]]
        for i in self.__unplaced:
            total_unplaced += self.__fragment_lengths[i]

        logger.info('%d mapped fragments of total length %d bp',
                    len(self.__anchors), total_mapped)
        logger.info('%d unlocalized fragments of total length %d bp',
                    len(self.__unlocalized), total_unlocalized)
        logger.info('%d unplaced fragments of total length %d bp',
                    len(self.__unplaced), total_unplaced)

        self.__anchor_fragments()

        return (self.__fragment_map, self.__unlocalized,
                self.__unplaced)

    def __anchor_fragments(self):
        """
        Build a fragment map from anchors.
        """
        # first, we split anchors by reference genome chromosomes
        chr_anchors = defaultdict(list)
        for anchor in self.__anchors.itervalues():
            chr_anchors[anchor.ref_chr].append(anchor)

        # second, we sort the anchors by their position on the
        # chromosomes
        for chr_name in chr_anchors.iterkeys():
            chr_anchors[chr_name] = sorted(
                chr_anchors[chr_name], key=attrgetter('ref_start')
            )

        # now we form a fragment map from the anchors
        total_inserted_gaps = 0
        self.__fragment_map = Map()
        for chr_name in chr_anchors.iterkeys():
            previous_end = 0
            for anchor in chr_anchors[chr_name]:
                try:
                    fragment_length = self.__fragment_lengths[
                        anchor.fragment]
                except KeyError:
                    logger.error('the fragment %s length is missing',
                                 anchor.fragment)
                    raise AlignmentToMapError

                # determine the fragment's start and end positions
                if anchor.fr_strand == '+':
                    ref_start = anchor.ref_start - anchor.fr_start
                    ref_end = ref_start + fragment_length
                else:
                    ref_end = anchor.ref_end + anchor.fr_start
                    ref_start = ref_end - fragment_length

                new_record = Map.Record(
                    fr_name=anchor.fragment,
                    fr_length=fragment_length,
                    fr_start=0,
                    fr_end=fragment_length,
                    fr_strand=anchor.fr_strand,
                    ref_chr=anchor.ref_chr,
                    ref_start=previous_end,
                    ref_end=previous_end + ref_end - ref_start
                )
                self.__fragment_map.add_record(new_record)
                previous_end += ref_end - ref_start

                # add a gap
                new_gap = Map.Record(
                    fr_name='GAP',
                    fr_length=self.__gap_size,
                    fr_start=0,
                    fr_end=self.__gap_size,
                    fr_strand='+',
                    ref_chr=anchor.ref_chr,
                    ref_start=previous_end,
                    ref_end=previous_end + self.__gap_size
                )
                previous_end += self.__gap_size
                self.__fragment_map.add_record(new_gap)
                total_inserted_gaps += self.__gap_size

        logger.info('%d chromosomes formed', len(chr_anchors))
        logger.info('%d bp of gaps inserted', total_inserted_gaps)


class Simulator(object):
    """
    The class describes routines to simulate genome fragments and
    chromosomes that are composed from them.
    """
    def __init__(self, fragment_length, fragment_number,
                 chromosome_number, unplaced_number, gap_size):
        """
        Create a fragment simulator object.

        :param fragment_length: the length of a fragment
        :param fragment_number: the number of fragments constituting
            the chromosomes
        :param chromosome_number: the number of chromosomes
        :param unplaced_number: the number of fragments not included
            in the chromosomes
        :param gap_size: the length of gaps between fragments in
            chromosomes
        :type fragment_length: int
        :type fragment_number: int
        :type chromosome_number: int
        :type unplaced_number: int
        :type gap_size: int
        """
        self.__fragment_length = fragment_length
        self.__fragment_number = fragment_number
        self.__chromosome_number = chromosome_number
        self.__gap_size = gap_size

        # create fragment sequences
        self.__fragments = {}
        seq_generator = RandomSequence(self.__fragment_length)
        for i in xrange(self.__fragment_number):
            fr_name = 'fragment{}'.format(i+1)
            self.__fragments[fr_name] = seq_generator.get()

        self.__map = Map()
        self.__create_map()
        self.__assemble_chromosomes()

        # add unplaced fragments
        for i in xrange(self.__fragment_number,
                        self.__fragment_number + unplaced_number):
            fr_name = 'fragment{}'.format(i+1)
            self.__fragments[fr_name] = seq_generator.get()

    def __create_map(self):
        """
        Assign fragments to chromosomes randomly and create a
        fragment map.
        """
        fragment_positions = [0] * self.__chromosome_number
        for i in xrange(self.__fragment_number):
            chr_num = random.randrange(self.__chromosome_number)
            fr_strand = random.choice(('+', '-'))
            self.__map.add_record(Map.Record(
                fr_name='fragment{}'.format(i+1),
                fr_length=self.__fragment_length,
                fr_start=0,
                fr_end=self.__fragment_length,
                fr_strand=fr_strand,
                ref_chr='chr{}'.format(chr_num+1),
                ref_start=fragment_positions[chr_num],
                ref_end=fragment_positions[chr_num] +
                self.__fragment_length
            ))
            fragment_positions[chr_num] += self.__fragment_length
            self.__map.add_record(Map.Record(
                fr_name='GAP',
                fr_length=self.__gap_size,
                fr_start=0,
                fr_end=self.__gap_size,
                fr_strand='+',
                ref_chr='chr{}'.format(chr_num+1),
                ref_start=fragment_positions[chr_num],
                ref_end=fragment_positions[chr_num] + self.__gap_size
            ))
            fragment_positions[chr_num] += self.__gap_size

    def __assemble_chromosomes(self):
        """
        Get chromosome sequences from fragments using the constructed
        fragment map.
        """
        complement = string.maketrans('ATCGatcgNnXx', 'TAGCtagcNnXx')
        chromosomes = defaultdict(list)
        for i in self.__map.chromosomes():
            for fr in self.__map.fragments(i):
                if fr.fr_name == 'GAP':
                    temp_fragment = 'N' * fr.fr_length
                else:
                    temp_fragment = self.__fragments[fr.fr_name]
                    if fr.fr_strand == '-':
                        temp_fragment = temp_fragment[::-1].translate(
                            complement)
                chromosomes[i].append(temp_fragment)
            chromosomes[i] = ''.join(chromosomes[i])

        self.__chromosomes = chromosomes

    def write(self, map_file, fragment_file, chromosome_file):
        """
        Write the produced data - a fragment map, a FASTA file of
        fragments and a FASTA file of chromosomes - to the specified
        files.

        :param map_file: a name of a file to write the fragment map to
        :param fragment_file: a name of a file to write fragment
            sequences to
        :param chromosome_file: a name of a file to write chromosome
            sequences to
        :type map_file: str
        :type fragment_file: str
        :type chromosome_file: str
        """
        self.__map.write(map_file)
        with Writer(fragment_file) as fragment_fasta:
            for name, seq in self.__fragments.iteritems():
                fragment_fasta.write(name, seq)
        with Writer(chromosome_file) as chromosome_fasta:
            for name, seq in self.__chromosomes.iteritems():
                chromosome_fasta.write(name, seq)

        logger.debug('a simulated map of %d fragments written to %s',
                     len(self.__map.records), map_file)
        logger.debug('%d simulated fragments written to %s',
                     len(self.__fragments), fragment_file)
        logger.debug('%d simulated chromosomes written to %s',
                     len(self.__chromosomes), chromosome_file)


class SeqLengths(object):
    """
    The class implements routines to handle fragment sequence lengths.
    """
    def __init__(self, filename):
        """
        Create a SeqLengths object to handle sequence lengths of the
        specified FASTA file.

        :param filename: a name of a FASTA file with sequences which
            lengths are to be derived
        :type filename: str
        """
        self.__filename = filename
        self.__lengths = {}

    def lengths(self):
        """
        Return a dictionary of sequence lengths.

        :return: a dictionary which keys are sequence names and
            values are their lengths
        :rtype: dict
        """
        total_length = 0
        if not self.__lengths:
            reader = pyfaidx.Fasta(self.__filename)
            for seq in reader.keys():
                self.__lengths[seq] = len(reader[seq])
                total_length += len(reader[seq])

        logger.debug('%d sequences analyzed with the total length of '
                     '%d bp', len(self.__lengths), total_length)

        return self.__lengths


def agp2map(agp_filename, map_filename):
    """
    Given a name of an AGP file, convert it to the fragment map format.

    :param agp_filename: a name of an AGP file
    :param map_filename: a name of an output fragment map file
    :type agp_filename: str
    :type map_filename: str
    """
    with open(agp_filename) as agp_file:
        with open(map_filename, 'w') as map_file:
            for line in agp_file:
                if line.startswith('#'):
                    continue
                line = line.rstrip()
                line = line.split(None, 8)
                if line[4] == 'N':
                    output = ('GAP', int(line[5]), 0, int(line[5]),
                              '+', line[0], int(line[1]) - 1,
                              int(line[2]))
                else:
                    frag_len = int(line[7]) - int(line[6]) + 1
                    output = (line[5], frag_len, 0, frag_len, line[8],
                              line[0], int(line[1]) - 1, int(line[2]))
                map_file.write('\t'.join(map(str, output)) + '\n')

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Copyright (C) 2015-2016 by <NAME>
# gaik (dot) tamazian (at) gmail (dot) com

import logging
import pyfaidx
import random
import string
from bioformats.blast import BlastTab
from chromosomer.exception import MapError
from chromosomer.exception import AlignmentToMapError
from bioformats.fasta import RandomSequence
from bioformats.fasta import Writer
from collections import defaultdict
from itertools import izip
from collections import namedtuple
from operator import attrgetter

logging.basicConfig()
logger = logging.getLogger(__name__)


class Map(object):
    """
    The class implements routines related to creation, reading and
    writing a fragment map that describes how genome fragments are
    situated on reference genome chromosomes.
    """

    numeric_values = (1, 2, 3, 6, 7)
    
    record_names = ('fr_name', 'fr_length', 'fr_start', 'fr_end',
                    'fr_strand', 'ref_chr', 'ref_start', 'ref_end')

    Record = namedtuple('Record', record_names)

    def __init__(self):
        """
        Initializes a Map object.
        """
        self.__fragments = defaultdict(list)
        self.__block_adding = False

    def add_record(self, new_record):
        """
        Given a new fragment record, add it to the fragment map.

        :param new_record: a record to be added to the map
        :type new_record: Map.Record
        """
        self.__fragments[new_record.ref_chr].append(new_record)

    def read(self, filename):
        """
        Read a fragment map from the specified file. The file records
        are added to the records in the map.

        :param filename: a name of a file to read a fragment map from
        :type: str
        """
        lineno = 0
        i = 0
        with open(filename) as input_map_file:
            for line in input_map_file:
                lineno += 1
                line_parts = line.split('\t', 8)
                if len(line_parts) < 8:
                    logger.error('line %d: the incorrect number of '
                                 'columns', lineno)
                    raise MapError
                for i in self.numeric_values:
                    try:
                        line_parts[i] = int(line_parts[i])
                    except ValueError:
                        logger.error('line %d: the incorrect numeric '
                                     'value %s', lineno, line_parts[i])
                        raise MapError
                new_record = Map.Record(*line_parts)
                self.add_record(new_record)
                i += 1
        logger.debug('map of %d fragments was successfully read from '
                     '%s', i, filename)

    @property
    def records(self):
        return self.__fragments

    def chromosomes(self):
        """
        Return an iterator to the chromosomes the fragment map
        describes.

        :return: an iterator to iterate through the fragment map
            chromosomes
        """
        sorted_chromosomes = sorted(self.__fragments.keys())
        for i in sorted_chromosomes:
            yield i

    def fragments(self, chromosome):
        """
        Return an iterator to fragments of the specified chromosome
        describes by the map. If the chromosome is absent, None is
        returned.

        :param chromosome: a chromosome which fragments are to be
            iterated
        :type chromosome: str
        :return: an iterator to iterate through the chromosome's
            fragments
        """
        if chromosome not in self.__fragments:
            logging.error('%s missing in the fragment map', chromosome)
            raise MapError

        sorted_fragments = sorted(self.__fragments[chromosome],
                                  key=attrgetter('ref_start'))

        for i in sorted_fragments:
            yield i

    def write(self, filename):
        """
        Write the fragment map to the specified file.

        :param filename: a name of a file to write the fragment map to
        :type filename: str
        """
        template = '\t'.join(['{}'] * len(self.record_names)) + '\n'
        i = 0
        with open(filename, 'w') as output_map_file:
            for chromosome in self.chromosomes():
                for fragment in self.fragments(chromosome):
                    new_line = template.format(*fragment)
                    output_map_file.write(new_line)
                    i += 1
        logger.debug('the map of %d fragments successfully written '
                     'to %s', i, filename)

    def assemble(self, fragment_filename, output_filename,
                 save_soft_mask=False):
        """
        Assemble chromosome sequences from fragments.

        :param fragment_filename: a name of a FASTA file of fragment
            sequences
        :param output_filename: a name of the output FASTA file of
            the assembled chromosomes
        :param save_soft_mask: save soft-masking in sequences being
            assembled or not
        :type fragment_filename: str
        :type output_filename: str
        :type save_soft_mask: bool
        """
        logger.debug('assembling chromosomes...')
        logger.debug('FASTA of fragments: %s', fragment_filename)
        logger.debug('FASTA of chromosomes: %s', output_filename)
        logger.debug('saving soft mask: %r', save_soft_mask)
        num_fragments = 0
        num_chromosomes = 0

        fragment_fasta = pyfaidx.Fasta(fragment_filename)
        complement = string.maketrans('ATCGatcgNnXx', 'TAGCtagcNnXx')
        with Writer(output_filename) as chromosome_writer:
            for chromosome in self.chromosomes():
                seq = []
                for record in self.fragments(chromosome):
                    if record.fr_name == 'GAP':
                        record_seq = 'N' * (record.fr_end -
                                            record.fr_start)
                    else:
                        if record.fr_name not in fragment_fasta:
                            logger.error('the fragment %s sequence '
                                         'missing', record.fr_name)
                            raise MapError
                        record_seq = fragment_fasta[record.fr_name][
                            record.fr_start:record.fr_end].seq
                        # convert the sequence to non-unicode
                        record_seq = str(record_seq)
                        if not save_soft_mask:
                            record_seq = record_seq.upper()
                        # if the fragment orientation is reverse, then
                        # the reverse complement of the fragment
                        # sequence is written
                        if record.fr_strand == '-':
                            record_seq = record_seq[::-1].translate(
                                complement)
                    seq.append(record_seq)
                    num_fragments += 1
                chromosome_writer.write(chromosome, ''.join(seq))
                num_chromosomes += 1

        logger.debug('%d fragments assembled to %d chromosomes',
                     num_fragments, num_chromosomes)

    def shrink_gaps(self, gap_size):
        """
        Shrink gaps inserted into the map to the specified size.

        :param gap_size: a required gap size
        :type gap_size: int
        """
        logger.debug('shrinking gaps to %d bp', gap_size)
        total_shift = 0

        # process each chromosome separately
        for chrom in self.__fragments.keys():
            if len(self.__fragments[chrom]) > 1:
                shifts = []
                # iterate through gaps
                for i in self.__fragments[chrom]:
                    if i.fr_name == 'GAP':
                        len_diff = i.fr_length - gap_size
                        shifts.append(len_diff)
                        total_shift += len_diff
                    else:
                        shifts.append(0)
                # calculate absolute shifts for chromosome fragments
                accumulated_shift = 0
                for i in xrange(len(shifts)):
                    accumulated_shift += shifts[i]
                    shifts[i] = accumulated_shift
                for i in xrange(len(self.__fragments[chrom])):
                    fragment = list(self.__fragments[chrom][i])
                    if fragment[0] == 'GAP':
                        # change gap length and end position
                        fragment[1] = gap_size
                        fragment[3] = gap_size
                        fragment[6] -= shifts[i-1]
                        fragment[7] = fragment[6] + gap_size
                    else:
                        fragment[6] -= shifts[i]
                        fragment[7] -= shifts[i]
                    self.__fragments[chrom][i] = Map.Record(*fragment)

        logger.debug('in total, gaps shrinked by %d bp', total_shift)

    def summary(self):
        """
        Return a summary on the fragment map.

        :return: a dictionary of tuples each describing one assembled
            chromosome
        :rtype: dict
        """
        summary = {}
        for chromosome in self.chromosomes():
            gaps = 0
            chr_fragments = list(self.fragments(chromosome))
            for fragment in chr_fragments:
                if fragment.fr_name == 'GAP':
                    gaps += fragment.fr_length
            chr_length = chr_fragments[-1].ref_end
            fr_num = len(chr_fragments)
            summary[chromosome] = (fr_num, gaps, chr_length)
        return summary

    def convert2bed(self, bed_filename):
        """
        Given a name of the output BED3 file, write the fragment map
        to it in the BED format.

        :param bed_filename: a name of the output BED file of the
            fragment map
        :type bed_filename: str
        """
        template = '\t'.join(['{}'] * (len(Map.record_names) + 1)) + \
                   '\n'
        with open(bed_filename, 'w') as bed_file:
            for chromosome in sorted(self.chromosomes()):
                for fragment in self.fragments(chromosome):
                    bed_file.write(template.format(
                        fragment.ref_chr,
                        fragment.ref_start,
                        fragment.ref_end,
                        fragment.fr_name,
                        1000,
                        fragment.fr_strand,
                        fragment.fr_start,
                        fragment.fr_end,
                        fragment.fr_length
                    ))


class AlignmentToMap(object):
    """
    The class implements routines to create a fragment map from a set
    of alignments between fragments to be assembled and reference
    chromosomes.
    """

    Anchor = namedtuple('Anchor', ('fragment', 'fr_start', 'fr_end',
                                   'fr_strand', 'ref_chr',
                                   'ref_start', 'ref_end'))

    def __init__(self, gap_size, fragment_lengths,
                 min_fragment_length=None, centromeres=None):
        """
        Create a converter object to create fragment maps from
        alignmets between reference chromosomes and fragments to be
        assembled.

        :param gap_size: a size of a gap between fragments
        :param fragment_lengths: a dictionary of fragment lengths
            which keys are their names and values are their lengths
        :param min_fragment_length: the minimal length of a fragment
            to be included in the map
        :param centromeres: a dictionary of reference chromosome
            centromere locations
        :type gap_size: int
        :type fragment_lengths: dict
        :type min_fragment_length: int
        :type centromeres: dict
        """
        self.__gap_size = gap_size
        self.__fragment_lengths = fragment_lengths
        self.__min_fragment_length = min_fragment_length
        self.__centromeres = centromeres

        self.__anchors = {}
        self.__unlocalized = []
        self.__unplaced = []
        self.__fragment_map = Map()

    def blast(self, blast_alignments, bitscore_ratio_threshold):
        """
        Create a fragment map from BLAST blast_alignments between
        fragments and reference chromosomes.

        :param blast_alignments: BLAST blast_alignments
        :param bitscore_ratio_threshold: the minimal ratio of two
            greatest fragment alignment bit scores to consider the
            fragment placed to a reference
        :type blast_alignments: BlastTab
        :type bitscore_ratio_threshold: float
        :return: a tuple containing the fragment map constructed from
            the provided BLAST alignments, the list of unlocalized
            fragments and a list of unplaced fragments
        :rtype: tuple
        """
        self.__anchors = {}
        self.__unlocalized = []
        self.__unplaced = []

        temp_anchors = defaultdict(list)

        for alignment in blast_alignments.alignments():
            if self.__min_fragment_length is not None:
                # check if the fragment length is equal or greater
                # than the threshold value
                try:
                    if self.__fragment_lengths[alignment.query] < \
                            self.__min_fragment_length:
                        # skip the alignment
                        continue
                except KeyError:
                    logger.error('the fragment %s length is missing',
                                 alignment.query)
                    raise AlignmentToMapError

            # consider the centromeres if required
            if self.__centromeres is not None and alignment.subject \
                    in self.__centromeres:
                # the chromosome a fragment was aligned to has a
                # centromere, so we determine which arm the alignment
                # refers to and modify the chromosome name by adding
                # '_1' or '_2' to it
                if min(alignment.s_start, alignment.s_end) < \
                        self.__centromeres[alignment.subject].start:
                    arm_prefix = '_1'
                else:
                    arm_prefix = '_2'
                new_alignment = list(alignment)
                new_alignment[1] += arm_prefix
                alignment = BlastTab.Alignment(*new_alignment)

            temp_anchors[alignment.query].append(alignment)
            # check if there is more than 2 alignments for the
            # fragment; if there is, then leave two fragments with
            # the greatest bit-score values
            if len(temp_anchors[alignment.query]) > 2:
                temp_anchors[alignment.query] = sorted(
                    temp_anchors[alignment.query],
                    key=attrgetter('bit_score'),
                    reverse=True
                )
                temp_anchors[alignment.query] = temp_anchors[
                    alignment.query][0:2]

        for fragment, alignments in temp_anchors.iteritems():
            if len(alignments) > 1:
                # check if the ratio of the alignment bit scores is
                # greater than the required threshold to consider a
                # fragment places
                if alignments[0].bit_score/alignments[1].bit_score > \
                        bitscore_ratio_threshold:
                    self.__anchors[fragment] = \
                        AlignmentToMap.Anchor(
                            fragment=alignments[0].query,
                            fr_start=alignments[0].q_start - 1,
                            fr_end=alignments[0].q_end,
                            fr_strand='+' if alignments[0].s_start <
                            alignments[0].s_end else '-',
                            ref_chr=alignments[0].subject,
                            ref_start=min(alignments[0].s_start,
                                          alignments[0].s_end) - 1,
                            ref_end=max(alignments[0].s_start,
                                        alignments[0].s_end)
                        )
                elif alignments[0].subject == alignments[1].subject:
                    # the fragment is considered unlocalized
                    self.__unlocalized.append(
                        (fragment, alignments[0].subject))
                else:
                    # the fragment is considered unplaced
                    self.__unplaced.append(fragment)
            else:
                # there is a single alignment, use it as an anchor
                self.__anchors[fragment] = \
                    AlignmentToMap.Anchor(
                        fragment=alignments[0].query,
                        fr_start=alignments[0].q_start - 1,
                        fr_end=alignments[0].q_end,
                        fr_strand='+' if alignments[0].s_start <
                        alignments[0].s_end else '-',
                        ref_chr=alignments[0].subject,
                        ref_start=min(alignments[0].s_start,
                                      alignments[0].s_end) - 1,
                        ref_end=max(alignments[0].s_start,
                                    alignments[0].s_end)
                    )

        # get total lengths of mapped, unlocalized and unplaced
        # fragments
        total_mapped = total_unlocalized = total_unplaced = 0
        for i in self.__anchors.itervalues():
            total_mapped += self.__fragment_lengths[i.fragment]
        for i in self.__unlocalized:
            total_unlocalized += self.__fragment_lengths[i[0]]
        for i in self.__unplaced:
            total_unplaced += self.__fragment_lengths[i]

        logger.info('%d mapped fragments of total length %d bp',
                    len(self.__anchors), total_mapped)
        logger.info('%d unlocalized fragments of total length %d bp',
                    len(self.__unlocalized), total_unlocalized)
        logger.info('%d unplaced fragments of total length %d bp',
                    len(self.__unplaced), total_unplaced)

        self.__anchor_fragments()

        return (self.__fragment_map, self.__unlocalized,
                self.__unplaced)

    def __anchor_fragments(self):
        """
        Build a fragment map from anchors.
        """
        # first, we split anchors by reference genome chromosomes
        chr_anchors = defaultdict(list)
        for anchor in self.__anchors.itervalues():
            chr_anchors[anchor.ref_chr].append(anchor)

        # second, we sort the anchors by their position on the
        # chromosomes
        for chr_name in chr_anchors.iterkeys():
            chr_anchors[chr_name] = sorted(
                chr_anchors[chr_name], key=attrgetter('ref_start')
            )

        # now we form a fragment map from the anchors
        total_inserted_gaps = 0
        self.__fragment_map = Map()
        for chr_name in chr_anchors.iterkeys():
            previous_end = 0
            for anchor in chr_anchors[chr_name]:
                try:
                    fragment_length = self.__fragment_lengths[
                        anchor.fragment]
                except KeyError:
                    logger.error('the fragment %s length is missing',
                                 anchor.fragment)
                    raise AlignmentToMapError

                # determine the fragment's start and end positions
                if anchor.fr_strand == '+':
                    ref_start = anchor.ref_start - anchor.fr_start
                    ref_end = ref_start + fragment_length
                else:
                    ref_end = anchor.ref_end + anchor.fr_start
                    ref_start = ref_end - fragment_length

                new_record = Map.Record(
                    fr_name=anchor.fragment,
                    fr_length=fragment_length,
                    fr_start=0,
                    fr_end=fragment_length,
                    fr_strand=anchor.fr_strand,
                    ref_chr=anchor.ref_chr,
                    ref_start=previous_end,
                    ref_end=previous_end + ref_end - ref_start
                )
                self.__fragment_map.add_record(new_record)
                previous_end += ref_end - ref_start

                # add a gap
                new_gap = Map.Record(
                    fr_name='GAP',
                    fr_length=self.__gap_size,
                    fr_start=0,
                    fr_end=self.__gap_size,
                    fr_strand='+',
                    ref_chr=anchor.ref_chr,
                    ref_start=previous_end,
                    ref_end=previous_end + self.__gap_size
                )
                previous_end += self.__gap_size
                self.__fragment_map.add_record(new_gap)
                total_inserted_gaps += self.__gap_size

        logger.info('%d chromosomes formed', len(chr_anchors))
        logger.info('%d bp of gaps inserted', total_inserted_gaps)


class Simulator(object):
    """
    The class describes routines to simulate genome fragments and
    chromosomes that are composed from them.
    """
    def __init__(self, fragment_length, fragment_number,
                 chromosome_number, unplaced_number, gap_size):
        """
        Create a fragment simulator object.

        :param fragment_length: the length of a fragment
        :param fragment_number: the number of fragments constituting
            the chromosomes
        :param chromosome_number: the number of chromosomes
        :param unplaced_number: the number of fragments not included
            in the chromosomes
        :param gap_size: the length of gaps between fragments in
            chromosomes
        :type fragment_length: int
        :type fragment_number: int
        :type chromosome_number: int
        :type unplaced_number: int
        :type gap_size: int
        """
        self.__fragment_length = fragment_length
        self.__fragment_number = fragment_number
        self.__chromosome_number = chromosome_number
        self.__gap_size = gap_size

        # create fragment sequences
        self.__fragments = {}
        seq_generator = RandomSequence(self.__fragment_length)
        for i in xrange(self.__fragment_number):
            fr_name = 'fragment{}'.format(i+1)
            self.__fragments[fr_name] = seq_generator.get()

        self.__map = Map()
        self.__create_map()
        self.__assemble_chromosomes()

        # add unplaced fragments
        for i in xrange(self.__fragment_number,
                        self.__fragment_number + unplaced_number):
            fr_name = 'fragment{}'.format(i+1)
            self.__fragments[fr_name] = seq_generator.get()

    def __create_map(self):
        """
        Assign fragments to chromosomes randomly and create a
        fragment map.
        """
        fragment_positions = [0] * self.__chromosome_number
        for i in xrange(self.__fragment_number):
            chr_num = random.randrange(self.__chromosome_number)
            fr_strand = random.choice(('+', '-'))
            self.__map.add_record(Map.Record(
                fr_name='fragment{}'.format(i+1),
                fr_length=self.__fragment_length,
                fr_start=0,
                fr_end=self.__fragment_length,
                fr_strand=fr_strand,
                ref_chr='chr{}'.format(chr_num+1),
                ref_start=fragment_positions[chr_num],
                ref_end=fragment_positions[chr_num] +
                self.__fragment_length
            ))
            fragment_positions[chr_num] += self.__fragment_length
            self.__map.add_record(Map.Record(
                fr_name='GAP',
                fr_length=self.__gap_size,
                fr_start=0,
                fr_end=self.__gap_size,
                fr_strand='+',
                ref_chr='chr{}'.format(chr_num+1),
                ref_start=fragment_positions[chr_num],
                ref_end=fragment_positions[chr_num] + self.__gap_size
            ))
            fragment_positions[chr_num] += self.__gap_size

    def __assemble_chromosomes(self):
        """
        Get chromosome sequences from fragments using the constructed
        fragment map.
        """
        complement = string.maketrans('ATCGatcgNnXx', 'TAGCtagcNnXx')
        chromosomes = defaultdict(list)
        for i in self.__map.chromosomes():
            for fr in self.__map.fragments(i):
                if fr.fr_name == 'GAP':
                    temp_fragment = 'N' * fr.fr_length
                else:
                    temp_fragment = self.__fragments[fr.fr_name]
                    if fr.fr_strand == '-':
                        temp_fragment = temp_fragment[::-1].translate(
                            complement)
                chromosomes[i].append(temp_fragment)
            chromosomes[i] = ''.join(chromosomes[i])

        self.__chromosomes = chromosomes

    def write(self, map_file, fragment_file, chromosome_file):
        """
        Write the produced data - a fragment map, a FASTA file of
        fragments and a FASTA file of chromosomes - to the specified
        files.

        :param map_file: a name of a file to write the fragment map to
        :param fragment_file: a name of a file to write fragment
            sequences to
        :param chromosome_file: a name of a file to write chromosome
            sequences to
        :type map_file: str
        :type fragment_file: str
        :type chromosome_file: str
        """
        self.__map.write(map_file)
        with Writer(fragment_file) as fragment_fasta:
            for name, seq in self.__fragments.iteritems():
                fragment_fasta.write(name, seq)
        with Writer(chromosome_file) as chromosome_fasta:
            for name, seq in self.__chromosomes.iteritems():
                chromosome_fasta.write(name, seq)

        logger.debug('a simulated map of %d fragments written to %s',
                     len(self.__map.records), map_file)
        logger.debug('%d simulated fragments written to %s',
                     len(self.__fragments), fragment_file)
        logger.debug('%d simulated chromosomes written to %s',
                     len(self.__chromosomes), chromosome_file)


class SeqLengths(object):
    """
    The class implements routines to handle fragment sequence lengths.
    """
    def __init__(self, filename):
        """
        Create a SeqLengths object to handle sequence lengths of the
        specified FASTA file.

        :param filename: a name of a FASTA file with sequences which
            lengths are to be derived
        :type filename: str
        """
        self.__filename = filename
        self.__lengths = {}

    def lengths(self):
        """
        Return a dictionary of sequence lengths.

        :return: a dictionary which keys are sequence names and
            values are their lengths
        :rtype: dict
        """
        total_length = 0
        if not self.__lengths:
            reader = pyfaidx.Fasta(self.__filename)
            for seq in reader.keys():
                self.__lengths[seq] = len(reader[seq])
                total_length += len(reader[seq])

        logger.debug('%d sequences analyzed with the total length of '
                     '%d bp', len(self.__lengths), total_length)

        return self.__lengths


def agp2map(agp_filename, map_filename):
    """
    Given a name of an AGP file, convert it to the fragment map format.

    :param agp_filename: a name of an AGP file
    :param map_filename: a name of an output fragment map file
    :type agp_filename: str
    :type map_filename: str
    """
    with open(agp_filename) as agp_file:
        with open(map_filename, 'w') as map_file:
            for line in agp_file:
                if line.startswith('#'):
                    continue
                line = line.rstrip()
                line = line.split(None, 8)
                if line[4] == 'N':
                    output = ('GAP', int(line[5]), 0, int(line[5]),
                              '+', line[0], int(line[1]) - 1,
                              int(line[2]))
                else:
                    frag_len = int(line[7]) - int(line[6]) + 1
                    output = (line[5], frag_len, 0, frag_len, line[8],
                              line[0], int(line[1]) - 1, int(line[2]))
                map_file.write('\t'.join(map(str, output)) + '\n')
#!/usr/bin/env python # -*- coding: utf-8 -*- # Copyright (C) 2015-2016 by <NAME> # gaik (dot) tamazian (at) gmail (dot) com The class implements routines related to creation, reading and     writing a fragment map that describes how genome fragments are     situated on reference genome chromosomes. Initializes a Map object. Given a new fragment record, add it to the fragment map.          :param new_record: a record to be added to the map         :type new_record: Map.Record Read a fragment map from the specified file. The file records         are added to the records in the map.          :param filename: a name of a file to read a fragment map from         :type: str Return an iterator to the chromosomes the fragment map         describes.          :return: an iterator to iterate through the fragment map             chromosomes Return an iterator to fragments of the specified chromosome         describes by the map. If the chromosome is absent, None is         returned.          :param chromosome: a chromosome which fragments are to be             iterated         :type chromosome: str         :return: an iterator to iterate through the chromosome's             fragments Write the fragment map to the specified file.          :param filename: a name of a file to write the fragment map to         :type filename: str Assemble chromosome sequences from fragments.          :param fragment_filename: a name of a FASTA file of fragment             sequences         :param output_filename: a name of the output FASTA file of             the assembled chromosomes         :param save_soft_mask: save soft-masking in sequences being             assembled or not         :type fragment_filename: str         :type output_filename: str         :type save_soft_mask: bool # convert the sequence to non-unicode # if the fragment orientation is reverse, then # the reverse complement of the fragment # sequence is written Shrink gaps inserted into the map to the specified size.          :param gap_size: a required gap size         :type gap_size: int # process each chromosome separately # iterate through gaps # calculate absolute shifts for chromosome fragments # change gap length and end position Return a summary on the fragment map.          :return: a dictionary of tuples each describing one assembled             chromosome         :rtype: dict Given a name of the output BED3 file, write the fragment map         to it in the BED format.          :param bed_filename: a name of the output BED file of the             fragment map         :type bed_filename: str The class implements routines to create a fragment map from a set     of alignments between fragments to be assembled and reference     chromosomes. Create a converter object to create fragment maps from         alignmets between reference chromosomes and fragments to be         assembled.          :param gap_size: a size of a gap between fragments         :param fragment_lengths: a dictionary of fragment lengths             which keys are their names and values are their lengths         :param min_fragment_length: the minimal length of a fragment             to be included in the map         :param centromeres: a dictionary of reference chromosome             centromere locations         :type gap_size: int         :type fragment_lengths: dict         :type min_fragment_length: int         :type centromeres: dict Create a fragment map from BLAST blast_alignments between         fragments and reference chromosomes.          :param blast_alignments: BLAST blast_alignments         :param bitscore_ratio_threshold: the minimal ratio of two             greatest fragment alignment bit scores to consider the             fragment placed to a reference         :type blast_alignments: BlastTab         :type bitscore_ratio_threshold: float         :return: a tuple containing the fragment map constructed from             the provided BLAST alignments, the list of unlocalized             fragments and a list of unplaced fragments         :rtype: tuple # check if the fragment length is equal or greater # than the threshold value # skip the alignment # consider the centromeres if required # the chromosome a fragment was aligned to has a # centromere, so we determine which arm the alignment # refers to and modify the chromosome name by adding # '_1' or '_2' to it # check if there is more than 2 alignments for the # fragment; if there is, then leave two fragments with # the greatest bit-score values # check if the ratio of the alignment bit scores is # greater than the required threshold to consider a # fragment places # the fragment is considered unlocalized # the fragment is considered unplaced # there is a single alignment, use it as an anchor # get total lengths of mapped, unlocalized and unplaced # fragments Build a fragment map from anchors. # first, we split anchors by reference genome chromosomes # second, we sort the anchors by their position on the # chromosomes # now we form a fragment map from the anchors # determine the fragment's start and end positions # add a gap The class describes routines to simulate genome fragments and     chromosomes that are composed from them. Create a fragment simulator object.          :param fragment_length: the length of a fragment         :param fragment_number: the number of fragments constituting             the chromosomes         :param chromosome_number: the number of chromosomes         :param unplaced_number: the number of fragments not included             in the chromosomes         :param gap_size: the length of gaps between fragments in             chromosomes         :type fragment_length: int         :type fragment_number: int         :type chromosome_number: int         :type unplaced_number: int         :type gap_size: int # create fragment sequences # add unplaced fragments Assign fragments to chromosomes randomly and create a         fragment map. Get chromosome sequences from fragments using the constructed         fragment map. Write the produced data - a fragment map, a FASTA file of         fragments and a FASTA file of chromosomes - to the specified         files.          :param map_file: a name of a file to write the fragment map to         :param fragment_file: a name of a file to write fragment             sequences to         :param chromosome_file: a name of a file to write chromosome             sequences to         :type map_file: str         :type fragment_file: str         :type chromosome_file: str The class implements routines to handle fragment sequence lengths. Create a SeqLengths object to handle sequence lengths of the         specified FASTA file.          :param filename: a name of a FASTA file with sequences which             lengths are to be derived         :type filename: str Return a dictionary of sequence lengths.          :return: a dictionary which keys are sequence names and             values are their lengths         :rtype: dict Given a name of an AGP file, convert it to the fragment map format.      :param agp_filename: a name of an AGP file     :param map_filename: a name of an output fragment map file     :type agp_filename: str     :type map_filename: str