annotate utils/maf_utilities.py @ 3:25b8736c627a draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit 34a6c9f94a5722bb7d2f887618aafa410a770e91"

#!/usr/bin/env python
"""
Provides wrappers and utilities for working with MAF files and alignments.
"""
# Dan Blankenberg
import bx.align.maf
import bx.intervals
import bx.interval_index_file
import sys
import os
import tempfile
import logging
from copy import deepcopy

try:
    maketrans = str.maketrans
except AttributeError:
    from string import maketrans

log = logging.getLogger(__name__)


GAP_CHARS = ['-']
SRC_SPLIT_CHAR = '.'


def src_split(src):
    fields = src.split(SRC_SPLIT_CHAR, 1)
    spec = fields.pop(0)
    if fields:
        chrom = fields.pop(0)
    else:
        chrom = spec
    return spec, chrom


def src_merge(spec, chrom, contig=None):
    if None in [spec, chrom]:
        spec = chrom = spec or chrom
    return bx.align.maf.src_merge(spec, chrom, contig)


def get_species_in_block(block):
    species = []
    for c in block.components:
        spec, chrom = src_split(c.src)
        if spec not in species:
            species.append(spec)
    return species


def tool_fail(msg="Unknown Error"):
    msg = "Fatal Error: %s" % msg
    sys.exit(msg)

# an object corresponding to a reference layered alignment


class RegionAlignment(object):

    DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca")

    def __init__(self, size, species=[]):
        self.size = size
        self.sequences = {}
        if not isinstance(species, list):
            species = [species]
        for spec in species:
            self.add_species(spec)

    # add a species to the alignment
    def add_species(self, species):
        # make temporary sequence files
        self.sequences[species] = tempfile.TemporaryFile()
        self.sequences[species].write("-" * self.size)

    # returns the names for species found in alignment, skipping names as requested
    def get_species_names(self, skip=[]):
        if not isinstance(skip, list):
            skip = [skip]
        names = self.sequences.keys()
        for name in skip:
            try:
                names.remove(name)
            except Exception:
                pass
        return names

    # returns the sequence for a species
    def get_sequence(self, species):
        self.sequences[species].seek(0)
        return self.sequences[species].read()

    # returns the reverse complement of the sequence for a species
    def get_sequence_reverse_complement(self, species):
        complement = [base for base in self.get_sequence(species).translate(self.DNA_COMPLEMENT)]
        complement.reverse()
        return "".join(complement)

    # sets a position for a species
    def set_position(self, index, species, base):
        if len(base) != 1:
            raise Exception("A genomic position can only have a length of 1.")
        return self.set_range(index, species, base)
    # sets a range for a species

    def set_range(self, index, species, bases):
        if index >= self.size or index < 0:
            raise Exception("Your index (%i) is out of range (0 - %i)." % (index, self.size - 1))
        if len(bases) == 0:
            raise Exception("A set of genomic positions can only have a positive length.")
        if species not in self.sequences.keys():
            self.add_species(species)
        self.sequences[species].seek(index)
        self.sequences[species].write(bases)

    # Flush temp file of specified species, or all species
    def flush(self, species=None):
        if species is None:
            species = self.sequences.keys()
        elif not isinstance(species, list):
            species = [species]
        for spec in species:
            self.sequences[spec].flush()


class GenomicRegionAlignment(RegionAlignment):

    def __init__(self, start, end, species=[]):
        RegionAlignment.__init__(self, end - start, species)
        self.start = start
        self.end = end


class SplicedAlignment(object):

    DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca")

    def __init__(self, exon_starts, exon_ends, species=[]):
        if not isinstance(exon_starts, list):
            exon_starts = [exon_starts]
        if not isinstance(exon_ends, list):
            exon_ends = [exon_ends]
        assert len(exon_starts) == len(exon_ends), "The number of starts does not match the number of sizes."
        self.exons = []
        for i in range(len(exon_starts)):
            self.exons.append(GenomicRegionAlignment(exon_starts[i], exon_ends[i], species))

    # returns the names for species found in alignment, skipping names as requested
    def get_species_names(self, skip=[]):
        if not isinstance(skip, list):
            skip = [skip]
        names = []
        for exon in self.exons:
            for name in exon.get_species_names(skip=skip):
                if name not in names:
                    names.append(name)
        return names

    # returns the sequence for a species
    def get_sequence(self, species):
        sequence = tempfile.TemporaryFile()
        for exon in self.exons:
            if species in exon.get_species_names():
                sequence.write(exon.get_sequence(species))
            else:
                sequence.write("-" * exon.size)
        sequence.seek(0)
        return sequence.read()

    # returns the reverse complement of the sequence for a species
    def get_sequence_reverse_complement(self, species):
        complement = [base for base in self.get_sequence(species).translate(self.DNA_COMPLEMENT)]
        complement.reverse()
        return "".join(complement)

    # Start and end of coding region
    @property
    def start(self):
        return self.exons[0].start

    @property
    def end(self):
        return self.exons[-1].end

# Open a MAF index using a UID


def maf_index_by_uid(maf_uid, index_location_file):
    for line in open(index_location_file):
        try:
            # read each line, if not enough fields, go to next line
            if line[0:1] == "#":
                continue
            fields = line.split('\t')
            if maf_uid == fields[1]:
                try:
                    maf_files = fields[4].replace("\n", "").replace("\r", "").split(",")
                    return bx.align.maf.MultiIndexed(maf_files, keep_open=True, parse_e_rows=False)
                except Exception as e:
                    raise Exception('MAF UID (%s) found, but configuration appears to be malformed: %s' % (maf_uid, e))
        except Exception:
            pass
    return None

# return ( index, temp_index_filename ) for user maf, if available, or build one and return it, return None when no tempfile is created


def open_or_build_maf_index(maf_file, index_filename, species=None):
    try:
        return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), None)
    except Exception:
        return build_maf_index(maf_file, species=species)


def build_maf_index_species_chromosomes(filename, index_species=None):
    species = []
    species_chromosomes = {}
    indexes = bx.interval_index_file.Indexes()
    blocks = 0
    try:
        maf_reader = bx.align.maf.Reader(open(filename))
        while True:
            pos = maf_reader.file.tell()
            block = maf_reader.next()
            if block is None:
                break
            blocks += 1
            for c in block.components:
                spec = c.src
                chrom = None
                if "." in spec:
                    spec, chrom = spec.split(".", 1)
                if spec not in species:
                    species.append(spec)
                    species_chromosomes[spec] = []
                if chrom and chrom not in species_chromosomes[spec]:
                    species_chromosomes[spec].append(chrom)
                if index_species is None or spec in index_species:
                    forward_strand_start = c.forward_strand_start
                    forward_strand_end = c.forward_strand_end
                    try:
                        forward_strand_start = int(forward_strand_start)
                        forward_strand_end = int(forward_strand_end)
                    except ValueError:
                        continue  # start and end are not integers, can't add component to index, goto next component
                        # this likely only occurs when parse_e_rows is True?
                        # could a species exist as only e rows? should the
                    if forward_strand_end > forward_strand_start:
                        # require positive length; i.e. certain lines have start = end = 0 and cannot be indexed
                        indexes.add(c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size)
    except Exception as e:
        # most likely a bad MAF
        log.debug('Building MAF index on %s failed: %s' % (filename, e))
        return (None, [], {}, 0)
    return (indexes, species, species_chromosomes, blocks)

# builds and returns ( index, index_filename ) for specified maf_file


def build_maf_index(maf_file, species=None):
    indexes, found_species, species_chromosomes, blocks = build_maf_index_species_chromosomes(maf_file, species)
    if indexes is not None:
        fd, index_filename = tempfile.mkstemp()
        out = os.fdopen(fd, 'w')
        indexes.write(out)
        out.close()
        return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), index_filename)
    return (None, None)


def component_overlaps_region(c, region):
    if c is None:
        return False
    start, end = c.get_forward_strand_start(), c.get_forward_strand_end()
    if region.start >= end or region.end <= start:
        return False
    return True


def chop_block_by_region(block, src, region, species=None, mincols=0):
    # This chopping method was designed to maintain consistency with how start/end padding gaps have been working in Galaxy thus far:
    #   behavior as seen when forcing blocks to be '+' relative to src sequence (ref) and using block.slice_by_component( ref, slice_start, slice_end )
    #   whether-or-not this is the 'correct' behavior is questionable, but this will at least maintain consistency
    # comments welcome
    slice_start = block.text_size  # max for the min()
    slice_end = 0  # min for the max()
    old_score = block.score  # save old score for later use
    # We no longer assume only one occurance of src per block, so we need to check them all
    for c in iter_components_by_src(block, src):
        if component_overlaps_region(c, region):
            if c.text is not None:
                rev_strand = False
                if c.strand == "-":
                    # We want our coord_to_col coordinates to be returned from positive stranded component
                    rev_strand = True
                    c = c.reverse_complement()
                start = max(region.start, c.start)
                end = min(region.end, c.end)
                start = c.coord_to_col(start)
                end = c.coord_to_col(end)
                if rev_strand:
                    # need to orient slice coordinates to the original block direction
                    slice_len = end - start
                    end = len(c.text) - start
                    start = end - slice_len
                slice_start = min(start, slice_start)
                slice_end = max(end, slice_end)

    if slice_start < slice_end:
        block = block.slice(slice_start, slice_end)
        if block.text_size > mincols:
            # restore old score, may not be accurate, but it is better than 0 for everything?
            block.score = old_score
            if species is not None:
                block = block.limit_to_species(species)
                block.remove_all_gap_columns()
            return block
    return None


def orient_block_by_region(block, src, region, force_strand=None):
    # loop through components matching src,
    # make sure each of these components overlap region
    # cache strand for each of overlaping regions
    # if force_strand / region.strand not in strand cache, reverse complement
    # we could have 2 sequences with same src, overlapping region, on different strands, this would cause no reverse_complementing
    strands = [c.strand for c in iter_components_by_src(block, src) if component_overlaps_region(c, region)]
    if strands and (force_strand is None and region.strand not in strands) or (force_strand is not None and force_strand not in strands):
        block = block.reverse_complement()
    return block


def get_oriented_chopped_blocks_for_region(index, src, region, species=None, mincols=0, force_strand=None):
    for block, idx, offset in get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols, force_strand):
        yield block


def get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0, force_strand=None):
    for block, idx, offset in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols):
        yield orient_block_by_region(block, src, region, force_strand), idx, offset

# split a block with multiple occurances of src into one block per src


def iter_blocks_split_by_src(block, src):
    for src_c in iter_components_by_src(block, src):
        new_block = bx.align.Alignment(score=block.score, attributes=deepcopy(block.attributes))
        new_block.text_size = block.text_size
        for c in block.components:
            if c == src_c or c.src != src:
                new_block.add_component(deepcopy(c))  # components have reference to alignment, dont want to loose reference to original alignment block in original components
        yield new_block

# split a block into multiple blocks with all combinations of a species appearing only once per block


def iter_blocks_split_by_species(block, species=None):
    def __split_components_by_species(components_by_species, new_block):
        if components_by_species:
            # more species with components to add to this block
            components_by_species = deepcopy(components_by_species)
            spec_comps = components_by_species.pop(0)
            for c in spec_comps:
                newer_block = deepcopy(new_block)
                newer_block.add_component(deepcopy(c))
                for value in __split_components_by_species(components_by_species, newer_block):
                    yield value
        else:
            # no more components to add, yield this block
            yield new_block

    # divide components by species
    spec_dict = {}
    if not species:
        species = []
        for c in block.components:
            spec, chrom = src_split(c.src)
            if spec not in spec_dict:
                spec_dict[spec] = []
                species.append(spec)
            spec_dict[spec].append(c)
    else:
        for spec in species:
            spec_dict[spec] = []
            for c in iter_components_by_src_start(block, spec):
                spec_dict[spec].append(c)

    empty_block = bx.align.Alignment(score=block.score, attributes=deepcopy(block.attributes))  # should we copy attributes?
    empty_block.text_size = block.text_size
    # call recursive function to split into each combo of spec/blocks
    for value in __split_components_by_species(spec_dict.values(), empty_block):
        sort_block_components_by_block(value, block)  # restore original component order
        yield value


# generator yielding only chopped and valid blocks for a specified region
def get_chopped_blocks_for_region(index, src, region, species=None, mincols=0):
    for block, idx, offset in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols):
        yield block


def get_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0):
    for block, idx, offset in index.get_as_iterator_with_index_and_offset(src, region.start, region.end):
        block = chop_block_by_region(block, src, region, species, mincols)
        if block is not None:
            yield block, idx, offset

# returns a filled region alignment for specified regions


def get_region_alignment(index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True):
    if species is not None:
        alignment = RegionAlignment(end - start, species)
    else:
        alignment = RegionAlignment(end - start, primary_species)
    return fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps)

# reduces a block to only positions exisiting in the src provided


def reduce_block_by_primary_genome(block, species, chromosome, region_start):
    # returns ( startIndex, {species:texts}
    # where texts' contents are reduced to only positions existing in the primary genome
    src = "%s.%s" % (species, chromosome)
    ref = block.get_component_by_src(src)
    start_offset = ref.start - region_start
    species_texts = {}
    for c in block.components:
        species_texts[c.src.split('.')[0]] = list(c.text)
    # remove locations which are gaps in the primary species, starting from the downstream end
    for i in range(len(species_texts[species]) - 1, -1, -1):
        if species_texts[species][i] == '-':
            for text in species_texts.values():
                text.pop(i)
    for spec, text in species_texts.items():
        species_texts[spec] = ''.join(text)
    return (start_offset, species_texts)

# fills a region alignment


def fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True):
    region = bx.intervals.Interval(start, end)
    region.chrom = chrom
    region.strand = strand
    primary_src = "%s.%s" % (primary_species, chrom)

    # Order blocks overlaping this position by score, lowest first
    blocks = []
    for block, idx, offset in index.get_as_iterator_with_index_and_offset(primary_src, start, end):
        score = float(block.score)
        for i in range(0, len(blocks)):
            if score < blocks[i][0]:
                blocks.insert(i, (score, idx, offset))
                break
        else:
            blocks.append((score, idx, offset))

    # gap_chars_tuple = tuple( GAP_CHARS )
    gap_chars_str = ''.join(GAP_CHARS)
    # Loop through ordered blocks and layer by increasing score
    for block_dict in blocks:
        for block in iter_blocks_split_by_species(block_dict[1].get_at_offset(block_dict[2])):  # need to handle each occurance of sequence in block seperately
            if component_overlaps_region(block.get_component_by_src(primary_src), region):
                block = chop_block_by_region(block, primary_src, region, species, mincols)  # chop block
                block = orient_block_by_region(block, primary_src, region)  # orient block
                start_offset, species_texts = reduce_block_by_primary_genome(block, primary_species, chrom, start)
                for spec, text in species_texts.items():
                    # we should trim gaps from both sides, since these are not positions in this species genome (sequence)
                    text = text.rstrip(gap_chars_str)
                    gap_offset = 0
                    while True in [text.startswith(gap_char) for gap_char in GAP_CHARS]:  # python2.4 doesn't accept a tuple for .startswith()
                        # while text.startswith( gap_chars_tuple ):
                        gap_offset += 1
                        text = text[1:]
                        if not text:
                            break
                    if text:
                        if overwrite_with_gaps:
                            alignment.set_range(start_offset + gap_offset, spec, text)
                        else:
                            for i, char in enumerate(text):
                                if char not in GAP_CHARS:
                                    alignment.set_position(start_offset + gap_offset + i, spec, char)
    return alignment

# returns a filled spliced region alignment for specified region with start and end lists


def get_spliced_region_alignment(index, primary_species, chrom, starts, ends, strand='+', species=None, mincols=0, overwrite_with_gaps=True):
    # create spliced alignment object
    if species is not None:
        alignment = SplicedAlignment(starts, ends, species)
    else:
        alignment = SplicedAlignment(starts, ends, [primary_species])
    for exon in alignment.exons:
        fill_region_alignment(exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps)
    return alignment

# loop through string array, only return non-commented lines


def line_enumerator(lines, comment_start='#'):
    i = 0
    for line in lines:
        if not line.startswith(comment_start):
            i += 1
            yield (i, line)

# read a GeneBed file, return list of starts, ends, raw fields


def get_starts_ends_fields_from_gene_bed(line):
    # Starts and ends for exons
    starts = []
    ends = []

    fields = line.split()
    # Requires atleast 12 BED columns
    if len(fields) < 12:
        raise Exception("Not a proper 12 column BED line (%s)." % line)
    tx_start = int(fields[1])
    strand = fields[5]
    if strand != '-':
        strand = '+'  # Default strand is +
    cds_start = int(fields[6])
    cds_end = int(fields[7])

    # Calculate and store starts and ends of coding exons
    region_start, region_end = cds_start, cds_end
    exon_starts = map(int, fields[11].rstrip(',\n').split(','))
    exon_starts = map((lambda x: x + tx_start), exon_starts)
    exon_ends = map(int, fields[10].rstrip(',').split(','))
    exon_ends = map((lambda x, y: x + y), exon_starts, exon_ends)
    for start, end in zip(exon_starts, exon_ends):
        start = max(start, region_start)
        end = min(end, region_end)
        if start < end:
            starts.append(start)
            ends.append(end)
    return (starts, ends, fields)


def iter_components_by_src(block, src):
    for c in block.components:
        if c.src == src:
            yield c


def get_components_by_src(block, src):
    return [value for value in iter_components_by_src(block, src)]


def iter_components_by_src_start(block, src):
    for c in block.components:
        if c.src.startswith(src):
            yield c


def get_components_by_src_start(block, src):
    return [value for value in iter_components_by_src_start(block, src)]


def sort_block_components_by_block(block1, block2):
    # orders the components in block1 by the index of the component in block2
    # block1 must be a subset of block2
    # occurs in-place
    return block1.components.sort(cmp=lambda x, y: block2.components.index(x) - block2.components.index(y))


def get_species_in_maf(maf_filename):
    species = []
    for block in bx.align.maf.Reader(open(maf_filename)):
        for spec in get_species_in_block(block):
            if spec not in species:
                species.append(spec)
    return species


def parse_species_option(species):
    if species:
        species = species.split(',')
        if 'None' not in species:
            return species
    return None  # provided species was '', None, or had 'None' in it


def remove_temp_index_file(index_filename):
    try:
        os.unlink(index_filename)
    except Exception:
        pass

# Below are methods to deal with FASTA files


def get_fasta_header(component, attributes={}, suffix=None):
    header = ">%s(%s):%i-%i|" % (component.src, component.strand, component.get_forward_strand_start(), component.get_forward_strand_end())
    for key, value in attributes.iteritems():
        header = "%s%s=%s|" % (header, key, value)
    if suffix:
        header = "%s%s" % (header, suffix)
    else:
        header = "%s%s" % (header, src_split(component.src)[0])
    return header


def get_attributes_from_fasta_header(header):
    if not header:
        return {}
    attributes = {}
    header = header.lstrip('>')
    header = header.strip()
    fields = header.split('|')
    try:
        region = fields[0]
        region = region.split('(', 1)
        temp = region[0].split('.', 1)
        attributes['species'] = temp[0]
        if len(temp) == 2:
            attributes['chrom'] = temp[1]
        else:
            attributes['chrom'] = temp[0]
        region = region[1].split(')', 1)
        attributes['strand'] = region[0]
        region = region[1].lstrip(':').split('-')
        attributes['start'] = int(region[0])
        attributes['end'] = int(region[1])
    except Exception:
        # fields 0 is not a region coordinate
        pass
    if len(fields) > 2:
        for i in range(1, len(fields) - 1):
            prop = fields[i].split('=', 1)
            if len(prop) == 2:
                attributes[prop[0]] = prop[1]
    if len(fields) > 1:
        attributes['__suffix__'] = fields[-1]
    return attributes


def iter_fasta_alignment(filename):
    class fastaComponent:
        def __init__(self, species, text=""):
            self.species = species
            self.text = text

        def extend(self, text):
            self.text = self.text + text.replace('\n', '').replace('\r', '').strip()
    # yields a list of fastaComponents for a FASTA file
    with open(filename, 'r') as f:
        components = []
        # cur_component = None
        while True:
            line = f.readline()
            if not line:
                if components:
                    yield components
                return
            line = line.strip()
            if not line:
                if components:
                    yield components
                components = []
            elif line.startswith('>'):
                attributes = get_attributes_from_fasta_header(line)
                components.append(fastaComponent(attributes['species']))
            elif components:
                components[-1].extend(line)