annotate extract_genomic_dna_utils.py @ 3:b71579ad576c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31

import copy
import os
import subprocess
import sys
import tempfile

from bx.intervals.io import Comment, GenomicInterval, Header
from bx.intervals.io import GenomicIntervalReader, NiceReaderWrapper, ParseError

# Default chrom, start, end, strand cols for a bed file
BED_DEFAULT_COLS = 0, 1, 2, 5


class GFFInterval(GenomicInterval):
    """
    A GFF interval, including attributes. If file is strictly a GFF file,
    only attribute is 'group.'
    """

    def __init__(self, reader, fields, chrom_col=0, feature_col=2, start_col=3, end_col=4,
                 strand_col=6, score_col=5, default_strand='.', fix_strand=False):
        # GFF format allows '.' for strand but GenomicInterval does not. To get around this,
        # temporarily set strand and then unset after initing GenomicInterval.
        unknown_strand = False
        if not fix_strand and fields[strand_col] == '.':
            unknown_strand = True
            fields[strand_col] = '+'
        GenomicInterval.__init__(self, reader, fields, chrom_col, start_col, end_col,
                                 strand_col, default_strand, fix_strand=fix_strand)
        if unknown_strand:
            self.strand = '.'
            self.fields[strand_col] = '.'
        # Handle feature, score column.
        self.feature_col = feature_col
        if self.feature_col >= self.nfields:
            stop_err("No field for feature_col (%d)" % feature_col)
        self.feature = self.fields[self.feature_col]
        self.score_col = score_col
        if self.score_col >= self.nfields:
            stop_err("No field for score_col (%d)" % score_col)
        self.score = self.fields[self.score_col]
        # GFF attributes.
        self.attributes = parse_gff_attributes(fields[8])

    def copy(self):
        return GFFInterval(self.reader, list(self.fields), self.chrom_col, self.feature_col,
                           self.start_col, self.end_col, self.strand_col, self.score_col, self.strand)


class GFFFeature(GFFInterval):
    """
    A GFF feature, which can include multiple intervals.
    """

    def __init__(self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4, strand_col=6,
                 score_col=5, default_strand='.', fix_strand=False, intervals=[], raw_size=0):
        # Use copy so that first interval and feature do not share fields.
        GFFInterval.__init__(self, reader, copy.deepcopy(intervals[0].fields), chrom_col, feature_col,
                             start_col, end_col, strand_col, score_col, default_strand, fix_strand=fix_strand)
        self.intervals = intervals
        self.raw_size = raw_size
        # Use intervals to set feature attributes.
        for interval in self.intervals:
            # Error checking. NOTE: intervals need not share the same strand.
            if interval.chrom != self.chrom:
                stop_err("interval chrom does not match self chrom: %s != %s" % (interval.chrom, self.chrom))
            # Set start, end of interval.
            if interval.start < self.start:
                self.start = interval.start
            if interval.end > self.end:
                self.end = interval.end

    def name(self):
        """
        Returns feature's name.
        """
        name = None
        # Preference for name:
        # GTF: 'gene_id', 'transcript_id'
        # GFF3: 'ID', 'id'
        # GFF: 'group'
        for attr_name in ['gene_id', 'transcript_id', 'ID', 'id', 'group']:
            name = self.attributes.get(attr_name, None)
            if name is not None:
                break
        return name

    def copy(self):
        intervals_copy = []
        for interval in self.intervals:
            intervals_copy.append(interval.copy())
        return GFFFeature(self.reader, self.chrom_col, self.feature_col, self.start_col, self.end_col,
                          self.strand_col, self.score_col, self.strand, intervals=intervals_copy)

    def lines(self):
        lines = []
        for interval in self.intervals:
            lines.append('\t'.join(interval.fields))
        return lines


class GFFReaderWrapper(NiceReaderWrapper):
    """
    Reader wrapper for GFF files which has two major functions:
    1. group entries for GFF file (via group column), GFF3 (via id attribute),
       or GTF (via gene_id/transcript id);
    2. convert coordinates from GFF format--starting and ending coordinates
       are 1-based, closed--to the 'traditional'/BED interval format--0 based,
       half-open. This is useful when using GFF files as inputs to tools that
       expect traditional interval format.
    """

    def __init__(self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4, strand_col=6,
                 score_col=5, fix_strand=False, convert_to_bed_coord=False, **kwargs):
        NiceReaderWrapper.__init__(self, reader, chrom_col=chrom_col, start_col=start_col, end_col=end_col,
                                   strand_col=strand_col, fix_strand=fix_strand, **kwargs)
        self.feature_col = feature_col
        self.score_col = score_col
        self.convert_to_bed_coord = convert_to_bed_coord
        self.last_line = None
        self.cur_offset = 0
        self.seed_interval = None
        self.seed_interval_line_len = 0

    def parse_row(self, line):
        interval = GFFInterval(self, line.split("\t"), self.chrom_col, self.feature_col, self.start_col,
                               self.end_col, self.strand_col, self.score_col, self.default_strand,
                               fix_strand=self.fix_strand)
        return interval

    def next(self):
        """
        Returns next GFFFeature.
        """

        def handle_parse_error(parse_error):
            """
            Actions to take when ParseError found.
            """
            if self.outstream:
                if self.print_delegate and hasattr(self.print_delegate, "__call__"):
                    self.print_delegate(self.outstream, e, self)
            self.skipped += 1
            # No reason to stuff an entire bad file into memory.
            if self.skipped < 10:
                self.skipped_lines.append((self.linenum, self.current_line, str(e)))
        # Get next GFFFeature
        raw_size = self.seed_interval_line_len
        # If there is no seed interval, set one. Also, if there are no more
        # intervals to read, this is where iterator dies.
        if not self.seed_interval:
            while not self.seed_interval:
                try:
                    self.seed_interval = GenomicIntervalReader.next(self)
                except ParseError as e:
                    handle_parse_error(e)
                finally:
                    raw_size += len(self.current_line)
        # If header or comment, clear seed interval and return it with its size.
        if isinstance(self.seed_interval, (Header, Comment)):
            return_val = self.seed_interval
            return_val.raw_size = len(self.current_line)
            self.seed_interval = None
            self.seed_interval_line_len = 0
            return return_val
        # Initialize feature identifier from seed.
        # For GFF.
        feature_group = self.seed_interval.attributes.get('group', None)
        # For GFF3
        feature_id = self.seed_interval.attributes.get('ID', None)
        # For GTF.
        feature_transcript_id = self.seed_interval.attributes.get('transcript_id', None)
        # Read all intervals associated with seed.
        feature_intervals = []
        feature_intervals.append(self.seed_interval)
        while True:
            try:
                interval = GenomicIntervalReader.next(self)
                raw_size += len(self.current_line)
            except StopIteration as e:
                # No more intervals to read, but last feature needs to be
                # returned.
                interval = None
                raw_size += len(self.current_line)
                break
            except ParseError as e:
                handle_parse_error(e)
                raw_size += len(self.current_line)
                continue
            # Ignore comments.
            if isinstance(interval, Comment):
                continue
            # Determine if interval is part of feature.
            part_of = False
            group = interval.attributes.get('group', None)
            # GFF test:
            if group and feature_group == group:
                part_of = True
            # GFF3 test:
            parent_id = interval.attributes.get('Parent', None)
            cur_id = interval.attributes.get('ID', None)
            if (cur_id and cur_id == feature_id) or (parent_id and parent_id == feature_id):
                part_of = True
            # GTF test:
            transcript_id = interval.attributes.get('transcript_id', None)
            if transcript_id and transcript_id == feature_transcript_id:
                part_of = True
            # If interval is not part of feature, clean up and break.
            if not part_of:
                # Adjust raw size because current line is not part of feature.
                raw_size -= len(self.current_line)
                break
            # Interval associated with feature.
            feature_intervals.append(interval)
        # Last interval read is the seed for the next interval.
        self.seed_interval = interval
        self.seed_interval_line_len = len(self.current_line)
        # Return feature.
        feature = GFFFeature(self, self.chrom_col, self.feature_col, self.start_col,
                             self.end_col, self.strand_col, self.score_col,
                             self.default_strand, fix_strand=self.fix_strand,
                             intervals=feature_intervals, raw_size=raw_size)
        # Convert to BED coords?
        if self.convert_to_bed_coord:
            convert_gff_coords_to_bed(feature)
        return feature


def convert_bed_coords_to_gff(interval):
    """
    Converts an interval object's coordinates from BED format to GFF format.
    Accepted object types include GenomicInterval and list (where the first
    element in the list is the interval's start, and the second element is
    the interval's end).
    """
    if isinstance(interval, GenomicInterval):
        interval.start += 1
        if isinstance(interval, GFFFeature):
            for subinterval in interval.intervals:
                convert_bed_coords_to_gff(subinterval)
    elif isinstance(interval, list):
        interval[0] += 1
    return interval


def convert_gff_coords_to_bed(interval):
    """
    Converts an interval object's coordinates from GFF format to BED format.
    Accepted object types include GFFFeature, GenomicInterval, and list (where
    the first element in the list is the interval's start, and the second
    element is the interval's end).
    """
    if isinstance(interval, GenomicInterval):
        interval.start -= 1
        if isinstance(interval, GFFFeature):
            for subinterval in interval.intervals:
                convert_gff_coords_to_bed(subinterval)
    elif isinstance(interval, list):
        interval[0] -= 1
    return interval


def convert_to_twobit(reference_genome):
    """
    Create 2bit file history fasta dataset.
    """
    try:
        seq_path = tempfile.NamedTemporaryFile(dir=".").name
        cmd = "faToTwoBit %s %s" % (reference_genome, seq_path)
        tmp_name = tempfile.NamedTemporaryFile(dir=".").name
        tmp_stderr = open(tmp_name, 'wb')
        proc = subprocess.Popen(args=cmd, shell=True, stderr=tmp_stderr.fileno())
        returncode = proc.wait()
        tmp_stderr.close()
        if returncode != 0:
            # Get stderr, allowing for case where it's very large.
            tmp_stderr = open(tmp_name, 'rb')
            stderr = ''
            buffsize = 1048576
            try:
                while True:
                    stderr += tmp_stderr.read(buffsize)
                    if not stderr or len(stderr) % buffsize != 0:
                        break
            except OverflowError:
                pass
            tmp_stderr.close()
            os.remove(tmp_name)
            stop_err(stderr)
        return seq_path
    except Exception as e:
        stop_err('Error running faToTwoBit. ' + str(e))


def get_bedtools_getfasta_default_header(chrom, start, end, strand, includes_strand_col):
    """
    Return a fasta header that is the default produced by the bedtools
    getfasta tool, assuming "force strandedness".  This will produce a
    header with this format: <chrom>:<start>-<end>(strand).  If the input
    data includes a strand column and the strand is '+' or '-', then use it.
    If the input data includes a strand column and the value of strand is
    anything but '+' or '-', set strand to '.' in the header.  If the input
    data does not include a strand column, set strand to '.' in the header.
    """
    if includes_strand_col and strand in ['+', '-']:
        strand_val = strand
    else:
        strand_val = '.'
    return '%s:%s-%s(%s)' % (chrom, start, end, strand_val)


def get_fasta_header_delimiter(delimiter):
    # Return a specified fasta header delimiter.
    if delimiter == 'underscore':
        return '_'
    if delimiter == 'semicolon':
        return ';'
    if delimiter == 'comma':
        return ','
    if delimiter == 'tilde':
        return '~'
    if delimiter == 'vertical_bar':
        return '|'
    # Set the default to underscore.
    return '_'


def get_lines(feature):
    # Get feature's line(s).
    if isinstance(feature, GFFFeature):
        return feature.lines()
    else:
        return [feature.rstrip('\r\n')]


def gff_attributes_to_str(attrs, gff_format):
    """
    Convert GFF attributes to string. Supported formats are GFF3, GTF.
    """
    if gff_format == 'GTF':
        format_string = '%s "%s"'
        # Convert group (GFF) and ID, parent (GFF3) attributes to
        # transcript_id, gene_id.
        id_attr = None
        if 'group' in attrs:
            id_attr = 'group'
        elif 'ID' in attrs:
            id_attr = 'ID'
        elif 'Parent' in attrs:
            id_attr = 'Parent'
        if id_attr:
            attrs['transcript_id'] = attrs['gene_id'] = attrs[id_attr]
    elif gff_format == 'GFF3':
        format_string = '%s=%s'
    attrs_strs = []
    for name, value in attrs.items():
        attrs_strs.append(format_string % (name, value))
    return " ; ".join(attrs_strs)


def parse_cols_arg(cols):
    """
    Parse a columns command line argument into a four-tuple.
    """
    if cols:
        # Handle case where no strand column included - in this case, cols
        # looks something like 1,2,3,
        if cols.endswith(','):
            cols += '0'
        col_list = map(lambda x: int(x) - 1, cols.split(","))
        return col_list
    else:
        return BED_DEFAULT_COLS


def parse_gff_attributes(attr_str):
    """
    Parses a GFF/GTF attribute string and returns a dictionary of name-value
    pairs. The general format for a GFF3 attributes string is
        name1=value1;name2=value2
    The general format for a GTF attribute string is
        name1 "value1" ; name2 "value2"
    The general format for a GFF attribute string is a single string that
    denotes the interval's group; in this case, method returns a dictionary
    with a single key-value pair, and key name is 'group'.
    """
    attributes_list = attr_str.split(";")
    attributes = {}
    for name_value_pair in attributes_list:
        # Try splitting by '=' (GFF3) first because spaces are allowed in GFF3
        # attribute; next, try double quotes for GTF.
        pair = name_value_pair.strip().split("=")
        if len(pair) == 1:
            pair = name_value_pair.strip().split("\"")
        if len(pair) == 1:
            # Could not split for some reason.
            continue
        if pair == '':
            continue
        name = pair[0].strip()
        if name == '':
            continue
        # Need to strip double quote from values
        value = pair[1].strip(" \"")
        attributes[name] = value
    if len(attributes) == 0:
        # Could not split attributes string, so entire string must be
        # 'group' attribute. This is the case for strictly GFF files.
        attributes['group'] = attr_str
    return attributes


def reverse_complement(s):
    complement_dna = {"A": "T", "T": "A", "C": "G", "G": "C", "a": "t", "t": "a", "c": "g", "g": "c", "N": "N", "n": "n"}
    reversed_s = []
    for i in s:
        reversed_s.append(complement_dna[i])
    reversed_s.reverse()
    return "".join(reversed_s)


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit(1)