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Source code for galaxy.datatypes.util.gff_util

Provides utilities for working with GFF files.
import copy

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

from galaxy.util import unicodify


[docs]class GFFInterval(GenomicInterval): """ A GFF interval, including attributes. If file is strictly a GFF file, only attribute is 'group.' """
[docs] 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): # HACK: 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.nfields <= self.feature_col: raise MissingFieldError("No field for feature_col (%d)" % feature_col) self.feature = self.fields[self.feature_col] self.score_col = score_col if self.nfields <= self.score_col: raise MissingFieldError("No field for score_col (%d)" % score_col) self.score = self.fields[self.score_col] # GFF attributes. if self.nfields < 9: raise MissingFieldError("No field for attribute column (8)") self.attributes = parse_gff_attributes(fields[8])
[docs] 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)
[docs]class GFFFeature(GFFInterval): """ A GFF feature, which can include multiple intervals. """
[docs] 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=None, raw_size=0): # Use copy so that first interval and feature do not share fields. intervals = intervals or [] 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: raise ValueError("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
[docs] def name(self): """ Returns feature's name. """ name = None # Preference for name: GTF, GFF3, GFF. for attr_name in [ # GTF: 'gene_id', 'transcript_id', # GFF3: 'ID', 'id', # GFF (TODO): 'group']: name = self.attributes.get(attr_name, None) if name is not None: break return name
[docs] 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)
[docs] def lines(self): lines = [] for interval in self.intervals: lines.append('\t'.join(interval.fields)) return lines
[docs]class GFFIntervalToBEDReaderWrapper(NiceReaderWrapper): """ Reader wrapper that reads GFF intervals/lines and automatically converts them to BED format. """
[docs] def parse_row(self, line): # HACK: this should return a GFF interval, but bx-python operations # require GenomicInterval objects and subclasses will not work. interval = GenomicInterval(self, line.split("\t"), self.chrom_col, self.start_col, self.end_col, self.strand_col, self.default_strand, fix_strand=self.fix_strand) interval = convert_gff_coords_to_bed(interval) return interval
[docs]class GFFReaderWrapper(NiceReaderWrapper): """ Reader wrapper for GFF files. Wrapper 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. """
[docs] 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 self.__end_of_intervals = False
[docs] 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. """ # # Helper function. # def handle_parse_error(e): """ Actions to take when ParseError found. """ if self.outstream: if self.print_delegate and callable(self.print_delegate): self.print_delegate(self.outstream, e, self) self.skipped += 1 # no reason to stuff an entire bad file into memmory if self.skipped < 10: self.skipped_lines.append((self.linenum, self.current_line, unicodify(e))) # For debugging, uncomment this to propogate parsing exceptions up. # I.e. the underlying reason for an unexpected StopIteration exception # can be found by uncommenting this. # raise e # # Get next GFFFeature # if self.__end_of_intervals: raise StopIteration("End of Intervals") 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 = super(GenomicIntervalReader, self).__next__() except ParseError as e: handle_parse_error(e) # TODO: When no longer supporting python 2.4 use finally: # 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. feature_group = self.seed_interval.attributes.get('group', None) # For GFF # 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 = super(GenomicIntervalReader, self).__next__() except StopIteration: # No more intervals to read, but last feature needs to be # returned. interval = None break except ParseError as e: handle_parse_error(e) continue finally: raw_size += len(self.current_line) # Ignore comments. if isinstance(interval, Comment): if self.current_line.rstrip() == FASTA_DIRECTIVE: self.__end_of_intervals = True break 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
[docs]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
[docs]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
[docs]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 -- raise exception? 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
[docs]def parse_gff3_attributes(attr_str): """ Parses a GFF3 attribute string and returns a dictionary of name-value pairs. The general format for a GFF3 attributes string is name1=value1;name2=value2 """ attributes_list = attr_str.split(";") attributes = {} for tag_value_pair in attributes_list: tag_value_pair = tag_value_pair.strip() if tag_value_pair == '': continue pair = tag_value_pair.split("=") if len(pair) == 1: raise Exception(f"Attribute '{tag_value_pair}' does not contain a '='") if pair == '': continue tag = pair[0].strip() if tag == '': raise Exception(f"Empty tag in attribute '{tag_value_pair}'") value = pair[1].strip() attributes[tag] = value return attributes
[docs]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)
[docs]def read_unordered_gtf(iterator, strict=False): """ Returns GTF features found in an iterator. GTF lines need not be ordered or clustered for reader to work. Reader returns GFFFeature objects sorted by transcript_id, chrom, and start position. """ # -- Get function that generates line/feature key. -- def get_transcript_id(fields): return parse_gff_attributes(fields[8])['transcript_id'] if strict: # Strict GTF parsing uses transcript_id only to group lines into feature. key_fn = get_transcript_id else: # Use lenient parsing where chromosome + transcript_id is the key. This allows # transcripts with same ID on different chromosomes; this occurs in some popular # datasources, such as RefGenes in UCSC. def key_fn(fields): return f"{fields[0]}_{get_transcript_id(fields)}" # Aggregate intervals by transcript_id and collect comments. feature_intervals = {} comments = [] for line in iterator: if line.startswith('#'): comments.append(Comment(line)) continue line_key = key_fn(line.split('\t')) if line_key in feature_intervals: feature = feature_intervals[line_key] else: feature = [] feature_intervals[line_key] = feature feature.append(GFFInterval(None, line.split('\t'))) # Create features. chroms_features = {} for intervals in feature_intervals.values(): # Sort intervals by start position. intervals.sort(key=lambda _: _.start) feature = GFFFeature(None, intervals=intervals) if feature.chrom not in chroms_features: chroms_features[feature.chrom] = [] chroms_features[feature.chrom].append(feature) # Sort features by chrom, start position. chroms_features_sorted = sorted(chroms_features.values(), key=lambda _: _[0].chrom) for features in chroms_features_sorted: features.sort(key=lambda _: _.start) # Yield comments first, then features. # FIXME: comments can appear anywhere in file, not just the beginning. # Ideally, then comments would be associated with features and output # just before feature/line. yield from comments for chrom_features in chroms_features_sorted: for feature in chrom_features: yield feature