def next(self):
""" Returns next GFFFeature. """
#
# Helper function.
#
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 memmory
if self.skipped < 10:
self.skipped_lines.append(
(self.linenum, self.current_line, str(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
#
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, e:
handle_parse_error(e)
# TODO: When no longer supporting python 2.4 use finally:
#finally:
raw_size += len(self.current_line)
def next( self ):
""" Returns next GFFFeature. """
#
# Helper function.
#
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 memmory
if self.skipped < 10:
self.skipped_lines.append( ( self.linenum, self.current_line, str( 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
#
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, e:
handle_parse_error( e )
# TODO: When no longer supporting python 2.4 use finally:
#finally:
raw_size += len( self.current_line )
def next( self ):
""" Returns next GFFFeature. """
#
# Helper function.
#
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 memmory
if self.skipped < 10:
self.skipped_lines.append( ( self.linenum, self.current_line, str( 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
#
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 )
# 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 = 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
# TODO: When no longer supporting python 2.4 use finally:
# finally:
# raw_size += len( self.current_line )
# 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
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.
"""
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. """
#
# Helper function.
#
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 memmory
if self.skipped < 10:
self.skipped_lines.append(
(self.linenum, self.current_line, str(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
#
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, 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 = GenomicIntervalReader.next(self)
raw_size += len(self.current_line)
except StopIteration, e:
# No more intervals to read, but last feature needs to be
# returned.
interval = None
raw_size += len(self.current_line)
break
except ParseError, e:
handle_parse_error(e)
raw_size += len(self.current_line)
continue
