##Dan Blankenberg
import math
import string
import transform
from sequence import SequencingRead
from fasta import fastaSequence
[docs]class fastqSequencingRead( SequencingRead ):
format = 'sanger' #sanger is default
ascii_min = 33
ascii_max = 126
quality_min = 0
quality_max = 93
score_system = 'phred' #phred or solexa
sequence_space = 'base' #base or color
@classmethod
@classmethod
[docs] def convert_score_phred_to_solexa( cls, decimal_score_list ):
def phred_to_solexa( score ):
if score <= 0: #can't take log10( 1 - 1 ); make <= 0 into -5
return -5
return int( round( 10.0 * math.log10( math.pow( 10.0, ( float( score ) / 10.0 ) ) - 1.0 ) ) )
return map( phred_to_solexa, decimal_score_list )
@classmethod
[docs] def convert_score_solexa_to_phred( cls, decimal_score_list ):
def solexa_to_phred( score ):
return int( round( 10.0 * math.log10( math.pow( 10.0, ( float( score ) / 10.0 ) ) + 1.0 ) ) )
return map( solexa_to_phred, decimal_score_list )
@classmethod
[docs] def restrict_scores_to_valid_range( cls, decimal_score_list ):
def restrict_score( score ):
return max( min( score, cls.quality_max ), cls.quality_min )
return map( restrict_score, decimal_score_list )
@classmethod
@classmethod
@classmethod
[docs] def convert_base_to_color_space( cls, sequence ):
return cls.color_space_converter.to_color_space( sequence )
@classmethod
[docs] def convert_color_to_base_space( cls, sequence ):
return cls.color_space_converter.to_base_space( sequence )
[docs] def is_ascii_encoded( self ):
#as per fastq definition only decimal quality strings can have spaces (and TABs for our purposes) in them (and must have a trailing space)
if ' ' in self.quality:
return False
if '\t' in self.quality:
return False
return True
[docs] def get_ascii_quality_scores( self ):
if self.is_ascii_encoded():
return list( self.quality )
else:
quality = self.quality.rstrip() #decimal scores should have a trailing space
if quality:
try:
to_quality = self.ascii_min - self.quality_min
return [ chr( int( val ) + to_quality ) for val in quality.split() ]
except ValueError, e:
raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) )
else:
return []
[docs] def get_ascii_quality_scores_len( self ):
"""
Compute ascii quality score length, without generating relatively
expensive qualty score array.
"""
if self.is_ascii_encoded():
return len( self.quality )
else:
quality = self.quality.rstrip()
if quality:
try:
return len( quality.split() )
except ValueError, e:
raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) )
else:
return 0
[docs] def get_decimal_quality_scores( self ):
return self.__get_decimal_quality_scores(self.is_ascii_encoded())
def __get_decimal_quality_scores( self, ascii ):
if ascii:
to_quality = self.quality_min - self.ascii_min
return [ ord( val ) + to_quality for val in self.quality ]
else:
quality = self.quality.rstrip() #decimal scores should have a trailing space
if quality:
return [ int( val ) for val in quality.split() if val.strip() ]
else:
return []
[docs] def get_sequence( self ):
return self.sequence
[docs] def slice( self, left_column_offset, right_column_offset ):
new_read = fastqSequencingRead.get_class_by_format( self.format )()
new_read.identifier = self.identifier
new_read.sequence = self.get_sequence()[left_column_offset:right_column_offset]
new_read.description = self.description
if self.is_ascii_encoded():
new_read.quality = self.quality[left_column_offset:right_column_offset]
else:
quality = map( str, self.get_decimal_quality_scores()[left_column_offset:right_column_offset] )
if quality:
new_read.quality = "%s " % " ".join( quality )
else:
new_read.quality = ''
return new_read
[docs] def is_valid_sequence( self ):
for base in self.get_sequence():
if base not in self.valid_sequence_list:
return False
return True
[docs] def insufficient_quality_length( self ):
return self.get_ascii_quality_scores_len() < len( self.sequence )
[docs] def assert_sequence_quality_lengths( self ):
qual_len = self.get_ascii_quality_scores_len()
seq_len = len( self.sequence )
assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len )
[docs] def reverse( self, clone = True ):
#need to override how decimal quality scores are reversed
if clone:
rval = self.clone()
else:
rval = self
rval.sequence = transform.reverse( self.sequence )
if rval.is_ascii_encoded():
rval.quality = rval.quality[::-1]
else:
rval.quality = reversed( rval.get_decimal_quality_scores() )
rval.quality = "%s " % " ".join( map( str, rval.quality ) )
return rval
[docs] def apply_galaxy_conventions( self ):
pass
[docs]class fastqSangerRead( fastqSequencingRead ):
format = 'sanger'
ascii_min = 33
ascii_max = 126
quality_min = 0
quality_max = 93
score_system = 'phred'
sequence_space = 'base'
[docs]class fastqIlluminaRead( fastqSequencingRead ):
format = 'illumina'
ascii_min = 64
ascii_max = 126
quality_min = 0
quality_max = 62
score_system = 'phred'
sequence_space = 'base'
[docs]class fastqSolexaRead( fastqSequencingRead ):
format = 'solexa'
ascii_min = 59
ascii_max = 126
quality_min = -5
quality_max = 62
score_system = 'solexa'
sequence_space = 'base'
[docs]class fastqCSSangerRead( fastqSequencingRead ):
format = 'cssanger' #color space
ascii_min = 33
ascii_max = 126
quality_min = 0
quality_max = 93
score_system = 'phred'
sequence_space = 'color'
valid_sequence_list = map( str, range( 7 ) ) + [ '.' ]
def __len__( self ):
if self.has_adapter_base(): #Adapter base is not counted in length of read
return len( self.sequence ) - 1
return fastqSequencingRead.__len__( self )
[docs] def has_adapter_base( self ):
if self.sequence and self.sequence[0] in string.letters: #adapter base must be a letter
return True
return False
[docs] def insufficient_quality_length( self ):
if self.has_adapter_base():
return self.get_ascii_quality_scores_len() + 1 < len( self.sequence )
return fastqSequencingRead.insufficient_quality_length( self )
[docs] def assert_sequence_quality_lengths( self ):
if self.has_adapter_base():
qual_len = self.get_ascii_quality_scores_len()
seq_len = len( self.sequence )
assert ( qual_len + 1 == seq_len ) or ( qual_len == seq_len ), "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i with adapter base)" % ( qual_len, seq_len ) #SRA adds FAKE/DUMMY quality scores to the adapter base, we'll allow the reading of the Improper score here, but remove it in the Reader when "apply_galaxy_conventions" is set to True
else:
return fastqSequencingRead.assert_sequence_quality_lengths( self )
[docs] def get_sequence( self ):
if self.has_adapter_base():
return self.sequence[1:]
return self.sequence
[docs] def reverse( self, clone = True ):
#need to override how color space is reversed
if clone:
rval = self.clone()
else:
rval = self
if rval.has_adapter_base():
adapter = rval.sequence[0]
#sequence = rval.sequence[1:]
rval.sequence = self.color_space_converter.to_color_space( transform.reverse( self.color_space_converter.to_base_space( rval.sequence ) ), adapter_base = adapter )
else:
rval.sequence = transform.reverse( rval.sequence )
if rval.is_ascii_encoded():
rval.quality = rval.quality[::-1]
else:
rval.quality = reversed( rval.get_decimal_quality_scores() )
rval.quality = "%s " % " ".join( map( str, rval.quality ) )
return rval
[docs] def complement( self, clone = True ):
#need to override how color space is complemented
if clone:
rval = self.clone()
else:
rval = self
if rval.has_adapter_base(): #No adapter, color space stays the same
adapter = rval.sequence[0]
sequence = rval.sequence[1:]
if adapter.lower() != 'u':
adapter = transform.DNA_complement( adapter )
else:
adapter = transform.RNA_complement( adapter )
rval.sequence = "%s%s" % ( adapter, sequence )
return rval
[docs] def change_adapter( self, new_adapter, clone = True ):
#if new_adapter is empty, remove adapter, otherwise replace with new_adapter
if clone:
rval = self.clone()
else:
rval = self
if rval.has_adapter_base():
if new_adapter:
if new_adapter != rval.sequence[0]:
rval.sequence = rval.color_space_converter.to_color_space( rval.color_space_converter.to_base_space( rval.sequence ), adapter_base = new_adapter )
else:
rval.sequence = rval.sequence[1:]
elif new_adapter:
rval.sequence = "%s%s" % ( new_adapter, rval.sequence )
return rval
[docs] def apply_galaxy_conventions( self ):
if self.has_adapter_base() and len( self.sequence ) == len( self.get_ascii_quality_scores() ): #SRA adds FAKE/DUMMY quality scores to the adapter base, we remove them here
if self.is_ascii_encoded():
self.quality = self.quality[1:]
else:
self.quality = " ".join( map( str, self.get_decimal_quality_scores()[1:] ) )
FASTQ_FORMATS = {}
for format in [ fastqIlluminaRead, fastqSolexaRead, fastqSangerRead, fastqCSSangerRead ]:
FASTQ_FORMATS[ format.format ] = format
[docs]class fastqAggregator( object ):
VALID_FORMATS = FASTQ_FORMATS.keys()
def __init__( self, ):
self.ascii_values_used = [] #quick lookup of all ascii chars used
self.seq_lens = {} #counts of seqs by read len
self.nuc_index_quality = [] #counts of scores by read column
self.nuc_index_base = [] #counts of bases by read column
[docs] def consume_read( self, fastq_read ):
#ascii values used
for val in fastq_read.get_ascii_quality_scores():
if val not in self.ascii_values_used:
self.ascii_values_used.append( val )
#lengths
seq_len = len( fastq_read )
self.seq_lens[ seq_len ] = self.seq_lens.get( seq_len, 0 ) + 1
#decimal qualities by column
for i, val in enumerate( fastq_read.get_decimal_quality_scores() ):
if i == len( self.nuc_index_quality ):
self.nuc_index_quality.append( {} )
self.nuc_index_quality[ i ][ val ] = self.nuc_index_quality[ i ].get( val, 0 ) + 1
#bases by column
for i, nuc in enumerate( fastq_read.get_sequence() ):
if i == len( self.nuc_index_base ):
self.nuc_index_base.append( {} )
nuc = nuc.upper()
self.nuc_index_base[ i ][ nuc ] = self.nuc_index_base[ i ].get( nuc, 0 ) + 1
[docs] def get_ascii_range( self ):
if not self.ascii_values_used:
return None
return ( min( self.ascii_values_used ), max( self.ascii_values_used ) )
[docs] def get_decimal_range( self ):
if not self.nuc_index_quality:
return None
decimal_values_used = []
for scores in self.nuc_index_quality:
decimal_values_used.extend( scores.keys() )
return ( min( decimal_values_used ), max( decimal_values_used ) )
[docs] def get_length_counts( self ):
return self.seq_lens
[docs] def get_max_read_length( self ):
return len( self.nuc_index_quality )
[docs] def get_read_count_for_column( self, column ):
if column >= len( self.nuc_index_quality ):
return 0
return sum( self.nuc_index_quality[ column ].values() )
[docs] def get_read_count( self ):
return self.get_read_count_for_column( 0 )
[docs] def get_base_counts_for_column( self, column ):
return self.nuc_index_base[ column ]
[docs] def get_score_list_for_column( self, column ):
return self.nuc_index_quality[ column ].keys()
[docs] def get_score_min_for_column( self, column ):
return min( self.nuc_index_quality[ column ].keys() )
[docs] def get_score_max_for_column( self, column ):
return max( self.nuc_index_quality[ column ].keys() )
[docs] def get_score_sum_for_column( self, column ):
return sum( score * count for score, count in self.nuc_index_quality[ column ].iteritems() )
[docs] def get_score_at_position_for_column( self, column, position ):
score_value_dict = self.nuc_index_quality[ column ]
scores = sorted( score_value_dict.keys() )
for score in scores:
if score_value_dict[ score ] <= position:
position -= score_value_dict[ score ]
else:
return score
[docs] def get_summary_statistics_for_column( self, i ):
def _get_med_pos( size ):
halfed = int( size / 2 )
if size % 2 == 1:
return [ halfed ]
return[ halfed - 1, halfed ]
read_count = self.get_read_count_for_column( i )
min_score = self.get_score_min_for_column( i )
max_score = self.get_score_max_for_column( i )
sum_score = self.get_score_sum_for_column( i )
mean_score = float( sum_score ) / float( read_count )
#get positions
med_pos = _get_med_pos( read_count )
if 0 in med_pos:
q1_pos = [ 0 ]
q3_pos = [ read_count - 1 ]
else:
q1_pos = _get_med_pos( min( med_pos ) )
q3_pos = []
for pos in q1_pos:
q3_pos.append( max( med_pos ) + 1 + pos )
#get scores at position
med_score = float( sum( [ self.get_score_at_position_for_column( i, pos ) for pos in med_pos ] ) ) / float( len( med_pos ) )
q1 = float( sum( [ self.get_score_at_position_for_column( i, pos ) for pos in q1_pos ] ) ) / float( len( q1_pos ) )
q3 = float( sum( [ self.get_score_at_position_for_column( i, pos ) for pos in q3_pos ] ) ) / float( len( q3_pos ) )
#determine iqr and step
iqr = q3 - q1
step = 1.5 * iqr
#Determine whiskers and outliers
outliers = []
score_list = sorted( self.get_score_list_for_column( i ) )
left_whisker = q1 - step
for score in score_list:
if left_whisker <= score:
left_whisker = score
break
else:
outliers.append( score )
right_whisker = q3 + step
score_list.reverse()
for score in score_list:
if right_whisker >= score:
right_whisker = score
break
else:
outliers.append( score )
column_stats = { 'read_count': read_count,
'min_score': min_score,
'max_score': max_score,
'sum_score': sum_score,
'mean_score': mean_score,
'q1': q1,
'med_score': med_score,
'q3': q3,
'iqr': iqr,
'left_whisker': left_whisker,
'right_whisker': right_whisker,
'outliers': outliers }
return column_stats
[docs]class fastqReader( object ):
def __init__( self, fh, format = 'sanger', apply_galaxy_conventions = False ):
self.file = fh
self.format = format
self.apply_galaxy_conventions = apply_galaxy_conventions
[docs] def close( self ):
return self.file.close()
[docs] def next(self):
while True:
fastq_header = self.file.readline()
if not fastq_header:
raise StopIteration
fastq_header = fastq_header.rstrip( '\n\r' )
#remove empty lines, apparently extra new lines at end of file is common?
if fastq_header:
break
assert fastq_header.startswith( '@' ), 'Invalid fastq header: %s' % fastq_header
rval = fastqSequencingRead.get_class_by_format( self.format )()
rval.identifier = fastq_header
while True:
line = self.file.readline()
if not line:
raise Exception( 'Invalid FASTQ file: could not find quality score of sequence identifier %s.' % rval.identifier )
line = line.rstrip( '\n\r' )
if line.startswith( '+' ) and ( len( line ) == 1 or line[1:].startswith( fastq_header[1:] ) ):
rval.description = line
break
rval.append_sequence( line )
while rval.insufficient_quality_length():
line = self.file.readline()
if not line:
break
rval.append_quality( line )
rval.assert_sequence_quality_lengths()
if self.apply_galaxy_conventions:
rval.apply_galaxy_conventions()
return rval
def __iter__( self ):
while True:
yield self.next()
[docs]class ReadlineCountFile( object ):
def __init__( self, f ):
self.__file = f
self.readline_count = 0
[docs] def readline( self, *args, **kwds ):
self.readline_count += 1
return self.__file.readline( *args, **kwds )
def __getattr__( self, name ):
return getattr( self.__file, name )
[docs]class fastqVerboseErrorReader( fastqReader ):
MAX_PRINT_ERROR_BYTES = 1024
def __init__( self, fh, **kwds ):
super( fastqVerboseErrorReader, self ).__init__( ReadlineCountFile( fh ), **kwds )
self.last_good_identifier = None
[docs] def next( self ):
last_good_end_offset = self.file.tell()
last_readline_count = self.file.readline_count
try:
block = super( fastqVerboseErrorReader, self ).next()
self.last_good_identifier = block.identifier
return block
except StopIteration, e:
raise e
except Exception, e:
print "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: '%s'." % e
if self.last_good_identifier is not None:
print "The last valid FASTQ read had an identifier of '%s'." % self.last_good_identifier
else:
print "The error occurred at the start of your file and no valid FASTQ reads were found."
error_offset = self.file.tell()
error_byte_count = error_offset - last_good_end_offset
print_error_bytes = min( self.MAX_PRINT_ERROR_BYTES, error_byte_count )
print "The error in your file occurs between lines '%i' and '%i', which corresponds to byte-offsets '%i' and '%i', and contains the text (%i of %i bytes shown):\n" % ( last_readline_count + 1, self.file.readline_count, last_good_end_offset, error_offset, print_error_bytes, error_byte_count )
self.file.seek( last_good_end_offset )
print self.file.read( print_error_bytes )
raise e
[docs]class fastqNamedReader( object ):
def __init__( self, fh, format = 'sanger', apply_galaxy_conventions = False ):
self.file = fh
self.format = format
self.reader = fastqReader( self.file, self.format )
#self.last_offset = self.file.tell()
self.offset_dict = {}
self.eof = False
self.apply_galaxy_conventions = apply_galaxy_conventions
[docs] def close( self ):
return self.file.close()
[docs] def get( self, sequence_identifier ):
# Input is either a sequence ID or a sequence object
if not isinstance( sequence_identifier, basestring ):
# Input was a sequence object (not a sequence ID). Get the sequence ID
sequence_identifier = sequence_identifier.identifier
# Get only the ID part of the sequence header
sequence_id, sequence_sep, sequence_desc = sequence_identifier.partition(' ')
rval = None
if sequence_id in self.offset_dict:
initial_offset = self.file.tell()
seq_offset = self.offset_dict[ sequence_id ].pop( 0 )
if not self.offset_dict[ sequence_id ]:
del self.offset_dict[ sequence_id ]
self.file.seek( seq_offset )
rval = self.reader.next()
#assert rval.id == sequence_id, 'seq id mismatch' #should be able to remove this
self.file.seek( initial_offset )
else:
while True:
offset = self.file.tell()
try:
fastq_read = self.reader.next()
except StopIteration:
self.eof = True
break #eof, id not found, will return None
fastq_read_id, fastq_read_sep, fastq_read_desc = fastq_read.identifier.partition(' ')
if fastq_read_id == sequence_id:
rval = fastq_read
break
else:
if fastq_read_id not in self.offset_dict:
self.offset_dict[ fastq_read_id ] = []
self.offset_dict[ fastq_read_id ].append( offset )
if rval is not None and self.apply_galaxy_conventions:
rval.apply_galaxy_conventions()
return rval
[docs] def has_data( self ):
#returns a string representation of remaining data, or empty string (False) if no data remaining
eof = self.eof
count = 0
rval = ''
if self.offset_dict:
count = sum( map( len, self.offset_dict.values() ) )
if not eof:
offset = self.file.tell()
try:
fastq_read = self.reader.next()
except StopIteration:
eof = True
self.file.seek( offset )
if count:
rval = "There were %i known sequence reads not utilized. " % count
if not eof:
rval = "%s%s" % ( rval, "An additional unknown number of reads exist in the input that were not utilized." )
return rval
[docs]class fastqWriter( object ):
def __init__( self, fh, format = None, force_quality_encoding = None ):
self.file = fh
self.format = format
self.force_quality_encoding = force_quality_encoding
[docs] def write( self, fastq_read ):
if self.format:
fastq_read = fastq_read.convert_read_to_format( self.format, force_quality_encoding = self.force_quality_encoding )
self.file.write( str( fastq_read ) )
[docs] def close( self ):
return self.file.close()
[docs]class fastqJoiner( object ):
def __init__( self, format, force_quality_encoding = None ):
self.format = format
self.force_quality_encoding = force_quality_encoding
[docs] def join( self, read1, read2 ):
read1_id, read1_sep, read1_desc = read1.identifier.partition(' ')
read2_id, read2_sep, read2_desc = read2.identifier.partition(' ')
if read1_id.endswith( '/2' ) and read2_id.endswith( '/1' ):
#swap 1 and 2
tmp = read1
read1 = read2
read2 = tmp
del tmp
if read1_id.endswith( '/1' ) and read2_id.endswith( '/2' ):
read1_id = read1_id[:-2]
identifier = read1_id
if read1_desc:
identifier = identifier + ' ' + read1_desc
#use force quality encoding, if not present force to encoding of first read
force_quality_encoding = self.force_quality_encoding
if not force_quality_encoding:
if read1.is_ascii_encoded():
force_quality_encoding = 'ascii'
else:
force_quality_encoding = 'decimal'
new_read1 = read1.convert_read_to_format( self.format, force_quality_encoding = force_quality_encoding )
new_read2 = read2.convert_read_to_format( self.format, force_quality_encoding = force_quality_encoding )
rval = FASTQ_FORMATS[ self.format ]()
rval.identifier = identifier
if len( read1.description ) > 1:
rval.description = "+%s" % ( identifier[1:] )
else:
rval.description = '+'
if rval.sequence_space == 'color':
#need to handle color space joining differently
#convert to nuc space, join, then convert back
rval.sequence = rval.convert_base_to_color_space( new_read1.convert_color_to_base_space( new_read1.sequence ) + new_read2.convert_color_to_base_space( new_read2.sequence ) )
else:
rval.sequence = new_read1.sequence + new_read2.sequence
if force_quality_encoding == 'ascii':
rval.quality = new_read1.quality + new_read2.quality
else:
rval.quality = "%s %s" % ( new_read1.quality.strip(), new_read2.quality.strip() )
return rval
[docs] def get_paired_identifier( self, fastq_read ):
read_id, read_sep, read_desc = fastq_read.identifier.partition(' ')
if read_id[-2] == '/':
if read_id[-1] == "1":
read_id = "%s2" % read_id[:-1]
elif read_id[-1] == "2":
read_id = "%s1" % read_id[:-1]
return read_id
[docs] def is_first_mate( self, sequence_id ):
is_first = None
if not isinstance( sequence_id, basestring ):
sequence_id = sequence_id.identifier
sequence_id, sequence_sep, sequence_desc = sequence_id.partition(' ')
if sequence_id[-2] == '/':
if sequence_id[-1] == "1":
is_first = True
else:
is_first = False
return is_first
[docs]class fastqSplitter( object ):
[docs] def split( self, fastq_read ):
length = len( fastq_read )
#Only reads of even lengths can be split
if length % 2 != 0:
return None, None
half = int( length / 2 )
read1 = fastq_read.slice( 0, half )
read1.identifier += "/1"
if len( read1.description ) > 1:
read1.description += "/1"
read2 = fastq_read.slice( half, None )
read2.identifier += "/2"
if len( read2.description ) > 1:
read2.description += "/2"
return read1, read2
[docs]class fastqCombiner( object ):
def __init__( self, format ):
self.format = format
[docs] def combine(self, fasta_seq, quality_seq ):
fastq_read = fastqSequencingRead.get_class_by_format( self.format )()
fastq_read.identifier = "@%s" % fasta_seq.identifier[1:]
fastq_read.description = '+'
fastq_read.sequence = fasta_seq.sequence
fastq_read.quality = quality_seq.sequence
return fastq_read
[docs]class fastqFakeFastaScoreReader( object ):
def __init__( self, format = 'sanger', quality_encoding = None ):
self.fastq_read = fastqSequencingRead.get_class_by_format( format )()
if quality_encoding != 'decimal':
quality_encoding = 'ascii'
self.quality_encoding = quality_encoding
[docs] def close( self ):
return #nothing to close
[docs] def get( self, sequence ):
assert isinstance( sequence, fastaSequence ), 'fastqFakeFastaScoreReader requires a fastaSequence object as the parameter'
#add sequence to fastq_read, then get_sequence(), color space adapters do not have quality score values
self.fastq_read.sequence = sequence.sequence
new_sequence = fastaSequence()
new_sequence.identifier = sequence.identifier
if self.quality_encoding == 'ascii':
new_sequence.sequence = chr( self.fastq_read.ascii_max ) * len( self.fastq_read.get_sequence() )
else:
new_sequence.sequence = ( "%i " % self.fastq_read.quality_max ) * len( self.fastq_read.get_sequence() )
return new_sequence
[docs] def has_data( self ):
return '' #No actual data exist, none can be remaining