def __init__(self, seq, name=None, qual=None, use_mut_str=False):
"""
Constructor for FastqSequence class; see class level documentation for
descriptions of parameters.
"""
if len(seq) != len(qual):
msg = (
"failed to create FastqSequence object -- length of sequence "
+ "data (" + str(len(seq)) +
") does not match length of quality " + "string (" +
str(len(qual)) + "). seq data: " + seq + " qual data: " +
qual)
raise NGSReadError(msg)
Sequence.__init__(self, name, seq, use_mut_str)
self.seq_qual = qual
# for quality scores
# ILLUMINA 1.3+ Phred+64
self.LOWSET_SCORE = 64
self.HIGHEST_SCORE = 104
# Illumina 1.8+ Phred+33
self.LOWSET_SCORE_ILL_18_PHRD_33 = 33
self.HIGHEST_SCORE_ILL_18_PHRD_33 = 74
def __init__(self, seq, name=None, qual=None, use_mut_str=False):
"""
Constructor for FastqSequence class; see class level documentation for
descriptions of parameters.
"""
if len(seq) != len(qual):
msg = (
"failed to create FastqSequence object -- length of sequence "
+ "data ("
+ str(len(seq))
+ ") does not match length of quality "
+ "string ("
+ str(len(qual))
+ "). seq data: "
+ seq
+ " qual data: "
+ qual
)
raise NGSReadError(msg)
Sequence.__init__(self, name, seq, use_mut_str)
self.seq_qual = qual
# for quality scores
self.LOWSET_SCORE = 64
self.HIGHEST_SCORE = 104
