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Reduce to minimal required change

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This commit is contained in:
Wolfgang Maier
2019-07-11 16:47:25 +02:00
parent 37b3a0fe13
commit ff6f1084a7
1 changed files with 4 additions and 20 deletions
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lib/galaxy/datatypes/sequence.py
+4 -20
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@@ -694,6 +694,9 @@ class BaseFastq(Sequence):
>>> fname = get_test_fname('1.fastqsanger')
>>> FastqSanger().sniff(fname)
True
>>> fname = get_test_fname('4.fastqsanger')
>>> FastqSanger().sniff(fname)
True
>>> fname = get_test_fname('3.fastq')
>>> FastqSanger().sniff(fname)
False
@@ -714,9 +717,6 @@ class BaseFastq(Sequence):
True
>>> FastqCSSanger().sniff(fname)
True
>>> fname = get_test_fname('4.fastqsanger')
>>> FastqSanger().sniff(fname)
True
"""
compressed = file_prefix.compressed_format is not None
if compressed and not isinstance(self, Binary):
@@ -821,25 +821,9 @@ class FastqSanger(Fastq):
@staticmethod
def quality_check(lines):
"""Presuming lines are lines from a fastq file, return True if the qualities are compatible with sanger encoding"""
is_ambiguous = True
within_typical_upper_bound = True
for line in islice(lines, 3, None, 4):
if ' ' in line:
if not all(_ >= '!' and _ <= 'S' for _ in line[0]) or ' ' in line:
return False
if is_ambiguous:
for q in line[0]:
if q < '!' or q > '~':
return False
if q < ';':
# encoding is Phred+33
is_ambiguous = False
elif q > 'M':
within_typical_upper_bound = False
else:
if any(_ < '!' or _ > '~' for _ in line[0]):
return False
if is_ambiguous and not within_typical_upper_bound:
return False
return True