def compare_record(self, old, new, fmt=None, msg=None):
"""Quality aware SeqRecord comparison.
This will check the mapping between Solexa and PHRED scores.
It knows to ignore UnknownSeq objects for string matching (i.e. QUAL files).
"""
super().compare_record(old, new, msg=None)
if fmt in ["fastq-solexa", "fastq-illumina"]:
truncate = 62
elif fmt in ["fastq", "fastq-sanger"]:
truncate = 93
else:
assert fmt in ["fasta", "qual", "phd", "sff", "tab", None]
truncate = None
for keyword in ("phred_quality", "solexa_quality"):
q_old = old.letter_annotations.get(keyword)
q_new = new.letter_annotations.get(keyword)
if q_old is None or q_new is None:
continue
if truncate is not None and q_old != q_new:
q_old = [min(q, truncate) for q in q_old]
q_new = [min(q, truncate) for q in q_new]
err_msg = "mismatch in %s" % keyword
if msg is not None:
err_msg = "%s: %s" % (msg, err_msg)
self.assertEqual(q_old, q_new, msg=err_msg)
q_old = old.letter_annotations.get("phred_quality")
q_new = new.letter_annotations.get("solexa_quality")
if q_old is not None and q_new is not None:
# Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
# Assume "old" is the original, and "new" has been converted.
converted = [
round(QualityIO.solexa_quality_from_phred(q)) for q in q_old
]
if truncate is not None:
converted = [min(q, truncate) for q in converted]
err_msg = "mismatch converting phred_quality %s to solexa_quality" % q_old
if msg is not None:
err_msg = "%s: %s" % (msg, err_msg)
self.assertEqual(converted, q_new, msg=err_msg)
q_old = old.letter_annotations.get("solexa_quality")
q_new = new.letter_annotations.get("phred_quality")
if q_old is not None and q_new is not None:
# Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
# Assume "old" is the original, and "new" has been converted.
converted = [
round(QualityIO.phred_quality_from_solexa(q)) for q in q_old
]
if truncate is not None:
converted = [min(q, truncate) for q in converted]
err_msg = "mismatch converting solexa_quality %s to phred_quality" % q_old
if msg is not None:
err_msg = "%s: %s" % (msg, err_msg)
self.assertEqual(converted, q_new, msg=err_msg)
def test_sanger_to_solexa(self):
"""Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62)"""
# The point of this test is the writing code doesn't actually use the
# solexa_quality_from_phred function directly. For speed it uses a
# cached dictionary of the mappings.
seq = "N"*94
qual = "".join(chr(33+q) for q in range(0, 94))
expected_sol = [min(62, int(round(QualityIO.solexa_quality_from_phred(q))))
for q in range(0, 94)]
in_handle = StringIO("@Test\n%s\n+\n%s" % (seq, qual))
out_handle = StringIO()
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", BiopythonWarning)
SeqIO.write(SeqIO.parse(in_handle, "fastq-sanger"),
out_handle, "fastq-solexa")
self.assertTrue(len(w) <= 1, w)
out_handle.seek(0)
record = SeqIO.read(out_handle, "fastq-solexa")
self.assertEqual(str(record.seq), seq)
self.assertEqual(record.letter_annotations["solexa_quality"],
expected_sol)
def test_sanger_to_solexa(self):
"""Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62)"""
# The point of this test is the writing code doesn't actually use the
# solexa_quality_from_phred function directly. For speed it uses a
# cached dictionary of the mappings.
seq = "N" * 94
qual = "".join(chr(33 + q) for q in range(0, 94))
expected_sol = [min(62, int(round(QualityIO.solexa_quality_from_phred(q))))
for q in range(0, 94)]
in_handle = StringIO("@Test\n%s\n+\n%s" % (seq, qual))
out_handle = StringIO()
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", BiopythonWarning)
SeqIO.write(SeqIO.parse(in_handle, "fastq-sanger"),
out_handle, "fastq-solexa")
self.assertTrue(len(w) <= 1, w)
out_handle.seek(0)
record = SeqIO.read(out_handle, "fastq-solexa")
self.assertEqual(str(record.seq), seq)
self.assertEqual(record.letter_annotations["solexa_quality"],
expected_sol)
def test_sanger_to_solexa(self):
"""Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62)"""
#The point of this test is the writing code doesn't actually use the
#solexa_quality_from_phred function directly. For speed it uses a
#cached dictionary of the mappings.
seq = "N"*94
qual = "".join(chr(33+q) for q in range(0,94))
expected_sol = [min(62,int(round(QualityIO.solexa_quality_from_phred(q))))
for q in range(0,94)]
in_handle = StringIO("@Test\n%s\n+\n%s" % (seq,qual))
out_handle = StringIO("")
#Want to ignore the data loss warning
#(on Python 2.6 we could check for it!)
warnings.simplefilter('ignore', BiopythonWarning)
SeqIO.write(SeqIO.parse(in_handle, "fastq-sanger"),
out_handle, "fastq-solexa")
warnings.filters.pop()
out_handle.seek(0)
record = SeqIO.read(out_handle, "fastq-solexa")
self.assertEqual(str(record.seq), seq)
self.assertEqual(record.letter_annotations["solexa_quality"],
expected_sol)
def test_sanger_to_solexa(self):
"""Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62)"""
#The point of this test is the writing code doesn't actually use the
#solexa_quality_from_phred function directly. For speed it uses a
#cached dictionary of the mappings.
seq = "N" * 94
qual = "".join(chr(33 + q) for q in range(0, 94))
expected_sol = [min(62,int(round(QualityIO.solexa_quality_from_phred(q)))) \
for q in range(0,94)]
in_handle = StringIO("@Test\n%s\n+\n%s" % (seq, qual))
out_handle = StringIO("")
#Want to ignore the data loss warning
#(on Python 2.6 we could check for it!)
warnings.simplefilter('ignore', UserWarning)
SeqIO.write(SeqIO.parse(in_handle, "fastq-sanger"), out_handle,
"fastq-solexa")
warnings.resetwarnings()
out_handle.seek(0)
record = SeqIO.read(out_handle, "fastq-solexa")
self.assertEqual(str(record.seq), seq)
self.assertEqual(record.letter_annotations["solexa_quality"],
expected_sol)
def compare_record(self, old, new, truncate, msg):
"""Quality aware SeqRecord comparison.
This will check the mapping between Solexa and PHRED scores.
It knows to ignore UnknownSeq objects for string matching (i.e. QUAL files).
"""
super().compare_record(old, new, msg=msg)
for keyword in ("phred_quality", "solexa_quality"):
q_old = old.letter_annotations.get(keyword)
q_new = new.letter_annotations.get(keyword)
if q_old is None or q_new is None:
continue
if truncate and q_old != q_new:
q_old = [min(q, truncate) for q in q_old]
q_new = [min(q, truncate) for q in q_new]
err_msg = "%s: mismatch in %s" % (msg, keyword)
self.assertEqual(q_old, q_new, msg=err_msg)
q_old = old.letter_annotations.get("phred_quality")
q_new = new.letter_annotations.get("solexa_quality")
if q_old is not None and q_new is not None:
# Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
# Assume "old" is the original, and "new" has been converted.
converted = [round(QualityIO.solexa_quality_from_phred(q)) for q in q_old]
if truncate:
converted = [min(q, truncate) for q in converted]
err_msg = "%s: mismatch in phred_quality vs solexa_quality" % msg
self.assertEqual(converted, q_new, msg=err_msg)
q_old = old.letter_annotations.get("solexa_quality")
q_new = new.letter_annotations.get("phred_quality")
if q_old is not None and q_new is not None:
# Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
# Assume "old" is the original, and "new" has been converted.
converted = [round(QualityIO.phred_quality_from_solexa(q)) for q in q_old]
if truncate:
converted = [min(q, truncate) for q in converted]
err_msg = "%s: mismatch in solexa_quality vs phred_quality" % msg
self.assertEqual(converted, q_new, msg=err_msg)
def test_solexa_quality_from_phred(self):
"""Mapping check for function solexa_quality_from_phred"""
self.assertEqual(-5, round(QualityIO.solexa_quality_from_phred(0)))
self.assertEqual(-5, round(QualityIO.solexa_quality_from_phred(1)))
self.assertEqual(-2, round(QualityIO.solexa_quality_from_phred(2)))
self.assertEqual(0, round(QualityIO.solexa_quality_from_phred(3)))
self.assertEqual(2, round(QualityIO.solexa_quality_from_phred(4)))
self.assertEqual(3, round(QualityIO.solexa_quality_from_phred(5)))
self.assertEqual(5, round(QualityIO.solexa_quality_from_phred(6)))
self.assertEqual(6, round(QualityIO.solexa_quality_from_phred(7)))
self.assertEqual(7, round(QualityIO.solexa_quality_from_phred(8)))
self.assertEqual(8, round(QualityIO.solexa_quality_from_phred(9)))
for i in range(10,100):
self.assertEqual(i, round(QualityIO.solexa_quality_from_phred(i)))
def compare_record(old, new, truncate=None):
"""Quality aware SeqRecord comparison.
This will check the mapping between Solexa and PHRED scores.
It knows to ignore UnknownSeq objects for string matching (i.e. QUAL files).
"""
if old.id != new.id:
raise ValueError("'%s' vs '%s' " % (old.id, new.id))
if old.description != new.description \
and (old.id+" "+old.description).strip() != new.description:
raise ValueError("'%s' vs '%s' " % (old.description, new.description))
if len(old.seq) != len(new.seq):
raise ValueError("%i vs %i" % (len(old.seq), len(new.seq)))
if isinstance(old.seq, UnknownSeq) or isinstance(new.seq, UnknownSeq):
pass
elif str(old.seq) != str(new.seq):
if len(old.seq) < 200:
raise ValueError("'%s' vs '%s'" % (old.seq, new.seq))
else:
raise ValueError("'%s...' vs '%s...'" % (old.seq[:100], new.seq[:100]))
if "phred_quality" in old.letter_annotations \
and "phred_quality" in new.letter_annotations \
and old.letter_annotations["phred_quality"] != new.letter_annotations["phred_quality"]:
if truncate and [min(q,truncate) for q in old.letter_annotations["phred_quality"]] == \
[min(q,truncate) for q in new.letter_annotations["phred_quality"]]:
pass
else:
raise ValuerError("Mismatch in phred_quality")
if "solexa_quality" in old.letter_annotations \
and "solexa_quality" in new.letter_annotations \
and old.letter_annotations["solexa_quality"] != new.letter_annotations["solexa_quality"]:
if truncate and [min(q,truncate) for q in old.letter_annotations["solexa_quality"]] == \
[min(q,truncate) for q in new.letter_annotations["solexa_quality"]]:
pass
else:
raise ValueError("Mismatch in phred_quality")
if "phred_quality" in old.letter_annotations \
and "solexa_quality" in new.letter_annotations:
#Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
#Assume "old" is the original, and "new" has been converted.
converted = [round(QualityIO.solexa_quality_from_phred(q))
for q in old.letter_annotations["phred_quality"]]
if truncate:
converted = [min(q,truncate) for q in converted]
if converted != new.letter_annotations["solexa_quality"]:
print
print(old.letter_annotations["phred_quality"])
print(converted)
print(new.letter_annotations["solexa_quality"])
raise ValueError("Mismatch in phred_quality vs solexa_quality")
if "solexa_quality" in old.letter_annotations \
and "phred_quality" in new.letter_annotations:
#Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
#Assume "old" is the original, and "new" has been converted.
converted = [round(QualityIO.phred_quality_from_solexa(q))
for q in old.letter_annotations["solexa_quality"]]
if truncate:
converted = [min(q,truncate) for q in converted]
if converted != new.letter_annotations["phred_quality"]:
print(old.letter_annotations["solexa_quality"])
print(converted)
print(new.letter_annotations["phred_quality"])
raise ValueError("Mismatch in solexa_quality vs phred_quality")
return True
def test_solexa_quality_from_phred(self):
"""Mapping check for function solexa_quality_from_phred"""
self.assertEqual(-5, round(QualityIO.solexa_quality_from_phred(0)))
self.assertEqual(-5, round(QualityIO.solexa_quality_from_phred(1)))
self.assertEqual(-2, round(QualityIO.solexa_quality_from_phred(2)))
self.assertEqual(0, round(QualityIO.solexa_quality_from_phred(3)))
self.assertEqual(2, round(QualityIO.solexa_quality_from_phred(4)))
self.assertEqual(3, round(QualityIO.solexa_quality_from_phred(5)))
self.assertEqual(5, round(QualityIO.solexa_quality_from_phred(6)))
self.assertEqual(6, round(QualityIO.solexa_quality_from_phred(7)))
self.assertEqual(7, round(QualityIO.solexa_quality_from_phred(8)))
self.assertEqual(8, round(QualityIO.solexa_quality_from_phred(9)))
for i in range(10, 100):
self.assertEqual(i, round(QualityIO.solexa_quality_from_phred(i)))
def compare_record(old, new, truncate=None):
"""Quality aware SeqRecord comparison.
This will check the mapping between Solexa and PHRED scores.
It knows to ignore UnknownSeq objects for string matching (i.e. QUAL files).
"""
if old.id != new.id:
raise ValueError("'%s' vs '%s' " % (old.id, new.id))
if old.description != new.description \
and (old.id+" "+old.description).strip() != new.description:
raise ValueError("'%s' vs '%s' " % (old.description, new.description))
if len(old.seq) != len(new.seq):
raise ValueError("%i vs %i" % (len(old.seq), len(new.seq)))
if isinstance(old.seq, UnknownSeq) or isinstance(new.seq, UnknownSeq):
pass
elif str(old.seq) != str(new.seq):
if len(old.seq) < 200:
raise ValueError("'%s' vs '%s'" % (old.seq, new.seq))
else:
raise ValueError("'%s...' vs '%s...'" %
(old.seq[:100], new.seq[:100]))
if "phred_quality" in old.letter_annotations \
and "phred_quality" in new.letter_annotations \
and old.letter_annotations["phred_quality"] != new.letter_annotations["phred_quality"]:
if truncate and [min(q,truncate) for q in old.letter_annotations["phred_quality"]] == \
[min(q,truncate) for q in new.letter_annotations["phred_quality"]]:
pass
else:
raise ValuerError("Mismatch in phred_quality")
if "solexa_quality" in old.letter_annotations \
and "solexa_quality" in new.letter_annotations \
and old.letter_annotations["solexa_quality"] != new.letter_annotations["solexa_quality"]:
if truncate and [min(q,truncate) for q in old.letter_annotations["solexa_quality"]] == \
[min(q,truncate) for q in new.letter_annotations["solexa_quality"]]:
pass
else:
raise ValueError("Mismatch in phred_quality")
if "phred_quality" in old.letter_annotations \
and "solexa_quality" in new.letter_annotations:
#Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
#Assume "old" is the original, and "new" has been converted.
converted = [
round(QualityIO.solexa_quality_from_phred(q))
for q in old.letter_annotations["phred_quality"]
]
if truncate:
converted = [min(q, truncate) for q in converted]
if converted != new.letter_annotations["solexa_quality"]:
print
print(old.letter_annotations["phred_quality"])
print(converted)
print(new.letter_annotations["solexa_quality"])
raise ValueError("Mismatch in phred_quality vs solexa_quality")
if "solexa_quality" in old.letter_annotations \
and "phred_quality" in new.letter_annotations:
#Mapping from Solexa to PHRED is lossy, but so is PHRED to Solexa.
#Assume "old" is the original, and "new" has been converted.
converted = [
round(QualityIO.phred_quality_from_solexa(q))
for q in old.letter_annotations["solexa_quality"]
]
if truncate:
converted = [min(q, truncate) for q in converted]
if converted != new.letter_annotations["phred_quality"]:
print(old.letter_annotations["solexa_quality"])
print(converted)
print(new.letter_annotations["phred_quality"])
raise ValueError("Mismatch in solexa_quality vs phred_quality")
return True
