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# Copyright 2009 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for Bio.SeqIO.convert(...) function."""
from __future__ import print_function
import unittest
import warnings
from Bio.Seq import UnknownSeq
from Bio import SeqIO
from Bio.SeqIO import QualityIO
from Bio.SeqIO._convert import _converter as converter_dict
from Bio._py3k import StringIO
from Bio.Alphabet import generic_protein, generic_nucleotide, generic_dna
# TODO - share this with the QualityIO tests...
def truncation_expected(format):
if format in ["fastq-solexa", "fastq-illumina"]:
return 62
elif format in ["fastq", "fastq-sanger"]:
return 93
else:
return None
# Top level function as this makes it easier to use for debugging:
def check_convert(in_filename, in_format, out_format, alphabet=None):
records = list(SeqIO.parse(in_filename, in_format, alphabet))
# Write it out...
handle = StringIO()
qual_truncate = truncation_expected(out_format)
with warnings.catch_warnings():
if qual_truncate:
warnings.simplefilter('ignore', UserWarning)
SeqIO.write(records, handle, out_format)
handle.seek(0)
# Now load it back and check it agrees,
records2 = list(SeqIO.parse(handle, out_format, alphabet))
compare_records(records, records2, qual_truncate)
# Finally, use the convert function, and check that agrees:
handle2 = StringIO()
with warnings.catch_warnings():
if qual_truncate:
warnings.simplefilter('ignore', UserWarning)
SeqIO.convert(in_filename, in_format, handle2, out_format, alphabet)
# We could re-parse this, but it is simpler and stricter:
assert handle.getvalue() == handle2.getvalue()
def check_convert_fails(in_filename, in_format, out_format, alphabet=None):
qual_truncate = truncation_expected(out_format)
# We want the SAME error message from parse/write as convert!
err1 = None
try:
records = list(SeqIO.parse(in_filename, in_format, alphabet))
handle = StringIO()
with warnings.catch_warnings():
if qual_truncate:
warnings.simplefilter('ignore', UserWarning)
SeqIO.write(records, handle, out_format)
handle.seek(0)
assert False, "Parse or write should have failed!"
except ValueError as err:
err1 = err
# Now do the conversion...
try:
handle2 = StringIO()
with warnings.catch_warnings():
if qual_truncate:
warnings.simplefilter('ignore', UserWarning)
SeqIO.convert(in_filename, in_format, handle2, out_format, alphabet)
assert False, "Convert should have failed!"
except ValueError as err2:
assert str(err1) == str(err2), \
"Different failures, parse/write:\n%s\nconvert:\n%s" \
% (err1, err2)
# TODO - move this to a shared test module...
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 \
and new.description != "<unknown description>" \
and new.description != "": # e.g. tab format
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 compare_records(old_list, new_list, truncate_qual=None):
"""Check two lists of SeqRecords agree, raises a ValueError if mismatch."""
if len(old_list) != len(new_list):
raise ValueError("%i vs %i records" % (len(old_list), len(new_list)))
for old, new in zip(old_list, new_list):
if not compare_record(old, new, truncate_qual):
return False
return True
class ConvertTests(unittest.TestCase):
"""Cunning unit test where methods are added at run time."""
def simple_check(self, filename, in_format, out_format, alphabet):
check_convert(filename, in_format, out_format, alphabet)
def failure_check(self, filename, in_format, out_format, alphabet):
check_convert_fails(filename, in_format, out_format, alphabet)
tests = [
("Quality/example.fastq", "fastq", None),
("Quality/example.fastq", "fastq-sanger", generic_dna),
("Quality/tricky.fastq", "fastq", generic_nucleotide),
("Quality/sanger_93.fastq", "fastq-sanger", None),
("Quality/sanger_faked.fastq", "fastq-sanger", generic_dna),
("Quality/solexa_faked.fastq", "fastq-solexa", generic_dna),
("Quality/illumina_faked.fastq", "fastq-illumina", generic_dna),
("EMBL/U87107.embl", "embl", None),
("EMBL/TRBG361.embl", "embl", None),
("GenBank/NC_005816.gb", "gb", None),
("GenBank/cor6_6.gb", "genbank", None),
]
for filename, format, alphabet in tests:
for (in_format, out_format) in converter_dict:
if in_format != format:
continue
def funct(fn, fmt1, fmt2, alpha):
f = lambda x: x.simple_check(fn, fmt1, fmt2, alpha)
f.__doc__ = "Convert %s from %s to %s" % (fn, fmt1, fmt2)
return f
setattr(ConvertTests, "test_%s_%s_to_%s"
% (filename.replace("/", "_").replace(".", "_"), in_format, out_format),
funct(filename, in_format, out_format, alphabet))
del funct
# Fail tests:
tests = [
("Quality/error_diff_ids.fastq", "fastq", None),
("Quality/error_long_qual.fastq", "fastq", None),
("Quality/error_no_qual.fastq", "fastq", None),
("Quality/error_qual_del.fastq", "fastq", None),
("Quality/error_qual_escape.fastq", "fastq", None),
("Quality/error_qual_null.fastq", "fastq", None),
("Quality/error_qual_space.fastq", "fastq", None),
("Quality/error_qual_tab.fastq", "fastq", None),
("Quality/error_qual_unit_sep.fastq", "fastq", None),
("Quality/error_qual_vtab.fastq", "fastq", None),
("Quality/error_short_qual.fastq", "fastq", None),
("Quality/error_spaces.fastq", "fastq", None),
("Quality/error_tabs.fastq", "fastq", None),
("Quality/error_trunc_at_plus.fastq", "fastq", None),
("Quality/error_trunc_at_qual.fastq", "fastq", None),
("Quality/error_trunc_at_seq.fastq", "fastq", None),
("Quality/error_trunc_in_title.fastq", "fastq", generic_dna),
("Quality/error_trunc_in_seq.fastq", "fastq", generic_nucleotide),
("Quality/error_trunc_in_plus.fastq", "fastq", None),
("Quality/error_trunc_in_qual.fastq", "fastq", generic_dna),
("Quality/error_double_seq.fastq", "fastq", generic_dna),
("Quality/error_double_qual.fastq", "fastq", generic_dna),
]
for filename, format, alphabet in tests:
for (in_format, out_format) in converter_dict:
if in_format != format:
continue
if in_format in ["fastq", "fastq-sanger", "fastq-solexa", "fastq-illumina"] \
and out_format in ["fasta", "tab"] and filename.startswith("Quality/error_qual_"):
# TODO? These conversions don't check for bad characters in the quality,
# and in order to pass this strict test they should.
continue
def funct(fn, fmt1, fmt2, alpha):
f = lambda x: x.failure_check(fn, fmt1, fmt2, alpha)
f.__doc__ = "Convert %s from %s to %s" % (fn, fmt1, fmt2)
return f
setattr(ConvertTests, "test_%s_%s_to_%s"
% (filename.replace("/", "_").replace(".", "_"), in_format, out_format),
funct(filename, in_format, out_format, alphabet))
del funct
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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