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ex-278 (dkriti/cgates) modified varscan error messages to check hc and
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vcf file matching
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dkriti committed Jun 16, 2015
1 parent 693e667 commit 049dd04
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Showing 2 changed files with 78 additions and 38 deletions.
77 changes: 43 additions & 34 deletions jacquard/variant_caller_transforms/varscan.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -238,28 +238,28 @@ def _raise_invalid_filter_exception(invalid_filter_files):
omitted_files)

@staticmethod
def _validate_file_pairing(unpaired_hc_files, unpaired_vcf_files):
if unpaired_hc_files:
for unpaired_hc_file in unpaired_hc_files[:5]:
msg = ("The VarScan high-confidence file [{}] has no matching "
"VCF file.")
logger.error(msg, unpaired_hc_file.file_name)

msg = ("[{}] VarScan high-confidence file(s) did not have a "
"matching VCF file. See log for more details. Review inputs "
"and try again.")
raise utils.JQException(msg, len(unpaired_hc_files))

if unpaired_vcf_files:
for unpaired_vcf_file in unpaired_vcf_files[:5]:
msg = ("The VarScan VCF file [{}] has no matching "
"high-confidence file.")
logger.error(msg, unpaired_vcf_file.file_name)

msg = ("[{}] VarScan VCF file(s) did not have a matching "
"high-confidence file. See log for more details. Review "
"inputs and try again.")
raise utils.JQException(msg, len(unpaired_vcf_files))
def _raise_error_for_unpaired_files(unpaired_files, found_orphan, missing_counterpart):
_SINGLETON_ERROR_MSG = ("The VarScan {0} [{{}}] has no "
"matching {1}.").format(found_orphan,
missing_counterpart)
_MULTIPLE_ERROR_MSG = ("[{{1}}] VarScan {0}s [{{}}] did "
"not have a matching {1}. See log for more "
"details. Review inputs and try "
"again.").format(found_orphan,
missing_counterpart)
total_unpaired_files = len(unpaired_files)
msg = None
if total_unpaired_files == 1:
msg = _SINGLETON_ERROR_MSG.format(unpaired_files[0])
else:
cutoff = 5
unpaired_hc_files_list = ", ".join(unpaired_files[0:min(cutoff, total_unpaired_files)])
if total_unpaired_files > cutoff:
omitted = total_unpaired_files - cutoff
unpaired_hc_files_list += ", ...({} file(s) omitted)".format(omitted)
msg = _MULTIPLE_ERROR_MSG.format(total_unpaired_files,
unpaired_hc_files_list)
raise utils.UsageError(msg)

def _find_varscan_files(self, file_readers):
unclaimed_set = set()
Expand Down Expand Up @@ -354,19 +354,28 @@ def _pair_files(self, prefixes, filter_files):

return self._dictionaries_to_tuples(vcf_dict, filter_dict)

def _validate_file_pairs(self, tuples):
def _validate_vcf_hc_pairs(self, vcf_hc_pairs):
hc_files = [i[1] for i in vcf_hc_pairs if i[1]]
if not hc_files:
return

unpaired_vcf_files = []
unpaired_hc_files = []

hc_values = set([i[1] for i in tuples])
if len(hc_values) != 1:
for vcf_file_reader, hc_file_reader in tuples:
if vcf_file_reader and not hc_file_reader:
unpaired_vcf_files.append(vcf_file_reader)
if hc_file_reader and not vcf_file_reader:
unpaired_hc_files.append(hc_file_reader)
for vcf_file_reader, hc_file_reader in vcf_hc_pairs:
if vcf_file_reader and not hc_file_reader:
unpaired_vcf_files.append(vcf_file_reader.file_name)
if hc_file_reader and not vcf_file_reader:
unpaired_hc_files.append(hc_file_reader.file_name)

self._validate_file_pairing(unpaired_hc_files, unpaired_vcf_files)
if unpaired_hc_files:
self._raise_error_for_unpaired_files(unpaired_hc_files,
"high-confidence file",
"VCF file")
elif unpaired_vcf_files:
self._raise_error_for_unpaired_files(unpaired_vcf_files,
"VCF file",
"high-confidence file")

@staticmethod
def _create_vcf_readers(pair_tuples):
Expand Down Expand Up @@ -402,9 +411,9 @@ def claim(self, file_readers):

prefix_by_patients = self._split_prefix_by_patient(prefix_to_readers)
self._validate_vcf_readers(prefix_by_patients)
vcf_filter_tuples = self._pair_files(prefix_to_readers, filter_files)
self._validate_file_pairs(vcf_filter_tuples)
vcf_readers = self._create_vcf_readers(vcf_filter_tuples)
vcf_hc_pairs = self._pair_files(prefix_to_readers, filter_files)
self._validate_vcf_hc_pairs(vcf_hc_pairs)
vcf_readers = self._create_vcf_readers(vcf_hc_pairs)

return list(unclaimed_set), vcf_readers

Expand Down
39 changes: 35 additions & 4 deletions test/variant_caller_transforms/varscan_test.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,11 @@ def tearDown(self):
super(VarscanTestCase, self).tearDown()

@staticmethod
def append_hc_files(readers, file1="snp.somatic.hc.fpfilter.pass", file2="indel.somatic.hc.fpfilter.pass", content1=None, content2=None):
def append_hc_files(readers,
file1="snp.somatic.hc.fpfilter.pass",
file2="indel.somatic.hc.fpfilter.pass",
content1=None,
content2=None):
if not content1:
content1 = []
if not content2:
Expand All @@ -189,6 +193,33 @@ def append_hc_files(readers, file1="snp.somatic.hc.fpfilter.pass", file2="indel.
def _get_tag_class_names(vcf_reader):
return [tag.__class__.__name__ for tag in vcf_reader.tags]

def test_validate_vcf_hc_pairs(self):
self.caller._validate_vcf_hc_pairs([(MockFileReader("A.vcf"), MockFileReader("A.hc")),
(MockFileReader("B.vcf"), MockFileReader("B.hc"))])
self.ok()

def test_validate_vcf_hc_pairs_okIfNoHcFiles(self):
self.caller._validate_vcf_hc_pairs([(MockFileReader("A.vcf"), None),
(MockFileReader("B.vcf"), None)])
self.ok()

def test_validate_vcf_hc_pairs_raisesIfMissingHcFiles(self):
vcf_hc_pairs = [(MockFileReader("A.vcf"), MockFileReader("A.hc")),
(MockFileReader("B.vcf"), None)]
self.assertRaisesRegexp(utils.UsageError,
"The VarScan VCF file \[B.vcf\] has no matching high-confidence file.",
self.caller._validate_vcf_hc_pairs,
vcf_hc_pairs)

def test_validate_vcf_hc_pairs_raisesIfNoMissingVcfFiles(self):
vcf_hc_pairs = [(MockFileReader("A.vcf"), MockFileReader("A.hc")),
(None, MockFileReader("B.hc"))]
self.assertRaisesRegexp(utils.UsageError,
"The VarScan high-confidence file \[B.hc\] has no matching VCF file.",
self.caller._validate_vcf_hc_pairs,
vcf_hc_pairs)


def test_get_hc_file_pattern(self):
args = Namespace(varscan_hc_filter_file_regex="foo.*")
compiled_regex = varscan.Varscan._get_hc_file_pattern(args)
Expand Down Expand Up @@ -373,7 +404,7 @@ def test_claim_hcHasNoMatchingVCF(self):

caller = varscan.Varscan()
self.assertRaisesRegexp(utils.JQException,
r"\[1\] VarScan high-confidence file\(s\) did not have a matching VCF file. See log for more details. Review inputs and try again.",
r"The VarScan high-confidence file \[patientB.snp.Somatic.hc.fpfilter.pass\] has no matching VCF file.",
caller.claim,
file_readers)

Expand All @@ -388,8 +419,8 @@ def test_claim_VCFHasNoMatchingHc(self):
file_readers = [reader1, reader2, reader3]

caller = varscan.Varscan()
self.assertRaisesRegexp(utils.JQException,
r"\[1\] VarScan VCF file\(s\) did not have a matching high-confidence file. See log for more details. Review inputs and try again.",
self.assertRaisesRegexp(utils.UsageError,
r"The VarScan VCF file \[patientA.vcf\] has no matching high-confidence file.",
caller.claim,
file_readers)

Expand Down

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