def __init__(self, args, out=sys.stdout):
if not os.path.isfile(args.file):
raise IOError("Not a file: %s" % args.file)
self.file_name = args.file
self.silent = args.xunit_out is not None
base, ext = os.path.splitext(args.file)
if ext == ".gz":
ext_ = ext
base, ext = os.path.splitext(base)
if args.quiet:
out = StringIO()
self.t_start = time.time()
if (args.file_type == "Fasta" or
(args.file_type is None and ext in [".fasta", ".fa", ".fna"])):
self.errors, self.metrics = fasta.validate_fasta(
file_name=args.file,
strict=args.strict,
validate_index=args.validate_index,
quick=args.quick)
elif (args.file_type == "BAM" or
(args.file_type is None and ext in [".bam"])):
self.errors, self.metrics = bam.validate_bam(
file_name=args.file,
reference=args.reference,
aligned=args.aligned,
contents=args.contents,
quick=args.quick,
max_errors=args.max_errors,
max_records=args.max_records,
validate_index=args.validate_index,
permissive_headers=args.permissive_headers)
elif (args.file_type in ["AlignmentSet", "ReferenceSet", "SubreadSet"] or
ext in [".xml"]):
self.errors, self.metrics = dataset.validate_dataset(
file_name=args.file,
dataset_type=args.file_type,
reference=args.reference,
quick=args.quick,
max_errors=args.max_errors,
max_records=args.max_records,
aligned=args.aligned,
contents=args.contents,
validate_index=args.validate_index,
strict=args.strict,
permissive_headers=args.permissive_headers)
else:
raise NotImplementedError("No validator found for '%s'." % ext)
self.t_end = time.time()
if not args.quiet:
utils.show_validation_errors(self.errors, out=out,
use_termcolor=args.use_termcolor)
if args.xunit_out is not None:
doc = self.to_xml()
with open(args.xunit_out, "w") as xml_out:
xml_out.write(doc.toprettyxml(indent=" "))
def error_string(self):
err_out = StringIO()
utils.show_validation_errors(self.errors, out=err_out)
return err_out.getvalue()
