def testParams(self):
"""
When a BLAST XML file has been read, its parameters must be present
in the reader instance. We only test a subset of the parameters.
"""
mockOpener = mockOpen(read_data=RECORD)
with patch.object(builtins, 'open', mockOpener):
reader = XMLRecordsReader('file.xml')
list(reader.records())
self.assertEqual('BLASTN', reader.params['application'])
self.assertEqual('virus-nt-20130719', reader.params['database'])
def testXMLInput(self):
"""
Test conversion of a chunk of BLAST XML. This is highly incomplete
in what it tests.
"""
mockOpener = mockOpen(read_data=RECORD)
with patch.object(builtins, 'open', mockOpener):
reader = XMLRecordsReader('file.xml')
record1, record2 = list(reader.records())
self.assertEqual(0, len(record1.alignments))
self.assertEqual(2, len(record2.alignments))
def testXMLInput(self):
"""
Test conversion of a chunk of BLAST XML. This is highly incomplete
in what it tests.
"""
mockOpener = mockOpen(read_data=RECORD)
with patch.object(builtins, 'open', mockOpener):
reader = XMLRecordsReader('file.xml')
record1, record2 = list(reader.records())
self.assertEqual(0, len(record1.alignments))
self.assertEqual(2, len(record2.alignments))
def testParams(self):
"""
When a BLAST XML file has been read, its parameters must be present
in the reader instance. We only test a subset of the parameters.
"""
mockOpener = mockOpen(read_data=RECORD)
with patch.object(builtins, 'open', mockOpener):
reader = XMLRecordsReader('file.xml')
list(reader.records())
self.assertEqual('BLASTN', reader.params['application'])
self.assertEqual('virus-nt-20130719', reader.params['database'])
parser = argparse.ArgumentParser(
description='Convert a BLAST XML file to JSON.',
epilog=('Give a BLAST XML file and convert it to JSON. Optionally '
'compress the JSON output.')
)
parser.add_argument(
'--json', metavar='JSON-output-file',
help=('the JSON filename to write the converted XML to. If omitted, '
'standard output will be used.'))
parser.add_argument(
'--xml', metavar='BLAST-XML-file', default=sys.stdin,
help=('the BLAST XML output file to convert. If omitted, standard '
'input will be read.'))
parser.add_argument(
'--bzip2', default=False, action='store_true',
help='If True, compress the JSON output using bzip2.')
args = parser.parse_args()
if args.bzip2:
fp = bz2file.BZ2File(args.json or sys.stdout, 'w')
else:
fp = open(args.json, 'w') if args.json else sys.stdout
reader = XMLRecordsReader(args.xml)
reader.saveAsJSON(fp)
fp.close()
'compress the JSON output.'))
parser.add_argument(
'--json',
metavar='JSON-output-file',
help=('the JSON filename to write the converted XML to. If omitted, '
'standard output will be used.'))
parser.add_argument(
'--xml',
metavar='BLAST-XML-file',
default=sys.stdin,
help=('the BLAST XML output file to convert. If omitted, standard '
'input will be read.'))
parser.add_argument('--bzip2',
default=False,
action='store_true',
help='If True, compress the JSON output using bzip2.')
args = parser.parse_args()
if args.bzip2:
fp = bz2file.BZ2File(args.json or sys.stdout, 'w')
else:
fp = open(args.json, 'w') if args.json else sys.stdout
reader = XMLRecordsReader(args.xml)
reader.saveAsJSON(fp)
fp.close()
#!/usr/bin/env python
if __name__ == '__main__':
from dark.blast.conversion import XMLRecordsReader
import sys
if len(sys.argv) == 2:
reader = XMLRecordsReader(sys.argv[1])
reader.saveAsJSON(sys.stdout)
elif len(sys.argv) == 3:
reader = XMLRecordsReader(sys.argv[1])
with open(sys.argv[2], 'w') as fp:
reader.saveAsJSON(fp)
else:
print >>sys.stderr, 'Usage: %s infile.xml [outfile.json]' % sys.argv[0]
sys.exit(1)
