def test_parse_qa_cai(self):
qatest_text = '''
ID cai-ex
AP cai
CL AB009602
IN
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI ab009602.cai
FP /0\.188/
//
'''
acd_text = '''
application: cai [
documentation: "Calculate codon adaptation index"
groups: "Nucleic:Codon usage"
relations: "EDAM_topic:0107 Codon usage analysis"
relations: "EDAM_operation:0286 Codon usage analysis"
]
section: input [
information: "Input section"
type: "page"
]
seqall: seqall [
parameter: "Y"
type: "DNA"
relations: "EDAM_data:2887 Sequence record (nucleic acid)"
]
codon: cfile [
standard: "Y"
default: "Eyeast_cai.cut"
relations: "EDAM_data:1597 Codon usage table"
]
endsection: input
section: output [
information: "Output section"
type: "page"
]
outfile: outfile [
parameter: "Y"
knowntype: "cai output"
relations: "EDAM_data:2865 Codon usage bias"
]
endsection: output
'''
acd_def = parse_acd(acd_text)
qa_item = parse_qa(qatest_text)
qa_item.parse_command_lines(acd_def)
def testebeye_emblrel_con_multifield(self):
res = parse_qa('''ID ebeye-emblrel_con-multifield
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP textget
CL "tebeye:emblrelease_con-{keywords:Aspergillus fumigatus & description:BAC}"
CL stdout -auto
FI stdout
FP /BX649216/
FP /Aspergillus fumigatus BAC pilot project supercontig/
''')
def test_wsdbfetch_uniprot(self):
res = parse_qa('''ID wsdbfetch-uniprot
TI 120
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP seqret
CL fasta::twsdbfetch:uniprotkb:P06213 stdout -auto
FI stdout
FC = 25
FP 1 /^>INSR_HUMAN/
FP 1 /PS$/''')
def test_parse_qacc_not_srswww(self):
res = parse_qa('''
ID qacc-not-srswww
AP seqret
CL "srs:uniprot-acc{p00274 ! p0aa28}" stdout -auto
FI stdout
FP 5 /^>/
FP 0 /^>THIO_SALTY/
FP 1 /^>THIO_SHIFL/
FP 1 /^>THIO_ECOLI/
//''')
def test_wsdbfetch_noentry(self):
res = parse_qa('''ID wsdbfetch-noentry
RQ soapws
TI 120
CC requires (axis2C) SOAP webservices library enabled
AP seqret
CL fasta::twsdbfetch:uniprotkb:abcdefg stdout -auto
ER 1
FI stderr
FC = 2
FP 1 /Unable to read sequence/
''')
def test_parse_wsdbfetch(self):
res = parse_qa('''
ID wsdbfetch-uniprotxml
RQ soapws
CC requires (axis2C) SOAP webservices library enabled
AP xmlget
CL uniprotxml::twsdbfetch:uniprotkb:p12345 stdout -auto
FI stdout
FC > 160
FP 1 /<uniprot xmlns="http://uniprot.org/uniprot"/
FP 1 /<accession>P12345</accession>/
''')
def test_parse_qa_simple(self):
res = parse_qa('''
ID test-1
AP test
CL -u test -v test2
CL -w -x
IN toto.txt
IN tutu.dat
''')
self.assertEqual(res.id, 'test-1')
self.assertEqual(res.application_ref.name, 'test')
self.assertEqual(res.command_lines[0].command_line, '-u test -v test2')
self.assertEqual(res.command_lines[1].command_line, '-w -x')
self.assertEqual(res.input_lines[0].input_line, 'toto.txt')
self.assertEqual(res.input_lines[1].input_line, 'tutu.dat')
def test_parse_command_line(self, acd_path, qa_string, qa_name, app_name):
try:
if app_name in ['acdc', 'acdpretty', 'acdtable', 'acdvalid']:
raise unittest.SkipTest('ACD file {0} is not well-defined, skipping test on {1}'\
.format(acd_path, qa_name))
if not (os.path.isfile(acd_path)):
raise unittest.SkipTest('ACD file {0} does not exist, skipping test on {1}'\
.format(acd_path, qa_name))
acd_string = open(acd_path, 'r').read()
acd_object = parse_acd(acd_string)
qa_test = parse_qa(qa_string)
job_order = qa_test.parse_command_lines(acd_object)
except Exception as exc:
print "Failure parsing QA test {0} for ACD {1}".format(
qa_name, acd_path)
raise exc
def test_parse_backtranseq(self):
res = parse_qa('''
ID backtranseq-ex
UC Note that this is a human protein and so the default human codon frequency file is used ie. is not specified
AP backtranseq
IN tsw:opsd_human
IN
FI opsd_human.fasta
FP /^>OPSD_HUMAN/
FP /CGCCACCGGCGTGGTG\n/
FZ = 1101
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
''')
def test_parse_abiview(self):
res = parse_qa('''
ID abiview-ex
AP abiview
CL -graph cps
IN ../../data/abiview.abi
IN
FI stderr
FC = 2
FP 0 /Warning: /
FP 0 /Error: /
FP 0 /Died: /
FI stdout
FZ = 19
FP /^Created abiview\.ps\n/
FI abiview.fasta
FP /^>abiview\n/
FP /^GNNNNNNNNNG/
FZ = 861
FI abiview.ps
FP /^%%Title: PLplot Graph\n/
''')