def test4(self):
"""
Test 4.
"""
result = describe.describe(
'TAAGCACCAGGAGTCCATGAAGAAGATGGCTCCTGCCATGGAATCCCCTACTCTA',
'TAAGCACCAGGAGTCCATGAAGAAGCCATGTCCTGCCATGAATCCCCTACTCTA')
description = describe.alleleDescription(result)
assert description == '[26_29inv;30C>G;41del]'
def test2(self):
"""
Test 2.
"""
result = describe.describe(
'TAAGCACCAGGAGTCCATGAAGAAGATGGCTCCTGCCATGGAATCCCCTACTCTACTGTG',
'TAAGCACCAGGAGTCCATGAAGAAGCTGGATCCTCCCATGGAATCCCCTACTCTACTGTG')
description = describe.alleleDescription(result)
assert description == '[26A>C;30C>A;35G>C]'
def test1(self):
"""
Test 1.
"""
result = describe.describe(
'ATGATGATCAGATACAGTGTGATACAGGTAGTTAGACAA',
'ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA')
description = describe.alleleDescription(result)
assert description == '[5_6insTT;17del;26A>C;35dup]'
def description_extractor():
"""
The Variant Description Extractor (experimental service).
"""
reference_sequence = request.args.get('reference_sequence')
variant_sequence = request.args.get('variant_sequence')
if not (reference_sequence and variant_sequence):
return render_template('description-extractor.html')
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received Description Extract request from %s'
% request.remote_addr)
# Todo: Move this to the describe module.
if not util.is_dna(reference_sequence):
output.addMessage(__file__, 3, 'ENODNA',
'Reference sequence is not DNA.')
if not util.is_dna(variant_sequence):
output.addMessage(__file__, 3, 'ENODNA',
'Variant sequence is not DNA.')
raw_vars = describe.describe(reference_sequence, variant_sequence)
description = describe.alleleDescription(raw_vars)
errors, warnings, summary = output.Summary()
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO',
'Finished Description Extract request')
return render_template('description-extractor.html',
reference_sequence=reference_sequence,
variant_sequence=variant_sequence,
raw_vars=raw_vars,
description=description,
errors=errors,
summary=summary,
messages=messages)
def name_checker():
"""
Name checker.
"""
# For backwards compatibility with older LOVD versions, we support the
# `mutationName` argument. If present, we redirect and add `standalone=1`.
#
# Also for backwards compatibility, we support the `name` argument as an
# alias for `description`.
if 'name' in request.args:
return redirect(url_for('.name_checker',
description=request.args['name'],
standalone=request.args.get('standalone')),
code=301)
if 'mutationName' in request.args:
return redirect(url_for('.name_checker',
description=request.args['mutationName'],
standalone=1),
code=301)
description = request.args.get('description')
if not description:
return render_template('name-checker.html')
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO', 'Received variant %s from %s'
% (description, request.remote_addr))
stats.increment_counter('name-checker/website')
variantchecker.check_variant(description, output)
errors, warnings, summary = output.Summary()
parse_error = output.getOutput('parseError')
record_type = output.getIndexedOutput('recordType', 0, '')
reference = output.getIndexedOutput('reference', 0, '')
if reference:
if record_type == 'LRG':
reference_filename = reference + '.xml'
else :
reference_filename = reference + '.gb'
else:
reference_filename = None
genomic_dna = output.getIndexedOutput('molType', 0) != 'n'
genomic_description = output.getIndexedOutput('genomicDescription', 0, '')
# Create a link to the UCSC Genome Browser.
browser_link = None
raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
if raw_variants:
positions = [pos
for descr, (first, last) in raw_variants[2]
for pos in (first, last)]
bed_url = url_for('.bed', description=description, _external=True)
browser_link = ('http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&'
'position={chromosome}:{start}-{stop}&hgt.customText='
'{bed_file}'.format(chromosome=raw_variants[0],
start=min(positions) - 10,
stop=max(positions) + 10,
bed_file=urllib.quote(bed_url)))
# Experimental description extractor.
if (output.getIndexedOutput('original', 0) and
output.getIndexedOutput('mutated', 0)):
extracted = extractedProt = '(skipped)'
allele = describe.describe(output.getIndexedOutput('original', 0),
output.getIndexedOutput('mutated', 0))
if allele:
extracted = describe.alleleDescription(allele)
if output.getIndexedOutput('oldprotein', 0):
prot_allele = describe.describe(
output.getIndexedOutput('oldprotein', 0),
output.getIndexedOutput('newprotein', 0, default=''),
DNA=False)
if prot_allele:
extractedProt = describe.alleleDescription(prot_allele)
else:
extracted = extractedProt = ''
# Todo: Generate the fancy HTML views for the proteins here instead of in
# `mutalyzer.variantchecker`.
arguments = {
'description' : description,
'messages' : map(util.message_info, output.getMessages()),
'summary' : summary,
'parse_error' : parse_error,
'errors' : errors,
'genomicDescription' : genomic_description,
'chromDescription' : output.getIndexedOutput(
'genomicChromDescription', 0),
'genomicDNA' : genomic_dna,
'visualisation' : output.getOutput('visualisation'),
'descriptions' : output.getOutput('descriptions'),
'protDescriptions' : output.getOutput('protDescriptions'),
'oldProtein' : output.getOutput('oldProteinFancy'),
'altStart' : output.getIndexedOutput('altStart', 0),
'altProtein' : output.getOutput('altProteinFancy'),
'newProtein' : output.getOutput('newProteinFancy'),
'transcriptInfo' : output.getIndexedOutput('hasTranscriptInfo',
0, False),
'transcriptCoding' : output.getIndexedOutput('transcriptCoding', 0,
False),
'exonInfo' : output.getOutput('exonInfo'),
'cdsStart_g' : output.getIndexedOutput('cdsStart_g', 0),
'cdsStart_c' : output.getIndexedOutput('cdsStart_c', 0),
'cdsStop_g' : output.getIndexedOutput('cdsStop_g', 0),
'cdsStop_c' : output.getIndexedOutput('cdsStop_c', 0),
'restrictionSites' : output.getOutput('restrictionSites'),
'legends' : output.getOutput('legends'),
'reference_filename' : reference_filename, # Todo: Download link is not shown...
'browserLink' : browser_link,
'extractedDescription': extracted,
'extractedProtein' : extractedProt,
'standalone' : bool(request.args.get('standalone'))
}
output.addMessage(__file__, -1, 'INFO',
'Finished variant %s' % description)
return render_template('name-checker.html', **arguments)