def back_translator():
"""
Back translator.
"""
output = Output(__file__)
output.addMessage(
__file__, -1, 'INFO',
'Received Back Translate request from {}'.format(request.remote_addr))
stats.increment_counter('back-translator/website')
description = request.args.get('description')
variants = []
if description:
variants = backtranslator.backtranslate(output, description)
errors, warnings, summary = output.Summary()
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO', 'Finished Back Translate request')
return render_template('back-translator.html',
errors=errors,
summary=summary,
description=description or '',
messages=messages,
variants=variants)
def snp_converter():
"""
SNP converter.
Convert a dbSNP rs number to HGVS description(s) of the SNP specified on
the reference sequence(s) used by dbSNP.
"""
# Backwards compatibility.
if 'rsId' in request.args:
return redirect(url_for('.snp_converter', rs_id=request.args['rsId']),
code=301)
rs_id = request.args.get('rs_id')
if not rs_id:
return render_template('snp-converter.html')
output = Output(__file__)
output.addMessage(
__file__, -1, 'INFO', 'Received request snpConvert(%s) from %s' %
(rs_id, request.remote_addr))
stats.increment_counter('snp-converter/website')
descriptions = ncbi.rsid_to_descriptions(rs_id, output)
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO',
'Finished request snpConvert(%s)' % rs_id)
return render_template('snp-converter.html',
rs_id=rs_id,
descriptions=descriptions,
messages=messages,
summary=output.Summary()[2])
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 description_extractor_submit():
"""
The Variant Description Extractor (experimental service).
There multiple ways for the user to provide two sequences, corresponding to
the values for the `reference_method` and `sample_method` fields, each
requiring some additional fields to be defined:
`raw_method`
The reference and sample sequences are pasted into the form fields.
- `reference_sequence`: The reference sequence.
- `sample_sequence`: The sample sequence.
`file_method`
The reference and sample sequences are uploaded.
- `reference_file`: The reference file.
- `sample_file`: The sample file.
`refseq_method`
The reference and sample sequences are given by RefSeq accession numbers.
- `reference_accession_number`: RefSeq accession number for the reference
sequence.
- `sample_accession_number`: RefSeq accession number for the sample
sequence.
"""
output = Output(__file__)
output.addMessage(__file__, -1, 'INFO',
'Received Description Extract request from %s'
% request.remote_addr)
stats.increment_counter('description-extractor/website')
r = s = ''
reference_method = request.form.get('reference_method')
sample_method = request.form.get('sample_method')
reference_sequence = request.form.get('reference_sequence')
sample_sequence = request.form.get('sample_sequence')
reference_file = request.files.get('reference_file')
sample_file = request.files.get('sample_file')
reference_filename = ''
sample_filename = ''
reference_accession_number = request.form.get('reference_accession_number')
sample_accession_number = request.form.get('sample_accession_number')
if reference_method == 'refseq_method':
if reference_accession_number:
retriever = Retriever.GenBankRetriever(output)
genbank_record = retriever.loadrecord(reference_accession_number)
if genbank_record:
r = unicode(genbank_record.seq)
else:
output.addMessage(__file__, 3, 'EEMPTYFIELD',
'Reference accession number input fields is empty.')
elif reference_method == 'file_method':
if reference_file:
reference_filename = reference_file.filename
r = util.read_dna(reference_file)
else:
output.addMessage(__file__, 3, 'EEMPTYFIELD',
'No reference file provided.')
else: # raw_method
if reference_sequence:
r = util.read_dna(StringIO.StringIO(reference_sequence))
else:
output.addMessage(__file__, 3, 'EEMPTYFIELD',
'Reference sequence number input fields is empty.')
if sample_method == 'refseq_method':
if sample_accession_number:
retriever = Retriever.GenBankRetriever(output)
genbank_record = retriever.loadrecord(sample_accession_number)
if genbank_record:
s = unicode(genbank_record.seq)
else:
output.addMessage(__file__, 3, 'EEMPTYFIELD',
'Sample accession number input fields is empty.')
elif sample_method == 'file_method':
if sample_file:
sample_filename = sample_file.filename
s = util.read_dna(sample_file)
else:
output.addMessage(__file__, 3, 'EEMPTYFIELD',
'No sample file provided.')
else: # raw_method
if sample_sequence:
s = util.read_dna(StringIO.StringIO(sample_sequence))
else:
output.addMessage(__file__, 3, 'EEMPTYFIELD',
'Sample sequence number input fields is empty.')
# Todo: Move this to the describe module.
if not r or not util.is_dna(r):
output.addMessage(__file__, 3, 'ENODNA',
'Reference sequence is not DNA.')
if not s or not util.is_dna(s):
output.addMessage(__file__, 3, 'ENODNA',
'Sample sequence is not DNA.')
raw_vars = None
if r and s:
if (len(r) > settings.EXTRACTOR_MAX_INPUT_LENGTH or
len(s) > settings.EXTRACTOR_MAX_INPUT_LENGTH):
output.addMessage(__file__, 3, 'EMAXSIZE',
'Input sequences are restricted to {:,} bp.'
.format(settings.EXTRACTOR_MAX_INPUT_LENGTH))
else:
raw_vars = extractor.describe_dna(r, s)
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',
extractor_max_input_length=settings.EXTRACTOR_MAX_INPUT_LENGTH,
reference_sequence=reference_sequence or '',
sample_sequence=sample_sequence or '',
reference_accession_number=reference_accession_number or '',
sample_accession_number=sample_accession_number or '',
reference_filename=reference_filename or '',
sample_filename=sample_filename or '',
raw_vars=raw_vars, errors=errors, summary=summary, messages=messages,
reference_method=reference_method, sample_method=sample_method)
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)):
allele = extractor.describe_dna(output.getIndexedOutput('original', 0),
output.getIndexedOutput('mutated', 0))
extracted = '(skipped)'
if allele:
extracted = unicode(allele)
else:
extracted = ''
# 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,
'standalone' : bool(request.args.get('standalone'))
}
output.addMessage(__file__, -1, 'INFO',
'Finished variant %s' % description)
return render_template('name-checker.html', **arguments)
