本文整理汇总了Python中mutalyzer.output.Output.getIndexedOutput方法的典型用法代码示例。如果您正苦于以下问题：Python Output.getIndexedOutput方法的具体用法？Python Output.getIndexedOutput怎么用？Python Output.getIndexedOutput使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类mutalyzer.output.Output的用法示例。
在下文中一共展示了Output.getIndexedOutput方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: bed
# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getIndexedOutput [as 别名]
def bed():
"""
Create a BED track for the given variant, listing the positions of its raw
variants, e.g., for use in the UCSC Genome Browser.
This basically just runs the variant checker and extracts the raw variants
with positions.
"""
# Backwards compatibility.
if 'name' in request.args:
return redirect(url_for('.bed',
description=request.args['name']),
code=301)
description = request.args.get('description')
if not description:
abort(404)
output = Output(__file__)
variantchecker.check_variant(description, output)
raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
if not raw_variants:
abort(404)
# Todo: Hard-coded hg19.
fields = {
'name' : 'Mutalyzer',
'description': 'Mutalyzer track for ' + description,
'visibility' : 'pack',
'db' : 'hg19',
'url' : url_for('.name_checker',
description=description,
_external=True),
'color': '255,0,0'}
bed = ' '.join(['track'] +
['%s="%s"' % field for field in fields.items()]) + '\n'
for descr, positions in raw_variants[2]:
bed += '\t'.join([raw_variants[0],
unicode(min(positions) - 1),
unicode(max(positions)),
descr,
'0',
raw_variants[1]]) + '\n'
response = make_response(bed)
response.headers['Content-Type'] = 'text/plain; charset=utf-8'
return response示例2: name_checker
# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getIndexedOutput [as 别名]
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),
#.........这里部分代码省略.........