本文整理汇总了Python中dipper.utils.GraphUtils.GraphUtils.addType方法的典型用法代码示例。如果您正苦于以下问题：Python GraphUtils.addType方法的具体用法？Python GraphUtils.addType怎么用？Python GraphUtils.addType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dipper.utils.GraphUtils.GraphUtils的用法示例。
在下文中一共展示了GraphUtils.addType方法的5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: _process_data
# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addType [as 别名]
#.........这里部分代码省略.........
for o in omim_map:
# gene_id = 'OMIM:' + o # TODO unused
vslc_id = \
'_' + '-'.join(
[o + '.' + a for a in omim_map.get(o)])
if self.nobnodes:
vslc_id = ':'+vslc_id
vslc_label = vl
# we don't really know the zygosity of
# the alleles at all.
# so the vslcs are just a pot of them
gu.addIndividualToGraph(
g, vslc_id, vslc_label,
geno.genoparts[
'variant_single_locus_complement'])
for v in omim_map.get(o):
# this is actually a sequence alt
allele1_id = 'OMIM:'+o+'.'+v
geno.addSequenceAlteration(allele1_id, None)
# assume that the sa -> var_loc -> gene
# is taken care of in OMIM
geno.addPartsToVSLC(
vslc_id, allele1_id, None,
geno.zygosity['indeterminate'],
geno.object_properties[
'has_alternate_part'])
if vslc_id != gvc_id:
geno.addVSLCtoParent(vslc_id, gvc_id)
if affected == 'unaffected':
# let's just say that this person is wildtype
gu.addType(g, patient_id, geno.genoparts['wildtype'])
elif genotype_id is None:
# make an anonymous genotype id
genotype_id = '_geno'+catalog_id.strip()
if self.nobnodes:
genotype_id = ':'+genotype_id
# add the gvc
if gvc_id is not None:
gu.addIndividualToGraph(
g, gvc_id, gvc_label,
geno.genoparts['genomic_variation_complement'])
# add the gvc to the genotype
if genotype_id is not None:
if affected == 'unaffected':
rel = \
geno.object_properties[
'has_reference_part']
else:
rel = \
geno.object_properties[
'has_alternate_part']
geno.addParts(gvc_id, genotype_id, rel)
if karyotype_id is not None \
and self._is_normal_karyotype(karyotype):
if gvc_label is not None and gvc_label != '':
genotype_label = \
'; '.join((gvc_label, karyotype))
else:
genotype_label = karyotype
if genotype_id is None:
genotype_id = karyotype_id示例2: Feature
# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addType [as 别名]
#.........这里部分代码省略.........
# if we know only one of the coordinates,
# then we'll add an "unknown" other.
st = sp = 'UN'
strand = None
if self.start is not None and \
self.start['coordinate'] is not None:
st = str(self.start['coordinate'])
strand = self._getStrandStringFromPositionTypes(
self.start['type'])
if self.stop is not None and\
self.stop['coordinate'] is not None:
sp = str(self.stop['coordinate'])
if strand is not None:
strand = self._getStrandStringFromPositionTypes(
self.stop['type'])
# assume that the strand is the same for both start and stop.
# this will need to be fixed in the future
region_items = [regionchr, st, sp]
if strand is not None:
region_items += [strand]
region_id = '-'.join(region_items)
rid = region_id
rid = re.sub(r'\w+\:', '', rid, 1) # replace the id prefix
rid = '_'+rid+"-Region"
region_id = rid
if self.nobnodes:
region_id = ':'+region_id
self.gu.addTriple(graph, self.id, self.properties['location'],
region_id)
self.gu.addIndividualToGraph(
graph, region_id, None, 'faldo:Region')
else:
region_id = self.id
self.gu.addType(graph, region_id, 'faldo:Region')
# add the start/end positions to the region
beginp = endp = None
if self.start is not None:
beginp = self._makePositionId(self.start['reference'],
self.start['coordinate'],
self.start['type'])
self.addPositionToGraph(graph,
self.start['reference'],
self.start['coordinate'],
self.start['type'])
if self.stop is not None:
endp = self._makePositionId(self.stop['reference'],
self.stop['coordinate'],
self.stop['type'])
self.addPositionToGraph(graph,
self.stop['reference'],
self.stop['coordinate'],
self.stop['type'])
self.addRegionPositionToGraph(graph, region_id, beginp, endp)
# {coordinate : integer, reference : reference_id, types = []}
return
def _getStrandStringFromPositionTypes(self, tylist):
strand = None
if self.types['plus_strand'] in tylist:
strand = 'plus'
elif self.types['minus_strand'] in tylist:示例3: _process_data
# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addType [as 别名]
#.........这里部分代码省略.........
elif zygosity == 'homozygote':
allele2_label = allele1_label
allele2_id = allele1_id
allele2_rel = geno.object_properties['has_alternate_part']
elif zygosity == 'hemizygote':
allele2_label = re.sub(r'<.*', '<0>', allele1_label)
allele2_id = None
elif zygosity == 'not_applicable':
allele2_label = re.sub(r'<.*', '<?>', allele1_label)
allele2_id = None
else:
logger.warning("found unknown zygosity %s", zygosity)
break
vslc_name = '/'.join((allele1_label, allele2_label))
# Add the VSLC
vslc_id = '_' + '-'.join((marker_accession_id,
allele_accession_id, zygosity))
vslc_id = re.sub(r':', '', vslc_id)
if self.nobnodes:
vslc_id = ':'+vslc_id
gu.addIndividualToGraph(
g, vslc_id, vslc_name,
geno.genoparts['variant_single_locus_complement'])
geno.addPartsToVSLC(
vslc_id, allele1_id, allele2_id, zygosity_id,
geno.object_properties['has_alternate_part'],
allele2_rel)
# add vslc to genotype
geno.addVSLCtoParent(vslc_id, genotype_id)
# note that the vslc is also the gvc
gu.addType(
g, vslc_id,
Genotype.genoparts['genomic_variation_complement'])
# Add the genomic background
# create the genomic background id and name
if strain_accession_id != '':
genomic_background_id = strain_accession_id
else:
genomic_background_id = None
genotype_name = vslc_name
if genomic_background_id is not None:
geno.addGenotype(
genomic_background_id, strain_name,
geno.genoparts['genomic_background'])
# make a phenotyping-center-specific strain
# to use as the background
pheno_center_strain_label = \
strain_name + '/' + phenotyping_center
pheno_center_strain_id = \
'-'.join((re.sub(r':', '', genomic_background_id),
re.sub(r'\s', '_', phenotyping_center)))
if not re.match(r'^_', pheno_center_strain_id):
pheno_center_strain_id = '_'+pheno_center_strain_id
if self.nobnodes:
pheno_center_strain_id = ':'+pheno_center_strain_id
geno.addGenotype(pheno_center_strain_id,
pheno_center_strain_label,
geno.genoparts['genomic_background'])
geno.addSequenceDerivesFrom(pheno_center_strain_id,
genomic_background_id)示例4: Genotype
# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addType [as 别名]
#.........这里部分代码省略.........
This will add a has_part (or subproperty) relationship between a parent_id and the supplied part.
By default the relationship will be BFO:has_part, but any relationship could be given here.
:param part_id:
:param parent_id:
:param part_relationship:
:return:
"""
if part_relationship is None:
part_relationship = self.properties['has_part']
self.gu.addTriple(self.graph, parent_id, part_relationship, part_id)
return
def addSequenceAlteration(self, sa_id, sa_label, sa_type=None, sa_description=None):
if sa_type is None:
sa_type = self.genoparts['sequence_alteration']
self.gu.addIndividualToGraph(self.graph, sa_id, sa_label, sa_type, sa_description)
return
def addSequenceAlterationToVariantLocus(self, sa_id, vl_id):
self.addParts(sa_id, vl_id, self.properties['has_alternate_part'])
return
def addGenomicBackground(self, background_id, background_label, background_type=None, background_description=None):
if background_type is None:
background_type = self.genoparts['genomic_background']
self.gu.addIndividualToGraph(self.graph, background_id, background_label, background_type, background_description)
return
def addGenomicBackgroundToGenotype(self, background_id, genotype_id):
self.gu.addType(self.graph, background_id, self.genoparts['genomic_background'])
self.addParts(background_id, genotype_id, self.object_properties['has_reference_part'])
return
def addTaxon(self, taxon_id, genopart_id):
"""
The supplied geno part will have the specified taxon added with RO:in_taxon relation.
Generally the taxon is associated with a genomic_background, but could be added to any
genotype part (including a gene, regulatory element, or sequence alteration).
:param taxon_id:
:param genopart_id:
:return:
"""
in_taxon = self.gu.getNode(self.properties['in_taxon'])
s = self.gu.getNode(genopart_id)
self.graph.add((s, in_taxon, self.gu.getNode(taxon_id)))
return
def addGeneTargetingReagentToGenotype(self, reagent_id, genotype_id):
# for example, add a morphant reagent thingy to the genotype, assuming it's a extrinsic_genotype
p = self.object_properties['has_expression-variant_part']
self.gu.addTriple(self.graph, genotype_id, p, reagent_id)
return
def addGeneTargetingReagent(self, reagent_id, reagent_label, reagent_type, gene_id, description=None):
"""
Here, a gene-targeting reagent is added. The actual targets of this reagent should be added separately.
:param reagent_id:
:param reagent_label:
:param reagent_type:示例5: process_catalog
# 需要导入模块: from dipper.utils.GraphUtils import GraphUtils [as 别名]
# 或者: from dipper.utils.GraphUtils.GraphUtils import addType [as 别名]
#.........这里部分代码省略.........
pubmed_id = 'PMID:'+pubmed_num
r = Reference(
pubmed_id, Reference.ref_types['journal_article'])
r.addRefToGraph(g)
# create the chromosome
chrom_id = makeChromID(chrom_num, genome_version, 'CHR')
# add the feature to the graph
snp_description = None
if risk_allele_frequency != '' and \
risk_allele_frequency != 'NR':
snp_description = \
str(risk_allele_frequency) + \
' [risk allele frequency]'
f = Feature(
rs_id, strongest_snp_risk_allele.strip(),
Feature.types[r'SNP'], snp_description)
if chrom_num != '' and chrom_pos != '':
f.addFeatureStartLocation(chrom_pos, chrom_id)
f.addFeatureEndLocation(chrom_pos, chrom_id)
f.addFeatureToGraph(g)
f.addTaxonToFeature(g, tax_id)
# TODO consider adding allele frequency as property;
# but would need background info to do that
# also want to add other descriptive info about
# the variant from the context
for c in re.split(r';', context):
cid = self._map_variant_type(c.strip())
if cid is not None:
gu.addType(g, rs_id, cid)
# add deprecation information
if merged == 1 and str(snp_id_current.strip()) != '':
# get the current rs_id
current_rs_id = 'dbSNP:'
if not re.match(r'rs', snp_id_current):
current_rs_id += 'rs'
if loc is not None:
loc_to_id_hash[loc].append(current_rs_id)
current_rs_id += str(snp_id_current)
gu.addDeprecatedIndividual(g, rs_id, current_rs_id)
# TODO check on this
# should we add the annotations to the current
# or orig?
gu.makeLeader(g, current_rs_id)
else:
gu.makeLeader(g, rs_id)
# add the feature as a sequence alteration
# affecting various genes
# note that intronic variations don't necessarily list
# the genes such as for rs10448080 FIXME
if snp_gene_nums != '':
for s in re.split(r',', snp_gene_nums):
s = s.strip()
# still have to test for this,
# because sometimes there's a leading comma
if s != '':
gene_id = 'NCBIGene:'+s
geno.addAlleleOfGene(rs_id, gene_id)
# add the up and downstream genes if they are available