本文整理汇总了Python中dipper.models.Genotype.Genotype.addGenomicBackground方法的典型用法代码示例。如果您正苦于以下问题：Python Genotype.addGenomicBackground方法的具体用法？Python Genotype.addGenomicBackground怎么用？Python Genotype.addGenomicBackground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.models.Genotype.Genotype的用法示例。
在下文中一共展示了Genotype.addGenomicBackground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: _process_phenotype_data
# 需要导入模块: from dipper.models.Genotype import Genotype [as 别名]
# 或者: from dipper.models.Genotype.Genotype import addGenomicBackground [as 别名]
#.........这里部分代码省略.........
geno.genoparts['variant_locus'])
vl_set.add(vl_id)
if len(variants) == 1 and len(genes) == 1:
for gene in genes:
geno.addAlleleOfGene(vl_id, gene)
else:
geno.addAllele(vl_id, vl_symbol)
else: # len(vars) == 0
# it's just anonymous variants in some gene
for gene in genes:
vl_id = '_'+gene+'-VL'
vl_id = re.sub(r':', '', vl_id)
if self.nobnodes:
vl_id = ':'+vl_id
vl_symbol = self.id_label_hash[gene]+'<?>'
self.id_label_hash[vl_id] = vl_symbol
geno.addAllele(vl_id, vl_symbol,
geno.genoparts['variant_locus'])
geno.addGene(gene, self.id_label_hash[gene])
geno.addAlleleOfGene(vl_id, gene)
vl_set.add(vl_id)
# make the vslcs
vl_list = sorted(vl_set)
vslc_list = []
for vl in vl_list:
# for unknown zygosity
vslc_id = '_'+re.sub(r'^_', '', vl)+'U'
vslc_id = re.sub(r':', '', vslc_id)
if self.nobnodes:
vslc_id = ':' + vslc_id
vslc_label = self.id_label_hash[vl] + '/?'
self.id_label_hash[vslc_id] = vslc_label
vslc_list.append(vslc_id)
geno.addPartsToVSLC(
vslc_id, vl, None, geno.zygosity['indeterminate'],
geno.object_properties['has_alternate_part'], None)
gu.addIndividualToGraph(
g, vslc_id, vslc_label,
geno.genoparts['variant_single_locus_complement'])
if len(vslc_list) > 0:
if len(vslc_list) > 1:
gvc_id = '-'.join(vslc_list)
gvc_id = re.sub(r':', '', gvc_id)
if self.nobnodes:
gvc_id = ':'+gvc_id
gvc_label = \
'; '.join(self.id_label_hash[v] for v in vslc_list)
gu.addIndividualToGraph(
g, gvc_id, gvc_label,
geno.genoparts['genomic_variation_complement'])
for vslc_id in vslc_list:
geno.addVSLCtoParent(vslc_id, gvc_id)
else:
# the GVC == VSLC, so don't have to make an extra piece
gvc_id = vslc_list.pop()
gvc_label = self.id_label_hash[gvc_id]
genotype_label = gvc_label + ' [n.s.]'
bkgd_id = \
'_' + re.sub(r':', '', '-'.join(
(geno.genoparts['unspecified_genomic_background'],
s)))
genotype_id = '-'.join((gvc_id, bkgd_id))
if self.nobnodes:
bkgd_id = ':'+bkgd_id
geno.addTaxon(mouse_taxon, bkgd_id)
geno.addGenomicBackground(
bkgd_id, 'unspecified ('+s+')',
geno.genoparts['unspecified_genomic_background'],
"A placeholder for the " +
"unspecified genetic background for "+s)
geno.addGenomicBackgroundToGenotype(
bkgd_id, genotype_id,
geno.genoparts['unspecified_genomic_background'])
geno.addParts(
gvc_id, genotype_id,
geno.object_properties['has_alternate_part'])
geno.addGenotype(genotype_id, genotype_label)
gu.addTriple(
g, s, geno.object_properties['has_genotype'],
genotype_id)
else:
# logger.debug(
# "Strain %s is not making a proper genotype.", s)
pass
gu.loadProperties(
g, G2PAssoc.object_properties, G2PAssoc.OBJECTPROP)
gu.loadProperties(
g, G2PAssoc.datatype_properties, G2PAssoc.DATAPROP)
gu.loadProperties(
g, G2PAssoc.annotation_properties, G2PAssoc.ANNOTPROP)
gu.loadAllProperties(g)
logger.warning(
"The following gene symbols did not list identifiers: %s",
str(sorted(list(genes_with_no_ids))))
return示例2: _process_phenotype_data
# 需要导入模块: from dipper.models.Genotype import Genotype [as 别名]
# 或者: from dipper.models.Genotype.Genotype import addGenomicBackground [as 别名]
#.........这里部分代码省略.........
limit is not None and reader.line_num > limit):
break
# now that we've collected all of the variant information, build it
# we don't know their zygosities
for s in self.strain_hash:
h = self.strain_hash.get(s)
variants = h['variants']
genes = h['genes']
vl_set = set()
# make variant loci for each gene
if len(variants) > 0:
for var in variants:
vl_id = var.strip()
vl_symbol = self.id_label_hash[vl_id]
geno.addAllele(
vl_id, vl_symbol, self.globaltt['variant_locus'])
vl_set.add(vl_id)
if len(variants) == 1 and len(genes) == 1:
for gene in genes:
geno.addAlleleOfGene(vl_id, gene)
else:
geno.addAllele(vl_id, vl_symbol)
else: # len(vars) == 0
# it's just anonymous variants in some gene
for gene in genes:
vl_id = '_:' + re.sub(r':', '', gene) + '-VL'
vl_symbol = self.id_label_hash[gene]+'<?>'
self.id_label_hash[vl_id] = vl_symbol
geno.addAllele(
vl_id, vl_symbol, self.globaltt['variant_locus'])
geno.addGene(gene, self.id_label_hash[gene])
geno.addAlleleOfGene(vl_id, gene)
vl_set.add(vl_id)
# make the vslcs
vl_list = sorted(vl_set)
vslc_list = []
for vl in vl_list:
# for unknown zygosity
vslc_id = re.sub(r'^_', '', vl)+'U'
vslc_id = re.sub(r':', '', vslc_id)
vslc_id = '_:' + vslc_id
vslc_label = self.id_label_hash[vl] + '/?'
self.id_label_hash[vslc_id] = vslc_label
vslc_list.append(vslc_id)
geno.addPartsToVSLC(
vslc_id, vl, None, self.globaltt['indeterminate'],
self.globaltt['has_variant_part'], None)
model.addIndividualToGraph(
vslc_id, vslc_label,
self.globaltt['variant single locus complement'])
if len(vslc_list) > 0:
if len(vslc_list) > 1:
gvc_id = '-'.join(vslc_list)
gvc_id = re.sub(r'_|:', '', gvc_id)
gvc_id = '_:'+gvc_id
gvc_label = '; '.join(self.id_label_hash[v] for v in vslc_list)
model.addIndividualToGraph(
gvc_id, gvc_label,
self.globaltt['genomic_variation_complement'])
for vslc_id in vslc_list:
geno.addVSLCtoParent(vslc_id, gvc_id)
else:
# the GVC == VSLC, so don't have to make an extra piece
gvc_id = vslc_list.pop()
gvc_label = self.id_label_hash[gvc_id]
genotype_label = gvc_label + ' [n.s.]'
bkgd_id = re.sub(
r':', '', '-'.join((
self.globaltt['unspecified_genomic_background'], s)))
genotype_id = '-'.join((gvc_id, bkgd_id))
bkgd_id = '_:' + bkgd_id
geno.addTaxon(mouse_taxon, bkgd_id)
geno.addGenomicBackground(
bkgd_id, 'unspecified (' + s + ')',
self.globaltt['unspecified_genomic_background'],
"A placeholder for the unspecified genetic background for " + s)
geno.addGenomicBackgroundToGenotype(
bkgd_id, genotype_id,
self.globaltt['unspecified_genomic_background'])
geno.addParts(
gvc_id, genotype_id, self.globaltt['has_variant_part'])
geno.addGenotype(genotype_id, genotype_label)
graph.addTriple(
s, self.globaltt['has_genotype'], genotype_id)
else:
# LOG.debug(
# "Strain %s is not making a proper genotype.", s)
pass
LOG.warning(
"The following gene symbols did not list identifiers: %s",
str(sorted(list(genes_with_no_ids))))
LOG.error(
'%i symbols given are missing their gene identifiers',
len(genes_with_no_ids))
return