def gen_search_result(self):
"""
Get the info displayed in the search result table from the set of results computed in
the "search" function
"""
self.trait_list = []
species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name)
# result_set represents the results for each search term; a search of
# "shh grin2b" would have two sets of results, one for each term
print("self.results is:", pf(self.results))
for result in self.results:
if not result:
continue
#### Excel file needs to be generated ####
print("foo locals are:", locals())
trait_id = result[0]
this_trait = GeneralTrait(dataset=self.dataset, name=trait_id)
this_trait.retrieve_info(get_qtl_info=True)
self.trait_list.append(this_trait)
self.dataset.get_trait_info(self.trait_list, species)
def gen_search_result(self):
"""
Get the info displayed in the search result table from the set of results computed in
the "search" function
"""
self.trait_list = []
species = webqtlDatabaseFunction.retrieve_species(
self.dataset.group.name)
# result_set represents the results for each search term; a search of
# "shh grin2b" would have two sets of results, one for each term
print("self.results is:", pf(self.results))
for result in self.results:
if not result:
continue
#### Excel file needs to be generated ####
#print("foo locals are:", locals())
trait_id = result[0]
this_trait = GeneralTrait(dataset=self.dataset,
name=trait_id,
get_qtl_info=True,
get_sample_info=False)
self.trait_list.append(this_trait)
self.dataset.get_trait_info(self.trait_list, species)
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
print("dataset name:", dataset.name)
self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
if self.name == 'BXD300':
self.name = "BXD"
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
#print("parents/f1s: {}:{}".format(self.parlist, self.f1list))
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
self.allsamples = None
def __init__(self, kw):
self.type = kw['type']
self.terms = kw['terms']
if self.type == "gene":
sql = """
SELECT
Species.`Name` AS species_name,
InbredSet.`Name` AS inbredset_name,
Tissue.`Name` AS tissue_name,
ProbeSetFreeze.Name AS probesetfreeze_name,
ProbeSet.Name AS probeset_name,
ProbeSet.Symbol AS probeset_symbol,
ProbeSet.`description` AS probeset_description,
ProbeSet.Chr AS chr,
ProbeSet.Mb AS mb,
ProbeSetXRef.Mean AS mean,
ProbeSetXRef.LRS AS lrs,
ProbeSetXRef.`Locus` AS locus,
ProbeSetXRef.`pValue` AS pvalue,
ProbeSetXRef.`additive` AS additive
FROM Species, InbredSet, ProbeSetXRef, ProbeSet, ProbeFreeze, ProbeSetFreeze, Tissue
WHERE InbredSet.`SpeciesId`=Species.`Id`
AND ProbeFreeze.InbredSetId=InbredSet.`Id`
AND ProbeFreeze.`TissueId`=Tissue.`Id`
AND ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
AND ProbeSet.Id = ProbeSetXRef.ProbeSetId
AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
AND ProbeSetFreeze.public > 0
ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
LIMIT 5000
""" % (self.terms)
re = g.db.execute(sql).fetchall()
self.trait_list = []
for line in re:
dataset = create_dataset(line[3], "ProbeSet")
trait_id = line[4]
this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True)
self.trait_list.append(this_trait)
species = webqtlDatabaseFunction.retrieve_species(dataset.group.name)
dataset.get_trait_info([this_trait], species)
elif self.type == "phenotype":
sql = """
SELECT
Species.`Name`,
InbredSet.`Name`,
PublishFreeze.`Name`,
PublishXRef.`Id`,
Phenotype.`Post_publication_description`,
Publication.`Authors`,
Publication.`Year`,
PublishXRef.`LRS`,
PublishXRef.`Locus`,
PublishXRef.`additive`
FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
AND PublishFreeze.`InbredSetId`=InbredSet.`Id`
AND InbredSet.`SpeciesId`=Species.`Id`
AND PublishXRef.`PhenotypeId`=Phenotype.`Id`
AND PublishXRef.`PublicationId`=Publication.`Id`
AND (Phenotype.Post_publication_description REGEXP "[[:<:]]%s[[:>:]]"
OR Phenotype.Pre_publication_description REGEXP "[[:<:]]%s[[:>:]]"
OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]"
OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]"
OR Phenotype.Lab_code REGEXP "[[:<:]]%s[[:>:]]"
OR Publication.PubMed_ID REGEXP "[[:<:]]%s[[:>:]]"
OR Publication.Abstract REGEXP "[[:<:]]%s[[:>:]]"
OR Publication.Title REGEXP "[[:<:]]%s[[:>:]]"
OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]"
OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]")
ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
LIMIT 5000
""" % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
re = g.db.execute(sql).fetchall()
self.trait_list = []
for line in re:
dataset = create_dataset(line[2], "Publish")
trait_id = line[3]
this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True)
self.trait_list.append(this_trait)
species = webqtlDatabaseFunction.retrieve_species(dataset.group.name)
dataset.get_trait_info([this_trait], species)
def get_info(self):
"""For lots of traits just use get_trait_info in dataset instead...that will be way
more efficient"""
self.dataset.get_trait_info([self],
webqtlDatabaseFunction.retrieve_species(
self.dataset.group.name))
def get_info(self):
"""For lots of traits just use get_trait_info in dataset instead...that will be way
more efficient"""
self.dataset.get_trait_info([self], webqtlDatabaseFunction.retrieve_species(self.dataset.group.name))
