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-rw-r--r--[-rwxr-xr-x]wqflask/base/trait.py78
-rw-r--r--[-rwxr-xr-x]wqflask/wqflask/gsearch.py168
-rwxr-xr-xwqflask/wqflask/templates/gsearch_pheno.html2
3 files changed, 147 insertions, 101 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index acff38d9..ce3a7608 100755..100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -256,10 +256,10 @@ class GeneralTrait(object):
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id = %s
""" % (self.name, self.dataset.id)
-
- #print("query is:", query)
trait_info = g.db.execute(query).fetchone()
+
+
#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
#XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
elif self.dataset.type == 'ProbeSet':
@@ -294,7 +294,6 @@ class GeneralTrait(object):
escape(self.dataset.name),
escape(self.name))
trait_info = g.db.execute(query).fetchone()
- #print("trait_info is: ", pf(trait_info))
else: #Temp type
query = """SELECT %s FROM %s WHERE Name = %s"""
trait_info = g.db.execute(query,
@@ -305,7 +304,6 @@ class GeneralTrait(object):
#XZ: assign SQL query result to trait attributes.
for i, field in enumerate(self.dataset.display_fields):
- #print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i]))
holder = trait_info[i]
if isinstance(trait_info[i], basestring):
holder = unicode(trait_info[i], "utf8", "ignore")
@@ -315,12 +313,37 @@ class GeneralTrait(object):
self.confidential = 0
if self.pre_publication_description and not self.pubmed_id:
self.confidential = 1
+
+ description = self.post_publication_description
+
+ #If the dataset is confidential and the user has access to confidential
+ #phenotype traits, then display the pre-publication description instead
+ #of the post-publication description
+ if self.confidential:
+ self.description_display = ""
+
+ #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
+ # privilege=self.dataset.privilege,
+ # userName=self.dataset.userName,
+ # authorized_users=self.authorized_users):
+ #
+ # description = self.pre_publication_description
+
+ if len(description) > 0:
+ self.description_display = description.strip()
+ else:
+ self.description_display = ""
+ if not self.year.isdigit():
+ self.pubmed_text = "N/A"
+ else:
+ self.pubmed_text = self.year
+
+ if self.pubmed_id:
+ self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id
+
self.homologeneid = None
- #print("self.geneid is:", self.geneid)
- #print(" type:", type(self.geneid))
- #print("self.dataset.group.name is:", self.dataset.group.name)
if self.dataset.type == 'ProbeSet' and self.dataset.group and self.geneid:
#XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
#XZ: So I have to test if geneid is number before execute the query.
@@ -330,10 +353,7 @@ class GeneralTrait(object):
# geneidIsNumber = True
#except ValueError:
# geneidIsNumber = False
-
#if geneidIsNumber:
-
-
query = """
SELECT
HomologeneId
@@ -353,6 +373,11 @@ class GeneralTrait(object):
self.homologeneid = result[0]
if get_qtl_info:
+ #LRS and its location
+ self.LRS_score_repr = "N/A"
+ self.LRS_score_value = 0
+ self.LRS_location_repr = "N/A"
+ self.LRS_location_value = 1000000
if self.dataset.type == 'ProbeSet' and not self.cellid:
query = """
SELECT
@@ -365,12 +390,8 @@ class GeneralTrait(object):
ProbeSetXRef.ProbeSetFreezeId ={}
""".format(self.name, self.dataset.id)
trait_qtl = g.db.execute(query).fetchone()
- #self.cursor.execute(query)
- #trait_qtl = self.cursor.fetchone()
if trait_qtl:
- #print("trait_qtl:", trait_qtl)
self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl
- #print("self.locus:", self.locus)
if self.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
@@ -403,8 +424,37 @@ class GeneralTrait(object):
""", (self.name, self.dataset.id)).fetchone()
if trait_qtl:
self.locus, self.lrs, self.additive = trait_qtl
+ if self.locus:
+ query = """
+ select Geno.Chr, Geno.Mb from Geno, Species
+ where Species.Name = '{}' and
+ Geno.Name = '{}' and
+ Geno.SpeciesId = Species.Id
+ """.format(self.dataset.group.species, self.locus)
+ result = g.db.execute(query).fetchone()
+ if result:
+ self.locus_chr = result[0]
+ self.locus_mb = result[1]
+ else:
+ self.locus = self.locus_chr = self.locus_mb = ""
+ else:
+ self.locus = self.locus_chr = self.locus_mb = ""
else:
self.locus = self.lrs = self.additive = ""
+
+ if self.locus_chr != "" and self.locus_mb != "":
+ #XZ: LRS_location_value is used for sorting
+ try:
+ LRS_location_value = int(self.locus_chr)*1000 + float(self.locus_mb)
+ except:
+ if self.locus_chr.upper() == 'X':
+ LRS_location_value = 20*1000 + float(self.locus_mb)
+ else:
+ LRS_location_value = ord(str(self.locus_chr).upper()[0])*1000 + float(self.locus_mb)
+
+ self.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (self.locus_chr, float(self.locus_mb))
+ self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs
+ self.LRS_score_value = LRS_score_value = self.lrs
else:
raise KeyError, `self.name`+' information is not found in the database.'
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 179f054e..4cd3874c 100755..100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -9,90 +9,86 @@ from utility.benchmark import Bench
class GSearch(object):
- 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 6000
- """ % (self.terms)
- with Bench("Running query"):
- re = g.db.execute(sql).fetchall()
- self.trait_list = []
- with Bench("Creating trait objects"):
- for line in re:
- dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
- trait_id = line[4]
- #with Bench("Building trait object"):
- this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
- self.trait_list.append(this_trait)
- species = webqtlDatabaseFunction.retrieve_species(dataset.group.name)
- #with Bench("Getting trait info"):
- dataset.get_trait_info([this_trait], species)
+ 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 6000
+ """ % (self.terms)
+ with Bench("Running query"):
+ re = g.db.execute(sql).fetchall()
+ self.trait_list = []
+ with Bench("Creating trait objects"):
+ for line in re:
+ dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
+ trait_id = line[4]
+ #with Bench("Building trait object"):
+ this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+ self.trait_list.append(this_trait)
- 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 6000
- """ % (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, get_sample_info=False)
- 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 6000
+ """ % (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 = []
+ with Bench("Creating trait objects"):
+ 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, get_sample_info=False)
+ self.trait_list.append(this_trait)
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 0bdc4f4e..3c9f6841 100755
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -137,7 +137,7 @@
{ "type": "natural" },
{ "type": "natural" },
{ "type": "natural" },
- { "type": "natural" },
+ { "type": "natural", "width": "12%"},
{ "type": "natural" }
],
"order": [[ 1, "asc" ]],
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 23:24:51 +0000