aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/gsearch.py37
1 files changed, 22 insertions, 15 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 9e46c0c5..6ff57563 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,4 +1,6 @@
import json
+import datetime as dt
+from types import SimpleNamespace
from flask import Flask, g
from base.data_set import create_dataset
@@ -9,8 +11,9 @@ from base import webqtlConfig
from utility import hmac
-from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
from utility.benchmark import Bench
+from utility.authentication_tools import check_resource_availability
+from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
from utility.logger import getLogger
logger = getLogger(__name__)
@@ -42,15 +45,19 @@ class GSearch(object):
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
+ ProbeSetXRef.`additive` AS additive,
+ ProbeSetFreeze.Id AS probesetfreeze_id,
+ Geno.Chr as geno_chr,
+ Geno.Mb as geno_mb
+ FROM Species
+ INNER JOIN InbredSet ON InbredSet.`SpeciesId`=Species.`Id`
+ INNER JOIN ProbeFreeze ON ProbeFreeze.InbredSetId=InbredSet.`Id`
+ INNER JOIN Tissue ON ProbeFreeze.`TissueId`=Tissue.`Id`
+ INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
+ INNER JOIN ProbeSetXRef ON ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
+ INNER JOIN ProbeSet ON ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ LEFT JOIN Geno ON ProbeSetXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
+ WHERE ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,ProbeSet.alias,ProbeSet.GenbankId, ProbeSet.UniGeneId, ProbeSet.Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
AND ProbeSetFreeze.confidentiality < 1
AND ProbeSetFreeze.public > 0
ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
@@ -90,16 +97,16 @@ class GSearch(object):
this_trait['additive'] = "N/A"
if line[14] != "" and line[14] != None:
this_trait['additive'] = '%.3f' % line[14]
+ this_trait['dataset_id'] = line[15]
+ this_trait['locus_chr'] = line[16]
+ this_trait['locus_mb'] = line[17]
#dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
#trait_id = line[4]
#with Bench("Building trait object"):
- trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
- if not trait_ob:
- continue
max_lrs_text = "N/A"
- if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
- max_lrs_text = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb)
+ if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None:
+ max_lrs_text = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb'])
this_trait['max_lrs_text'] = max_lrs_text
trait_list.append(this_trait)