diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 37 |
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) |