aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base
diff options
context:
space:
mode:
authorzsloan2020-04-06 17:41:19 -0500
committerzsloan2020-04-06 17:41:19 -0500
commit9e6b8a2b2adfb4b41867ecd6932ce899872eea9e (patch)
tree3bfbcbd862fa8c935ded7bab0399e4beec795f4e /wqflask/base
parent984030cbff9c8f49a664df7c693f852f6d09b2e5 (diff)
downloadgenenetwork2-9e6b8a2b2adfb4b41867ecd6932ce899872eea9e.tar.gz
Added Mean column for phenotype traits in search and global search result tables
Diffstat (limited to 'wqflask/base')
-rw-r--r--wqflask/base/data_set.py2
-rw-r--r--wqflask/base/trait.py5
2 files changed, 5 insertions, 2 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5b32c5ae..ebf3f021 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -710,6 +710,7 @@ class PhenotypeDataSet(DataSet):
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
'Phenotype.Post_publication_abbreviation',
+ 'PublishXRef.mean',
'Phenotype.Lab_code',
'Publication.PubMed_ID',
'Publication.Abstract',
@@ -725,6 +726,7 @@ class PhenotypeDataSet(DataSet):
'original_description',
'pre_publication_abbreviation',
'post_publication_abbreviation',
+ 'mean',
'lab_code',
'submitter', 'owner',
'authorized_users',
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 8e779a11..5525472e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -354,7 +354,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
SELECT
PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
- Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+ Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
Publication.Authors, Publication.Title, Publication.Abstract,
Publication.Journal, Publication.Volume, Publication.Pages,
@@ -503,8 +503,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#LRS and its location
trait.LRS_score_repr = "N/A"
trait.LRS_location_repr = "N/A"
- trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = ""
+ trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
if dataset.type == 'ProbeSet' and not trait.cellid:
+ trait.mean = ""
query = """
SELECT
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive