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authorzsloan2019-05-17 14:08:07 -0500
committerzsloan2019-05-17 14:08:07 -0500
commita35498b0def3ab4bb950c407d5753eadb654277c (patch)
treebd065069f11c29b4c9737659345a90c9e18744c5
parent15d64a94eacf6b883fcc1ef2a49aa6ca7934eb96 (diff)
downloadgenenetwork2-a35498b0def3ab4bb950c407d5753eadb654277c.tar.gz
Fixed issue that caused error for traits with no unigene id
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py25
1 files changed, 22 insertions, 3 deletions
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index cf27a3d7..0e20722e 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -122,8 +122,8 @@ class ShowTrait(object):
self.UCSC_BLAT_URL = ""
self.UTHSC_BLAT_URL = ""
+ trait_units = get_trait_units(self.this_trait)
self.get_external_links()
-
self.build_correlation_tools()
#Get nearest marker for composite mapping
@@ -201,6 +201,7 @@ class ShowTrait(object):
#ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width
self.num_values = 0
self.binary = "true" #ZS: So it knows whether to display the Binary R/qtl mapping method, which doesn't work unless all values are 0 or 1
+ self.negative_vals_exist = "false" #ZS: Since we don't want to show log2 transform option for situations where it doesn't make sense
max_samplename_width = 1
for group in self.sample_groups:
for sample in group.sample_list:
@@ -210,6 +211,8 @@ class ShowTrait(object):
self.num_values += 1
if sample.display_value != 0 or sample.display_value != 1:
self.binary = "false"
+ if sample.value < 0:
+ self.negative_vals_exist = "true"
sample_column_width = max_samplename_width * 8
@@ -225,6 +228,7 @@ class ShowTrait(object):
js_data = dict(trait_id = self.trait_id,
trait_symbol = trait_symbol,
+ unit_type = trait_units,
dataset_type = self.dataset.type,
data_scale = self.dataset.data_scale,
sample_group_types = self.sample_group_types,
@@ -242,7 +246,7 @@ class ShowTrait(object):
self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if hasattr(self.this_trait, 'pubmed_id') else None
self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if hasattr(self.this_trait, 'geneid') else None
self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if hasattr(self.this_trait, 'omim') else None
- self.unigene_link = webqtlConfig.UNIGEN_ID % tuple(string.split(self.this_trait.unigeneid, '.')[:2]) if (hasattr(self.this_trait, 'unigeneid') and self.this_trait.unigeneid != "") else None
+ self.unigene_link = webqtlConfig.UNIGEN_ID % tuple(string.split(self.this_trait.unigeneid, '.')[:2]) if (hasattr(self.this_trait, 'unigeneid') and self.this_trait.unigeneid != "" and self.this_trait.unigeneid != None) else None
self.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if hasattr(self.this_trait, 'homologeneid') else None
self.genbank_link = None
@@ -497,4 +501,19 @@ def has_num_cases(this_trait):
has_n = True
break
- return has_n \ No newline at end of file
+ return has_n
+
+def get_trait_units(this_trait):
+ unit_type = ""
+ inside_brackets = False
+ if this_trait.description_fmt:
+ if ("[" in this_trait.description_fmt) and ("]" in this_trait.description_fmt):
+ for i in this_trait.description_fmt:
+ if inside_brackets:
+ if i != "]":
+ unit_type += i
+ else:
+ inside_brackets = False
+ if i == "[":
+ inside_brackets = True
+ return unit_type \ No newline at end of file