diff options
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 25 |
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 |