diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_details.html | 8 |
3 files changed, 12 insertions, 1 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 9dddc63e..018d5d54 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -57,6 +57,7 @@ DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s' PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s" OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s" UNIPROT_URL = "https://www.uniprot.org/uniprot/%s" +RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%s" # Temporary storage (note that this TMPDIR can be set as an # environment variable - use utility.tools.TEMPDIR when you diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 09004396..5d2f52cb 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -271,7 +271,7 @@ class ShowTrait(object): if check_if_attr_exists(self.this_trait, 'uniprotid'): self.uniprot_link = webqtlConfig.UNIPROT_URL % self.this_trait.uniprotid - self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None + self.genotation_link = self.rgd_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = self.ensembl_link = None if self.this_trait.symbol: self.genotation_link = webqtlConfig.GENOTATION_URL % self.this_trait.symbol @@ -283,6 +283,7 @@ class ShowTrait(object): #self.open_targets_link = webqtlConfig.OPEN_TARGETS_URL % self.this_trait.symbol if self.dataset.group.species == "mouse" or self.dataset.group.species == "human": + self.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize()) if self.dataset.group.species == "mouse": self.genemania_link = webqtlConfig.GENEMANIA_URL % ("mus-musculus", self.this_trait.symbol) else: @@ -307,6 +308,7 @@ class ShowTrait(object): self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end) if self.dataset.group.species == "rat": + self.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize()) self.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol) query = """SELECT kgID, chromosome, txStart, txEnd diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 7c2da752..b64b34d7 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -119,10 +119,18 @@ {% endif %} {% if this_trait.symbol %} + <!-- <a href="{{ genotation_link }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information"> Genotation </a> + --> + {% if rgd_link %} + <a href="{{ rgd_link }}" target="_blank"> + Rat Genome DB + </a> + + {% endif %} <a href="{{ gtex_link }}" target="_blank" title="GTEx Portal"> GTEx Portal </a> |