diff options
Diffstat (limited to 'gn2/base')
| -rw-r--r-- | gn2/base/trait.py | 31 | ||||
| -rw-r--r-- | gn2/base/webqtlConfig.py | 4 |
2 files changed, 34 insertions, 1 deletions
diff --git a/gn2/base/trait.py b/gn2/base/trait.py index 701958d7..24288ba1 100644 --- a/gn2/base/trait.py +++ b/gn2/base/trait.py @@ -611,3 +611,34 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): f"{repr(trait.name)} information is not found in the database " f"for dataset '{dataset.name}' with id '{dataset.id}'.") return trait + +def fetch_symbols(trait_db_list): + """ + Fetch list of trait symbols + + From a list of traits and datasets (where each item has + the trait and dataset name separated by a colon), return + + """ + + trimmed_trait_list = [trait_db for trait_db in trait_db_list + if 'Publish' not in trait_db and 'Geno' not in trait_db.split(":")[1]] + + symbol_list = [] + with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: + for trait_db in trimmed_trait_list: + symbol_query = """ + SELECT ps.Symbol + FROM ProbeSet as ps + INNER JOIN ProbeSetXRef psx ON psx.ProbeSetId = ps.Id + INNER JOIN ProbeSetFreeze psf ON psx.ProbeSetFreezeId = psf.Id + WHERE + ps.Name = %(trait_name)s AND + psf.Name = %(db_name)s + """ + + cursor.execute(symbol_query, {'trait_name': trait_db.split(":")[0], + 'db_name': trait_db.split(":")[1]}) + symbol_list.append(cursor.fetchone()[0]) + + return "+".join(symbol_list) \ No newline at end of file diff --git a/gn2/base/webqtlConfig.py b/gn2/base/webqtlConfig.py index 998c0efc..88f199f9 100644 --- a/gn2/base/webqtlConfig.py +++ b/gn2/base/webqtlConfig.py @@ -34,7 +34,7 @@ MAXLRS = 460.0 PUBLICTHRESH = 0 # Groups to treat as unique when drawing correlation dropdowns (not sure if this logic even makes sense or is necessary) -BXD_GROUP_EXCEPTIONS = ['BXD-Longevity', 'BXD-AE', 'BXD-Heart-Metals', 'BXD-NIA-AD'] +BXD_GROUP_EXCEPTIONS = ['BXD-Longevity', 'BXD-AE', 'BXD-Heart-Metals', 'BXD-NIA-AD', 'BXD-JAX-OFS'] # EXTERNAL LINK ADDRESSES PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" @@ -68,6 +68,8 @@ RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene& PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&genomeVer=rn7§ion=geneEQTL" RRID_MOUSE_URL = "https://www.jax.org/strain/%s" RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s" +GENE_CUP_URL = "https://genecup.org/progress?type=GWAS&type=addiction&type=drug&type=brain&type=stress&type=psychiatric&type=cell&type=function&query=%s" + # Temporary storage (note that this TMPDIR can be set as an # environment variable - use utility.tools.TEMPDIR when you |