diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 26 |
1 files changed, 4 insertions, 22 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 403f1b5e..3ce613e9 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -198,26 +198,6 @@ class PhenotypeSearch(DoSearch): query = self.compile_final_query(where_clause = self.get_fields_clause()) -# self.query = """SELECT PublishXRef.Id, -#PublishFreeze.createtime as thistable, -#Publication.PubMed_ID as Publication_PubMed_ID, -#Phenotype.Post_publication_description as Phenotype_Name FROM Phenotype, -#PublishFreeze, Publication, PublishXRef WHERE (Phenotype.Post_publication_description -#REGEXP "[[:<:]]brain[[:>:]]" OR Phenotype.Pre_publication_description REGEXP "[[:<:]]brain[[:>:]]" -#OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]brain[[:>:]]" -#OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]brain[[:>:]]" -#OR Phenotype.Lab_code REGEXP "[[:<:]]brain[[:>:]]" -#OR Publication.PubMed_ID REGEXP "[[:<:]]brain[[:>:]]" -#OR Publication.Abstract REGEXP "[[:<:]]brain[[:>:]]" -#OR Publication.Title REGEXP "[[:<:]]brain[[:>:]]" -#OR Publication.Authors REGEXP "[[:<:]]brain[[:>:]]" -#OR PublishXRef.Id REGEXP "[[:<:]]brain[[:>:]]") -#and PublishXRef.InbredSetId = 1 -#and PublishXRef.PhenotypeId = Phenotype.Id -#and PublishXRef.PublicationId = Publication.Id -#and PublishFreeze.Id = 1;""" - - results = self.execute(query) print("in [df] run results are:", results) return results @@ -461,7 +441,8 @@ class CisTransLrsSearch(LrsSearch): class CisLrsSearch(CisTransLrsSearch): - """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values + """ + Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values A cisLRS search can take 3 forms: - cisLRS=(min_LRS max_LRS) @@ -484,9 +465,10 @@ class CisLrsSearch(CisTransLrsSearch): class TransLrsSearch(CisTransLrsSearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values - A transLRS search can take 2 forms: + A transLRS search can take 3 forms: - transLRS=(min_LRS max_LRS) - transLRS=(min_LRS max_LRS mb_buffer) + - transLRS>min_LRS where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around a particular QTL where its eQTL would be considered "cis". If there is no third parameter, mb_buffer will default to 5 megabases. |