diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 90 |
1 files changed, 47 insertions, 43 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index ac6014e7..61bfbaba 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -7,19 +7,18 @@ from pprint import pformat as pf from dbFunction import webqtlDatabaseFunction - class DoSearch(object): """Parent class containing parameters/functions used for all searches""" - + # Used to translate search phrases into classes search_types = dict() - + def __init__(self, search_term, dataset, cursor, db_conn): self.search_term = search_term self.dataset = dataset self.db_conn = db_conn self.cursor = cursor - + #Get group information for dataset and the species id self.dataset.get_group() self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group) @@ -40,7 +39,7 @@ class DoSearch(object): """Strips out newlines/extra spaces and replaces them with just spaces""" step_one = " ".join(stringy.split()) return step_one - + @classmethod def get_search(cls, search_type): return cls.search_types[search_type] @@ -48,9 +47,9 @@ class DoSearch(object): class ProbeSetSearch(DoSearch): """A search within an mRNA expression dataset""" - + DoSearch.search_types['ProbeSet'] = "ProbeSetSearch" - + base_query = """SELECT ProbeSet.Name as TNAME, 0 as thistable, ProbeSetXRef.Mean as TMEAN, @@ -63,9 +62,10 @@ class ProbeSetSearch(DoSearch): FROM ProbeSetXRef, ProbeSet """ - def compile_final_query(self, from_clause, where_clause): + def compile_final_query(self, from_clause = '', where_clause = ''): """Generates the final query string""" + from_clause = '' from_clause = self.normalize_spaces(from_clause) query = (self.base_query + @@ -78,12 +78,12 @@ class ProbeSetSearch(DoSearch): self.escape(self.dataset.id))) print("query is:", pf(query)) - + return query def run(self): """Generates and runs a simple search of an mRNA expression dataset""" - + print("Running ProbeSetSearch") query = (self.base_query + """WHERE (MATCH (ProbeSet.Name, @@ -106,9 +106,9 @@ class ProbeSetSearch(DoSearch): class PhenotypeSearch(DoSearch): """A search within a phenotype dataset""" - + DoSearch.search_types['Publish'] = "PhenotypeSearch" - + base_query = """SELECT PublishXRef.Id, PublishFreeze.createtime as thistable, Publication.PubMed_ID as Publication_PubMed_ID, @@ -125,7 +125,7 @@ class PhenotypeSearch(DoSearch): 'Publication.Title', 'Publication.Authors', 'PublishXRef.Id') - + def get_where_clause(self): """Generate clause for WHERE portion of query""" @@ -140,7 +140,7 @@ class PhenotypeSearch(DoSearch): for field in self.search_fields: where_clause.append('''%s REGEXP "%s"''' % (field, search_term)) where_clause = "(%s)" % ' OR '.join(where_clause) - + return where_clause def run(self): @@ -164,7 +164,7 @@ class PhenotypeSearch(DoSearch): class GenotypeSearch(DoSearch): """A search within a genotype dataset""" - + DoSearch.search_types['Geno'] = "GenotypeSearch" base_query = """SELECT Geno.Name, @@ -185,7 +185,8 @@ class GenotypeSearch(DoSearch): where_clause = [] for field in self.search_fields: where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % (self.dataset.type, field), - self.search_term)) + self.escape(self.search_term))) + print("where_clause is:", pf(where_clause)) where_clause = "(%s)" % ' OR '.join(where_clause) return where_clause @@ -209,7 +210,7 @@ class GenotypeSearch(DoSearch): class RifSearch(ProbeSetSearch): """Searches for traits with a Gene RIF entry including the search term.""" - + DoSearch.search_types['RIF'] = "RifSearch" def run(self): @@ -224,9 +225,9 @@ class RifSearch(ProbeSetSearch): class WikiSearch(ProbeSetSearch): """Searches GeneWiki for traits other people have annotated""" - + DoSearch.search_types['WIKI'] = "WikiSearch" - + def run(self): where_clause = """%s.symbol = GeneRIF.symbol and GeneRIF.versionId=0 and GeneRIF.display>0 @@ -259,43 +260,44 @@ class GoSearch(ProbeSetSearch): from_clause = """ , db_GeneOntology.term as GOterm, db_GeneOntology.association as GOassociation, db_GeneOntology.gene_product as GOgene_product """ - + query = self.compile_final_query(from_clause, where_clause) return self.execute(query) +#ZS: Not sure what the best way to deal with LRS searches is class LrsSearch(ProbeSetSearch): """Searches for genes with a QTL within the given LRS values - + LRS searches can take 2 different forms: - LRS=(min_LRS max_LRS) - LRS=(min_LRS max_LRS chromosome start_Mb end_Mb) where min/max_LRS represent the range of LRS scores and start/end_Mb represent the range in megabases on the given chromosome - + """ - + DoSearch.search_types['LRS'] = 'LrsSearch' class CisLrsSearch(LrsSearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values - + A cisLRS search can take 2 forms: - cisLRS=(min_LRS max_LRS) - cisLRS=(min_LRS max_LRS mb_buffer) 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. - + A QTL is a cis-eQTL if a gene's expression is regulated by a QTL in roughly the same area (where the area is determined by the mb_buffer that the user can choose). - + """ - + # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps # between this and the LrsSearch code. In the original code, commands are divided by # the number of inputs they take, so these commands are completely separate - + DoSearch.search_types['CISLRS'] = "CisLrsSearch" def run(self): @@ -318,27 +320,28 @@ class CisLrsSearch(LrsSearch): self.dataset.type, min_threshold ) - else: - NeedSomeErrorHere + NeedSomeErrorHere - return None + query = self.compile_final_query(where_clause) + + return self.execute(query) class TransLrsSearch(LrsSearch): """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values - + A transLRS search can take 2 forms: - transLRS=(min_LRS max_LRS) - transLRS=(min_LRS max_LRS mb_buffer) 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. - + A QTL is a trans-eQTL if a gene's expression is regulated by a QTL in a different location/area (where the area is determined by the mb_buffer that the user can choose). Opposite of cis-eQTL. - + """ - + # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps # between this and the LrsSearch code. In the original code, commands are divided by # the number of inputs they take, so these commands are completely separate @@ -370,8 +373,8 @@ class TransLrsSearch(LrsSearch): NeedSomeErrorHere return None - - + + #itemCmd = item[0] #lowerLimit = float(item[1]) #upperLimit = float(item[2]) @@ -402,15 +405,15 @@ class TransLrsSearch(LrsSearch): # query.append(" (%s) " % clauseItem) # self.orderByDefalut = itemCmd # DescriptionText.append(HT.Span(' with ', HT.U(itemCmd), ' between %g and %g' % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit)))) - - + + class MeanSearch(ProbeSetSearch): """Searches for genes expressed within an interval (log2 units) determined by the user""" - + DoSearch.search_types['MEAN'] = "MeanSearch" - + def run(self): - + return None @@ -443,8 +446,9 @@ if __name__ == "__main__": #results = RifSearch("diabetes", dataset, cursor, db_conn).run() #results = WikiSearch("nicotine", dataset, cursor, db_conn).run() results = CisLrsSearch(['9','99','10'], dataset, cursor, db_conn).run() + #results = TransLrsSearch(['9', '999', '10'], dataset, cursor, db_conn).run() #results = PhenotypeSearch("brain", dataset, cursor, db_conn).run() #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run() #results = GoSearch("0045202", dataset, cursor, db_conn).run() - + print("results are:", pf(results))
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