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| author | zsloan | 2019-12-09 14:09:32 -0600 |
|---|---|---|
| committer | zsloan | 2019-12-09 14:09:32 -0600 |
| commit | aace2f31197115fa201a1a924d3d663ba43d0511 (patch) | |
| tree | 3bede35be1f0130bc734c97caa1cee67c709b39c /wqflask | |
| parent | 1da41f1c60b0f7f170841ad9584447a703cf4f06 (diff) | |
| download | genenetwork2-aace2f31197115fa201a1a924d3d663ba43d0511.tar.gz | |
Added optional fourth term to cis/transLRS searches so you can specify which chromosome you want the max LRS to be on
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 31 |
1 files changed, 21 insertions, 10 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 9aa41a87..12338401 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -577,21 +577,26 @@ class CisTransLrsSearch(DoSearch): return ", Geno" def get_where_clause(self, cis_trans): - self.search_term = [float(value) for value in self.search_term] self.mb_buffer = 5 # default + chromosome = None if cis_trans == "cis": the_operator = "<" else: the_operator = ">" if self.search_operator == "=": + if len(self.search_term) == 2 or len(self.search_term) == 3: + self.search_term = [float(value) for value in self.search_term] if len(self.search_term) == 2: lrs_min, lrs_max = self.search_term #[int(value) for value in self.search_term] - elif len(self.search_term) == 3: lrs_min, lrs_max, self.mb_buffer = self.search_term - + elif len(self.search_term) == 4: + lrs_min, lrs_max, self.mb_buffer = [float(value) for value in self.search_term[:3]] + chromosome = self.search_term[3] + if "Chr" in chromosome or "chr" in chromosome: + chromosome = float(chromosome[3:]) else: SomeError @@ -628,18 +633,24 @@ class CisTransLrsSearch(DoSearch): escape(self.dataset.type) ) else: + if chromosome: + location_clause = "(%s.Chr = %s and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = %s)" % (escape(self.dataset.type), + chromosome, + escape(self.dataset.type), + escape(self.dataset.type), + the_operator, + escape(str(self.mb_buffer)), + escape(self.dataset.type), + chromosome) + else: + location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type)) where_clause = sub_clause + """ %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and - ((ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or - (%s.Chr != Geno.Chr))""" % ( + (%s)""" % ( escape(self.dataset.type), escape(str(self.species_id)), - escape(self.dataset.type), - the_operator, - escape(str(self.mb_buffer)), - escape(self.dataset.type), - escape(self.dataset.type) + location_clause ) return where_clause |