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-rw-r--r--wqflask/wqflask/do_search.py79
-rw-r--r--wqflask/wqflask/parser.py7
-rw-r--r--wqflask/wqflask/search_results.py86
3 files changed, 99 insertions, 73 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 4517d9f5..ac6014e7 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -19,6 +19,10 @@ class DoSearch(object):
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)
def execute(self, query):
"""Executes query and returns results"""
@@ -47,10 +51,6 @@ class ProbeSetSearch(DoSearch):
DoSearch.search_types['ProbeSet'] = "ProbeSetSearch"
- #Get group information for dataset and the species id
- self.dataset.get_group()
- self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group)
-
base_query = """SELECT ProbeSet.Name as TNAME,
0 as thistable,
ProbeSetXRef.Mean as TMEAN,
@@ -62,6 +62,7 @@ class ProbeSetSearch(DoSearch):
ProbeSet.name_num as TNAME_NUM
FROM ProbeSetXRef, ProbeSet """
+
def compile_final_query(self, from_clause, where_clause):
"""Generates the final query string"""
@@ -268,7 +269,7 @@ class LrsSearch(ProbeSetSearch):
LRS searches can take 2 different forms:
- LRS=(min_LRS max_LRS)
- - LRS=(mine_LRS max_LRS chromosome start_Mb end_Mb)
+ - 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
@@ -276,9 +277,6 @@ class LrsSearch(ProbeSetSearch):
DoSearch.search_types['LRS'] = 'LrsSearch'
- self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor,
- self.dataset.group)
-
class CisLrsSearch(LrsSearch):
"""Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
@@ -290,8 +288,10 @@ class CisLrsSearch(LrsSearch):
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.
+ (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
@@ -300,7 +300,7 @@ class CisLrsSearch(LrsSearch):
def run(self):
if len(self.search_term) == 3:
- lower_limit, upper_limit, min_threshold = int(value) for value in self.search_term
+ lower_limit, upper_limit, min_threshold = [int(value) for value in self.search_term]
where_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s and
@@ -309,16 +309,65 @@ class CisLrsSearch(LrsSearch):
%s.Chr = Geno.Chr and
ABS(%s.Mb-Geno.Mb) < %s """ % (
self.dataset.type,
- min(lower_limit, upper_limit)
+ min(lower_limit, upper_limit),
+ self.dataset.type,
+ max(lower_limit, upper_limit),
+ self.dataset.type,
+ self.species_id,
self.dataset.type,
- max(lower_limit, upper_limit,
self.dataset.type,
-
+ min_threshold
)
else:
- NeedSomeErrorHere
-
+ NeedSomeErrorHere
+
+ return None
+
+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
+
+ DoSearch.search_types['TRANSLRS'] = "TransLrsSearch"
+
+ def run(self):
+ if len(self.search_term) == 3:
+ lower_limit, upper_limit, min_threshold = [int(value) for value in self.search_term]
+
+ where_clause = """ %sXRef.LRS > %s and
+ %sXRef.LRS < %s and
+ %sXRef.Locus = Geno.name and
+ Geno.SpeciesId = %s and
+ (%s.Chr != Geno.Chr or
+ ABS(%s.Mb-Geno.Mb) > %s) """ % (
+ self.dataset.type,
+ min(lower_limit, upper_limit),
+ self.dataset.type,
+ max(lower_limit, upper_limit),
+ self.dataset.type,
+ self.species_id,
+ self.dataset.type,
+ self.dataset.type,
+ min_threshold
+ )
+
+ else:
+ NeedSomeErrorHere
return None
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index e693b2b8..b220f837 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -27,6 +27,13 @@ def parse(pstring):
value = value[1:-1] # Get rid of the parenthesis
values = re.split(r"""\s+|,""", value)
value = [value.strip() for value in values if value.strip()]
+ # Brackets can also be used to encapsulate values
+ elif '[' in value:
+ assert value.startswith("["), "Invalid token"
+ assert value.endswith("]"), "Invalid token"
+ value = value[1:-1] # Get rid of the brackets
+ values = re.split(r"""\s+|,""", value)
+ value = [value.strip() for value in values if value.strip()]
term = dict(key=key,
seperator=seperator,
search_term=value)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 6ba4d94a..4aa1f2bc 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -213,56 +213,49 @@ class SearchResultPage(templatePage):
#### Excel file stuff stops
if self.dataset.type == "ProbeSet":
- #for item in result:
print("foo locals are:", locals())
probe_set_id = result[0]
- print("probe_set_id is:", pf(probe_set_id))
this_trait = webqtlTrait(db=self.dataset, name=probe_set_id, cursor=self.cursor)
this_trait.retrieveInfo(QTL=True)
print("this_trait is:", pf(this_trait))
self.trait_list.append(this_trait)
- elif self.dataset.type == "Publish":
- newrow += 1
- tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=mainfmName, worksheet=worksheet, newrow=newrow, species=species)
- elif self.dataset.type == "Geno":
- newrow += 1
- tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=form_name, worksheet=worksheet, newrow=newrow)
+ #elif self.dataset.type == "Publish":
+ # tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=mainfmName, worksheet=worksheet, species=species)
+ #elif self.dataset.type == "Geno":
+ # tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=form_name, worksheet=worksheet)
#traitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=thisFormName, submit=HT.Input(type='hidden'))
hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','group':group}
hddn['incparentsf1']='ON'
- # for key in hddn.keys():
- # traitForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
- #
- # traitForm.append(HT.P(),pageTable)
- #
- # TD_LR.append(traitForm)
- # if len(self.results) > 1 and i < len(self.results) - 1:
- # last_result = True
- #if last_result:
- # TD_LR.contents.pop()
-
+
if self.dataset.type == "ProbeSet":
- tblobj['body'] = self.getTableBodyForProbeSet(trait_list=self.trait_list, formName=self.form_name, newrow=newrow, species=species)
+ tblobj['body'] = self.getTableBodyForProbeSet(trait_list=self.trait_list, formName=self.form_name, species=species)
elif self.dataset.type == "Publish":
- tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=mainfmName, worksheet=worksheet, newrow=newrow, species=species)
+ tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=self.form_name, species=species)
elif self.dataset.type == "Geno":
- tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=form_name, worksheet=worksheet, newrow=newrow)
+ tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=self.form_name)
def search(self):
print("fd.search_terms:", self.fd['search_terms'])
self.search_terms = parser.parse(self.fd['search_terms'])
print("After parsing:", self.search_terms)
-
+
self.results = []
for a_search in self.search_terms:
print("[kodak] item is:", pf(a_search))
search_term = a_search['search_term']
- search_type = string.upper(a_search['key'])
- if not search_type:
+ if a_search['key']:
+ search_type = string.upper(a_search['key'])
+ else:
# We fall back to the dataset type as the key to get the right object
- search_type = self.dataset.type
+ search_type = self.dataset.type
+
+ # This is throwing an error when a_search['key'] is None, so I changed above
+ #search_type = string.upper(a_search['key'])
+ #if not search_type:
+ # # We fall back to the dataset type as the key to get the right object
+ # search_type = self.dataset.type
search_ob = do_search.DoSearch.get_search(search_type)
search_class = getattr(do_search, search_ob)
@@ -289,26 +282,9 @@ class SearchResultPage(templatePage):
keyword = string.replace(keyword,"?",".")
wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]'
return wildcardkeyword
+
-
- def getTableHeaderForGeno(self, worksheet=None, newrow=None, headingStyle=None):
-
- tblobj_header = []
-
- className = "fs13 fwb ffl b1 cw cbrb"
-
- tblobj_header = [[THCell(HT.TD(' ', Class=className), sort=0),
- THCell(HT.TD('Record', HT.BR(), 'ID', HT.BR(), Class=className), text='record_id', idx=1),
- THCell(HT.TD('Location', HT.BR(), 'Chr and Mb', HT.BR(), Class=className), text='location', idx=2)]]
-
- for ncol, item in enumerate(['Record ID', 'Location (Chr, Mb)']):
- worksheet.write([newrow, ncol], item, headingStyle)
- worksheet.set_column([ncol, ncol], 2*len(item))
-
- return tblobj_header
-
-
- def getTableBodyForGeno(self, trait_list, formName=None, worksheet=None, newrow=None):
+ def getTableBodyForGeno(self, trait_list, formName=None):
tblobj_body = []
@@ -345,15 +321,13 @@ class SearchResultPage(templatePage):
tblobj_body.append(tr)
- for ncol, item in enumerate([this_trait.name, trait_location_repr]):
- worksheet.write([newrow, ncol], item)
-
- newrow += 1
+ #for ncol, item in enumerate([this_trait.name, trait_location_repr]):
+ # worksheet.write([newrow, ncol], item)
return tblobj_body
-
- def getTableBodyForPublish(self, trait_list, formName=None, worksheet=None, newrow=None, species=''):
+
+ def getTableBodyForPublish(self, trait_list, formName=None, species=''):
tblobj_body = []
@@ -438,15 +412,13 @@ class SearchResultPage(templatePage):
tblobj_body.append(tr)
- for ncol, item in enumerate([this_trait.name, PhenotypeString, this_trait.authors, this_trait.year, this_trait.pubmed_id, LRS_score_repr, LRS_location_repr]):
- worksheet.write([newrow, ncol], item)
-
- newrow += 1
+ #for ncol, item in enumerate([this_trait.name, PhenotypeString, this_trait.authors, this_trait.year, this_trait.pubmed_id, LRS_score_repr, LRS_location_repr]):
+ # worksheet.write([newrow, ncol], item)
return tblobj_body
- def getTableBodyForProbeSet(self, trait_list=None, primaryTrait=None, formName=None, worksheet=None, newrow=None, species=''):
+ def getTableBodyForProbeSet(self, trait_list=None, primaryTrait=None, formName=None, species=''):
# Note: setting trait_list to [] is probably not a great idea.
tblobj_body = []
@@ -590,8 +562,6 @@ class SearchResultPage(templatePage):
tblobj_body.append(tr)
- newrow += 1
-
return tblobj_body
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-28 00:50:21 +0000