diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 67 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/input.py | 181 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 79 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pylmmKinship.py | 108 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 28 |
5 files changed, 267 insertions, 196 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 2e74d991..1b1b56fb 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -58,6 +58,7 @@ class DoSearch(object): @classmethod def get_search(cls, search_type): + print("search_types are:", pf(cls.search_types)) return cls.search_types[search_type] class QuickMrnaAssaySearch(DoSearch): @@ -66,9 +67,10 @@ class QuickMrnaAssaySearch(DoSearch): DoSearch.search_types['quick_mrna_assay'] = "QuickMrnaAssaySearch" base_query = """SELECT ProbeSet.Name as ProbeSet_Name, + ProbeSet.Symbol as ProbeSet_Symbol, + ProbeSet.description as ProbeSet_Description, ProbeSet.Chr_num as ProbeSet_Chr_Num, ProbeSet.Mb as ProbeSet_Mb, - ProbeSet.Symbol as ProbeSet_Symbol, ProbeSet.name_num as ProbeSet_name_num FROM ProbeSet """ @@ -76,14 +78,15 @@ class QuickMrnaAssaySearch(DoSearch): 'Record ID', 'Symbol', 'Location'] - + def run(self): """Generates and runs a search for assays across all mRNA expression datasets""" print("Running ProbeSetSearch") query = self.base_query + """WHERE (MATCH (ProbeSet.Name, ProbeSet.description, - ProbeSet.symbol) + ProbeSet.symbol, + ProbeSet.alias) AGAINST ('%s' IN BOOLEAN MODE)) """ % (escape(self.search_term[0])) @@ -156,9 +159,7 @@ class MrnaAssaySearch(DoSearch): return self.execute(query) - -#class QuickPhenotypeSearch(DoSearch): - + class PhenotypeSearch(DoSearch): """A search within a phenotype dataset""" @@ -232,9 +233,57 @@ class PhenotypeSearch(DoSearch): query = self.compile_final_query(where_clause = self.get_fields_clause()) - results = self.execute(query) - print("in [df] run results are:", results) - return results + return self.execute(query) + +class QuickPhenotypeSearch(PhenotypeSearch): + """A search across all phenotype datasets""" + + DoSearch.search_types['quick_phenotype'] = "QuickPhenotypeSearch" + + base_query = """SELECT Species.Name as Species_Name, + PublishFreeze.FullName as Dataset_Name, + PublishFreeze.Name, + 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, + InbredSet, + Species """ + + search_fields = ('Phenotype.Post_publication_description', + 'Phenotype.Pre_publication_description', + 'Phenotype.Pre_publication_abbreviation', + 'Phenotype.Post_publication_abbreviation', + 'Phenotype.Lab_code', + 'Publication.PubMed_ID', + 'Publication.Abstract', + 'Publication.Title', + 'Publication.Authors') + + def compile_final_query(self, where_clause = ''): + """Generates the final query string""" + + query = (self.base_query + + """WHERE %s + PublishXRef.PhenotypeId = Phenotype.Id and + PublishXRef.PublicationId = Publication.Id and + PublishXRef.InbredSetId = InbredSet.Id and + InbredSet.SpeciesId = Species.Id""" % where_clause) + + print("query is:", pf(query)) + + return query + + def run(self): + """Generates and runs a search across all phenotype datasets""" + + query = self.compile_final_query(where_clause = self.get_fields_clause()) + + return self.execute(query) class GenotypeSearch(DoSearch): """A search within a genotype dataset""" diff --git a/wqflask/wqflask/my_pylmm/pyLMM/input.py b/wqflask/wqflask/my_pylmm/pyLMM/input.py index 33666a0d..b8b76fd0 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/input.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/input.py @@ -1,20 +1,25 @@ # pylmm is a python-based linear mixed-model solver with applications to GWAS # Copyright (C) 2013 Nicholas A. Furlotte (nick.furlotte@gmail.com) -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU Affero General Public License as -# published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. - -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU Affero General Public License for more details. - -# You should have received a copy of the GNU Affero General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. +#The program is free for academic use. Please contact Nick Furlotte +#<nick.furlotte@gmail.com> if you are interested in using the software for +#commercial purposes. + +#The software must not be modified and distributed without prior +#permission of the author. + +#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +#A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR +#CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +#EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +#PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +#PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +#LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +#NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. import os import sys @@ -24,7 +29,6 @@ import pdb class plink: def __init__(self,fbase,kFile=None,phenoFile=None,type='b',normGenotype=True,readKFile=False): - self.fbase = fbase self.type = type self.indivs = self.getIndivs(self.fbase,type) @@ -33,34 +37,33 @@ class plink: self.normGenotype = normGenotype self.phenoFile = phenoFile # Originally I was using the fastLMM style that has indiv IDs embedded. - # NOW I want to use this module to just read SNPs so I'm allowing + # NOW I want to use this module to just read SNPs so I'm allowing # the programmer to turn off the kinship reading. self.readKFile = readKFile - - if self.kFile: - self.kFile = kFile - if self.readKFile: self.K = self.readKinship(self.kFile) - elif os.path.isfile("%s.kin" % fbase): + + if self.kFile: self.K = self.readKinship(self.kFile) + elif os.path.isfile("%s.kin" % fbase): self.kFile = "%s.kin" %fbase - if self.readKFile: self.K = self.readKinship(self.kFile) - else: + if self.readKFile: + self.K = self.readKinship(self.kFile) + else: self.kFile = None self.K = None - + self.getPhenos(self.phenoFile) - + self.fhandle = None self.snpFileHandle = None - - def __del__(self): + + def __del__(self): if self.fhandle: self.fhandle.close() if self.snpFileHandle: self.snpFileHandle.close() - + def getSNPIterator(self): - if not self.type == 'b': + if not self.type == 'b': sys.stderr.write("Have only implemented this for binary plink files (bed)\n") return - + # get the number of snps file = self.fbase + '.bim' i = 0 @@ -70,30 +73,32 @@ class plink: self.numSNPs = i self.have_read = 0 self.snpFileHandle = open(file,'r') - + self.BytestoRead = self.N / 4 + (self.N % 4 and 1 or 0) self._formatStr = 'c'*self.BytestoRead - + file = self.fbase + '.bed' self.fhandle = open(file,'rb') - + magicNumber = self.fhandle.read(2) order = self.fhandle.read(1) - if not order == '\x01': + if not order == '\x01': sys.stderr.write("This is not in SNP major order - you did not handle this case\n") raise StopIteration - + return self - - def __iter__(self): return self.getSNPIterator() - + + def __iter__(self): + return self.getSNPIterator() + def next(self): - if self.have_read == self.numSNPs: raise StopIteration + if self.have_read == self.numSNPs: + raise StopIteration X = self.fhandle.read(self.BytestoRead) XX = [bin(ord(x)) for x in struct.unpack(self._formatStr,X)] self.have_read += 1 return self.formatBinaryGenotypes(XX,self.normGenotype),self.snpFileHandle.readline().strip().split()[1] - + def formatBinaryGenotypes(self,X,norm=True): D = { \ '00': 0.0, \ @@ -101,41 +106,45 @@ class plink: '11': 1.0, \ '01': np.nan \ } - + D_tped = { \ '00': '1 1', \ '10': '1 2', \ '11': '2 2', \ '01': '0 0' \ } - + #D = D_tped - + G = [] for x in X: if not len(x) == 10: xx = x[2:] x = '0b' + '0'*(8 - len(xx)) + xx - a,b,c,d = (x[8:],x[6:8],x[4:6],x[2:4]) + a,b,c,d = (x[8:],x[6:8],x[4:6],x[2:4]) L = [D[y] for y in [a,b,c,d]] G += L # only take the leading values because whatever is left should be null G = G[:self.N] G = np.array(G) - if norm: G = self.normalizeGenotype(G) + if norm: + G = self.normalizeGenotype(G) return G - + def normalizeGenotype(self,G): x = True - np.isnan(G) m = G[x].mean() s = np.sqrt(G[x].var()) G[np.isnan(G)] = m - G = (G - m) / s + if s == 0: G = G - m + else: G = (G - m) / s + return G - + def getPhenos(self,phenoFile=None): - if not phenoFile: self.phenoFile = phenoFile = self.fbase+".phenos" - if not os.path.isfile(phenoFile): + if not phenoFile: + self.phenoFile = phenoFile = self.fbase+".phenos" + if not os.path.isfile(phenoFile): sys.stderr.write("Could not find phenotype file: %s\n" % (phenoFile)) return f = open(phenoFile,'r') @@ -147,81 +156,86 @@ class plink: P.append([(x == 'NA' or x == '-9') and np.nan or float(x) for x in v[2:]]) f.close() P = np.array(P) - + # reorder to match self.indivs D = {} L = [] for i in range(len(keys)): D[keys[i]] = i for i in range(len(self.indivs)): - if not D.has_key(self.indivs[i]): continue + if not D.has_key(self.indivs[i]): + continue L.append(D[self.indivs[i]]) P = P[L,:] - + self.phenos = P return P - + def getIndivs(self,base,type='b'): - if type == 't': famFile = "%s.tfam" % base - else: famFile = "%s.fam" % base - + if type == 't': + famFile = "%s.tfam" % base + else: + famFile = "%s.fam" % base keys = [] i = 0 f = open(famFile,'r') for line in f: - v = line.strip().split() - famId = v[0] - indivId = v[1] - k = (famId.strip(),indivId.strip()) - keys.append(k) - i += 1 + v = line.strip().split() + famId = v[0] + indivId = v[1] + k = (famId.strip(),indivId.strip()) + keys.append(k) + i += 1 f.close() - + self.N = len(keys) sys.stderr.write("Read %d individuals from %s\n" % (self.N, famFile)) - + return keys - + def readKinship(self,kFile): # Assume the fastLMM style # This will read in the kinship matrix and then reorder it - # according to self.indivs - additionally throwing out individuals + # according to self.indivs - additionally throwing out individuals # that are not in both sets if self.indivs == None or len(self.indivs) == 0: sys.stderr.write("Did not read any individuals so can't load kinship\n") - return - + return + sys.stderr.write("Reading kinship matrix from %s\n" % (kFile) ) - + f = open(kFile,'r') - # read indivs + # read indivs v = f.readline().strip().split("\t")[1:] keys = [tuple(y.split()) for y in v] D = {} for i in range(len(keys)): D[keys[i]] = i - + # read matrix K = [] - for line in f: K.append([float(x) for x in line.strip().split("\t")[1:]]) + for line in f: + K.append([float(x) for x in line.strip().split("\t")[1:]]) f.close() K = np.array(K) - + # reorder to match self.indivs L = [] KK = [] X = [] for i in range(len(self.indivs)): - if not D.has_key(self.indivs[i]): X.append(self.indivs[i]) - else: + if not D.has_key(self.indivs[i]): + X.append(self.indivs[i]) + else: KK.append(self.indivs[i]) L.append(D[self.indivs[i]]) K = K[L,:][:,L] self.indivs = KK self.indivs_removed = X - if len(self.indivs_removed): sys.stderr.write("Removed %d individuals that did not appear in Kinship\n" % (len(self.indivs_removed))) - return K - + if len(self.indivs_removed): + sys.stderr.write("Removed %d individuals that did not appear in Kinship\n" % (len(self.indivs_removed))) + return K + def getCovariates(self,covFile=None): - if not os.path.isfile(covFile): + if not os.path.isfile(covFile): sys.stderr.write("Could not find covariate file: %s\n" % (phenoFile)) return f = open(covFile,'r') @@ -233,14 +247,15 @@ class plink: P.append([x == 'NA' and np.nan or float(x) for x in v[2:]]) f.close() P = np.array(P) - + # reorder to match self.indivs D = {} L = [] - for i in range(len(keys)): D[keys[i]] = i + for i in range(len(keys)): + D[keys[i]] = i for i in range(len(self.indivs)): - if not D.has_key(self.indivs[i]): continue + if not D.has_key(self.indivs[i]): continue L.append(D[self.indivs[i]]) P = P[L,:] - + return P \ No newline at end of file diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 1e689e49..7ed0f3e5 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -26,46 +26,51 @@ from scipy import stats from pprint import pformat as pf -from utility.benchmark import Bench - -#np.seterr('raise') - -def run(pheno_vector, - genotype_matrix, - restricted_max_likelihood=True, - refit=False, - temp_data=None): - """Takes the phenotype vector and genotype matrix and returns a set of p-values and t-statistics - - restricted_max_likelihood -- whether to use restricted max likelihood; True or False - refit -- whether to refit the variance component for each marker - temp_data -- TempData object that stores the progress for each major step of the - calculations ("calculate_kinship" and "GWAS" take the majority of time) - - """ - - with Bench("Calculate Kinship"): - kinship_matrix = calculate_kinship(genotype_matrix, temp_data) - - with Bench("Create LMM object"): - lmm_ob = LMM(pheno_vector, kinship_matrix) - - with Bench("LMM_ob fitting"): - lmm_ob.fit() - - with Bench("Doing GWAS"): - t_stats, p_values = GWAS(pheno_vector, - genotype_matrix, - kinship_matrix, - restricted_max_likelihood=True, - refit=False, - temp_data=temp_data) - Bench().report() - return t_stats, p_values +#from utility.benchmark import Bench +# +##np.seterr('raise') +# +#def run(pheno_vector, +# genotype_matrix, +# restricted_max_likelihood=True, +# refit=False, +# temp_data=None): +# """Takes the phenotype vector and genotype matrix and returns a set of p-values and t-statistics +# +# restricted_max_likelihood -- whether to use restricted max likelihood; True or False +# refit -- whether to refit the variance component for each marker +# temp_data -- TempData object that stores the progress for each major step of the +# calculations ("calculate_kinship" and "GWAS" take the majority of time) +# +# """ +# +# with Bench("Calculate Kinship"): +# kinship_matrix = calculate_kinship(genotype_matrix, temp_data) +# +# with Bench("Create LMM object"): +# lmm_ob = LMM(pheno_vector, kinship_matrix) +# +# with Bench("LMM_ob fitting"): +# lmm_ob.fit() +# +# with Bench("Doing GWAS"): +# t_stats, p_values = GWAS(pheno_vector, +# genotype_matrix, +# kinship_matrix, +# restricted_max_likelihood=True, +# refit=False, +# temp_data=temp_data) +# Bench().report() +# return t_stats, p_values def matrixMult(A,B): - #return np.dot(A,B) + + # If there is no fblas then we will revert to np.dot() + try: + linalg.fblas + except AttributeError: + return np.dot(A,B) print("A is:", pf(A.shape)) print("B is:", pf(B.shape)) diff --git a/wqflask/wqflask/my_pylmm/pylmmKinship.py b/wqflask/wqflask/my_pylmm/pylmmKinship.py index db1449a4..cfba2936 100644 --- a/wqflask/wqflask/my_pylmm/pylmmKinship.py +++ b/wqflask/wqflask/my_pylmm/pylmmKinship.py @@ -3,19 +3,25 @@ # pylmm is a python-based linear mixed-model solver with applications to GWAS # Copyright (C) 2013 Nicholas A. Furlotte (nick.furlotte@gmail.com) -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU Affero General Public License as -# published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU Affero General Public License for more details. - -# You should have received a copy of the GNU Affero General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. +#The program is free for academic use. Please contact Nick Furlotte +#<nick.furlotte@gmail.com> if you are interested in using the software for +#commercial purposes. + +#The software must not be modified and distributed without prior +#permission of the author. + +#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +#A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR +#CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +#EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +#PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +#PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +#LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +#NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +#SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. from optparse import OptionParser,OptionGroup usage = """usage: %prog [options] --[t | b | p]file plinkFileBase outfile @@ -28,38 +34,25 @@ parser = OptionParser(usage=usage) basicGroup = OptionGroup(parser, "Basic Options") #advancedGroup = OptionGroup(parser, "Advanced Options") -basicGroup.add_option("--pfile", - dest="pfile", - help="The base for a PLINK ped file") -basicGroup.add_option("--tfile", - dest="tfile", - help="The base for a PLINK tped file") -basicGroup.add_option("--bfile", - dest="bfile", - help="The base for a PLINK binary ped file") - -basicGroup.add_option("-e", - "--efile", - dest="saveEig", - help="Save eigendecomposition to this file.") -basicGroup.add_option("-n", - default=1000, - dest="computeSize", - type="int", - help="""The maximum number of SNPs to read into memory at once (default 1000). - This is important when there is a large number of SNPs, because memory could - be an issue.""") +basicGroup.add_option("--pfile", dest="pfile", + help="The base for a PLINK ped file") +basicGroup.add_option("--tfile", dest="tfile", + help="The base for a PLINK tped file") +basicGroup.add_option("--bfile", dest="bfile", + help="The base for a PLINK binary ped file") + +basicGroup.add_option("-e", "--efile", dest="saveEig", help="Save eigendecomposition to this file.") +basicGroup.add_option("-n", default=1000,dest="computeSize", type="int", help="The maximum number of SNPs to read into memory at once (default 1000). This is important when there is a large number of SNPs, because memory could be an issue.") basicGroup.add_option("-v", "--verbose", - action="store_true", dest="verbose", default=False, - help="Print extra info") + action="store_true", dest="verbose", default=False, + help="Print extra info") parser.add_option_group(basicGroup) #parser.add_option_group(advancedGroup) (options, args) = parser.parse_args() -if len(args) != 1: - parser.error("Incorrect number of arguments") +if len(args) != 1: parser.error("Incorrect number of arguments") outFile = args[0] import sys @@ -72,16 +65,11 @@ from pyLMM import input if not options.pfile and not options.tfile and not options.bfile: parser.error("You must provide at least one PLINK input file base") -if options.verbose: - sys.stderr.write("Reading PLINK input...\n") -if options.bfile: - IN = input.plink(options.bfile,type='b') -elif options.tfile: - IN = input.plink(options.tfile,type='t') -elif options.pfile: - IN = input.plink(options.pfile,type='p') -else: - parser.error("You must provide at least one PLINK input file base") +if options.verbose: sys.stderr.write("Reading PLINK input...\n") +if options.bfile: IN = input.plink(options.bfile,type='b') +elif options.tfile: IN = input.plink(options.tfile,type='t') +elif options.pfile: IN = input.plink(options.pfile,type='p') +else: parser.error("You must provide at least one PLINK input file base") n = len(IN.indivs) m = options.computeSize @@ -98,32 +86,34 @@ while i < IN.numSNPs: i += 1 continue W[:,j] = snp - + i += 1 j += 1 - if j < options.computeSize: - W = W[:,range(0,j)] + if j < options.computeSize: W = W[:,range(0,j)] if options.verbose: sys.stderr.write("Processing first %d SNPs\n" % i) - if K == None: - K = linalg.fblas.dgemm(alpha=1.,a=W.T,b=W.T,trans_a=True,trans_b=False) # calculate_kinship(W) * j - #if K == None: - # K = np.dot(W,W.T) # calculate_kinship(W) * j + if K == None: + try: + K = linalg.fblas.dgemm(alpha=1.,a=W.T,b=W.T,trans_a=True,trans_b=False) # calculateKinship(W) * j + except AttributeError: + K = np.dot(W,W.T) else: - K_j = linalg.fblas.dgemm(alpha=1.,a=W.T,b=W.T,trans_a=True,trans_b=False) # calculate_kinship(W) * j + try: + K_j = linalg.fblas.dgemm(alpha=1.,a=W.T,b=W.T,trans_a=True,trans_b=False) # calculateKinship(W) * j + except AttributeError: + K_j = np.dot(W,W.T) K = K + K_j K = K / float(IN.numSNPs) -if options.verbose: - sys.stderr.write("Saving Kinship file to %s\n" % outFile) +if options.verbose: sys.stderr.write("Saving Kinship file to %s\n" % outFile) np.savetxt(outFile,K) if options.saveEig: if options.verbose: sys.stderr.write("Obtaining Eigendecomposition\n") - Kva, Kve = linalg.eigh(K) + Kva,Kve = linalg.eigh(K) if options.verbose: sys.stderr.write("Saving eigendecomposition to %s.[kva | kve]\n" % outFile) np.savetxt(outFile+".kva",Kva) - np.savetxt(outFile+".kve",Kve) \ No newline at end of file + np.savetxt(outFile+".kve",Kve) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 2d39a711..e1d81f37 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -104,15 +104,27 @@ class SearchResultPage(): self.search_terms = parser.parse(self.search_terms) print("After parsing:", self.search_terms) - for a_search in self.search_terms: - search_term = a_search['search_term'] - #Do mRNA assay search - search_ob = do_search.DoSearch.get_search("quick_mrna_assay") + search_types = ["quick_phenotype", "quick_mrna_assay"] + + for search_category in search_types: + search_ob = do_search.DoSearch.get_search(search_category) search_class = getattr(do_search, search_ob) - the_search = search_class(search_term) - - self.results.extend(the_search.run()) - print("in the search results are:", self.results) + for a_search in self.search_terms: + search_term = a_search['search_term'] + the_search = search_class(search_term) + self.results.extend(the_search.run()) + print("in the search results are:", self.results) + + #for a_search in self.search_terms: + # search_term = a_search['search_term'] + # + # #Do mRNA assay search + # search_ob = do_search.DoSearch.get_search("quick_mrna_assay") + # search_class = getattr(do_search, search_ob) + # the_search = search_class(search_term) + # + # self.results.extend(the_search.run()) + # print("in the search results are:", self.results) #return True |