diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/mrna_assay_tissue_data.py | 42 | ||||
| -rwxr-xr-x | wqflask/base/species.py | 38 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 44 | ||||
| -rwxr-xr-x | wqflask/base/webqtlCaseData.py | 6 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 2 |
5 files changed, 66 insertions, 66 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index ba82057a..039f5d1f 100755 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -12,30 +12,30 @@ from MySQLdb import escape_string as escape from pprint import pformat as pf class MrnaAssayTissueData(object): - + def __init__(self, gene_symbols=None): self.gene_symbols = gene_symbols self.have_data = False if self.gene_symbols == None: self.gene_symbols = [] - + #print("self.gene_symbols:", self.gene_symbols) - + self.data = collections.defaultdict(Bunch) - + #self.gene_id_dict ={} #self.data_id_dict = {} #self.chr_dict = {} #self.mb_dict = {} #self.desc_dict = {} #self.probe_target_desc_dict = {} - + query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description from ( select Symbol, max(Mean) as maxmean from TissueProbeSetXRef where TissueProbeSetFreezeId=1 and ''' - + # Note that inner join is necessary in this query to get distinct record in one symbol group # with highest mean value # Due to the limit size of TissueProbeSetFreezeId table in DB, @@ -43,11 +43,11 @@ class MrnaAssayTissueData(object): if len(gene_symbols) == 0: query += '''Symbol!='' and Symbol Is Not Null group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol - and t.Mean = x.maxmean; + and t.Mean = x.maxmean; ''' else: in_clause = db_tools.create_in_clause(gene_symbols) - + #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower query += ''' Symbol in {} group by Symbol) @@ -56,7 +56,7 @@ class MrnaAssayTissueData(object): '''.format(in_clause) results = g.db.execute(query).fetchall() - + lower_symbols = [] for gene_symbol in gene_symbols: if gene_symbol != None: @@ -68,7 +68,7 @@ class MrnaAssayTissueData(object): if symbol.lower() in lower_symbols: #gene_symbols.append(symbol) symbol = symbol.lower() - + self.data[symbol].gene_id = result.GeneId self.data[symbol].data_id = result.DataId self.data[symbol].chr = result.Chr @@ -85,21 +85,21 @@ class MrnaAssayTissueData(object): #function: get one dictionary whose key is gene symbol and value is tissue expression data (list type). #Attention! All keys are lower case! ########################################################################### - + def get_symbol_values_pairs(self): id_list = [self.data[symbol].data_id for symbol in self.data] print("id_list:", id_list) symbol_values_dict = {} - + query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value FROM TissueProbeSetXRef, TissueProbeSetData WHERE TissueProbeSetData.Id IN {} and TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list)) - + print("TISSUE QUERY:", query) - + results = g.db.execute(query).fetchall() for result in results: if result.Symbol.lower() not in symbol_values_dict: @@ -110,11 +110,11 @@ class MrnaAssayTissueData(object): #for symbol in self.data: # data_id = self.data[symbol].data_id # symbol_values_dict[symbol] = self.get_tissue_values(data_id) - - + + return symbol_values_dict - - + + #def get_tissue_values(self, data_id): # """Gets the tissue values for a particular gene""" # @@ -133,7 +133,7 @@ class MrnaAssayTissueData(object): # # symbol_values_pairs[symbol] = None # # return tissue_values - + ######################################################################################################## #input: cursor, symbolList (list), dataIdDict(Dict): key is symbol #output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair. @@ -154,7 +154,7 @@ class MrnaAssayTissueData(object): # #descDict, # #pTargetDescDict = getTissueProbeSetXRefInfo( # # GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId) -# +# # if len(tissue_data.gene_symbols): # return get_symbol_values_pairs(tissue_data) - + diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 52bd8297..79d867c8 100755 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -24,21 +24,21 @@ class TheSpecies(object): # for counter, genotype in enumerate(self.dataset.group.genotype): # if len(genotype) > 1: # chromosomes.append((genotype.name, counter)) - # - # print("chromosomes is: ", pf(chromosomes)) - # + # + # print("chromosomes is: ", pf(chromosomes)) + # # return chromosomes class IndChromosome(object): def __init__(self, name, length): self.name = name self.length = length - + @property def mb_length(self): """Chromosome length in megabases""" return self.length / 1000000 - + def set_cm_length(self, genofile_chr): self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM @@ -61,19 +61,19 @@ class Chromosomes(object): for item in results: self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) - + self.set_mb_graph_interval() #self.get_cm_length_list() def set_mb_graph_interval(self): """Empirical megabase interval""" - + if self.chromosomes: self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) else: self.mb_graph_interval = 1 - + #if self.chromosomes: #assert self.chromosomes, "Have to add some code back in apparently to set it to 1" #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) @@ -94,30 +94,30 @@ class Chromosomes(object): def get_cm_length_list(self): """Chromosome length in centimorgans - + Calculates the length in centimorgans by subtracting the centimorgan position of the last marker in a chromosome by the position of the first marker - + """ - + self.dataset.group.read_genotype_file() - + self.cm_length_list = [] - + for chromosome in self.dataset.group.genotype: self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM) - + print("self.cm_length_list:", pf(self.cm_length_list)) - + assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!" for counter, chromosome in enumerate(self.chromosomes.values()): chromosome.cm_length = self.cm_length_list[counter] #self.chromosomes[counter].cm_length = item - + for key, value in self.chromosomes.items(): print("bread - %s: %s" % (key, pf(vars(value)))) - -# Testing -#if __name__ == '__main__': + +# Testing +#if __name__ == '__main__': # foo = dict(bar=dict(length))
\ No newline at end of file diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index a71d8157..b51b8c72 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -69,11 +69,11 @@ class GeneralTrait(object): self.retrieve_info(get_qtl_info=get_qtl_info) if get_sample_info != False: self.retrieve_sample_data() - - + + def jsonable(self): """Return a dict suitable for using as json - + Actual turning into json doesn't happen here though""" return dict(name=self.name, dataset=self.dataset.name, @@ -258,10 +258,10 @@ class GeneralTrait(object): PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND PublishFreeze.Id = %s """ % (self.name, self.dataset.id) - + trait_info = g.db.execute(query).fetchone() - - + + #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms. elif self.dataset.type == 'ProbeSet': @@ -310,27 +310,27 @@ class GeneralTrait(object): if isinstance(trait_info[i], basestring): holder = unicode(trait_info[i], "utf8", "ignore") setattr(self, field, holder) - + if self.dataset.type == 'Publish': self.confidential = 0 if self.pre_publication_description and not self.pubmed_id: self.confidential = 1 - + description = self.post_publication_description - + #If the dataset is confidential and the user has access to confidential #phenotype traits, then display the pre-publication description instead #of the post-publication description if self.confidential: self.description_display = "" - + #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( # privilege=self.dataset.privilege, # userName=self.dataset.userName, # authorized_users=self.authorized_users): - # + # # description = self.pre_publication_description - + if description: self.description_display = description.strip() else: @@ -343,8 +343,8 @@ class GeneralTrait(object): if self.pubmed_id: self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id - - + + self.homologeneid = None if self.dataset.type == 'ProbeSet' and self.dataset.group: if self.geneid: @@ -374,7 +374,7 @@ class GeneralTrait(object): if result: self.homologeneid = result[0] - + description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') @@ -410,7 +410,7 @@ class GeneralTrait(object): #ZS: Put this in function currently called "convert_location_to_value" self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) self.location_value = trait_location_value - + if get_qtl_info: #LRS and its location @@ -481,7 +481,7 @@ class GeneralTrait(object): self.locus = self.locus_chr = self.locus_mb = self.additive = "" else: self.locus = self.lrs = self.additive = "" - + if (self.dataset.type == 'Publish' or self.dataset.type == "ProbeSet") and self.locus_chr != "" and self.locus_mb != "": #XZ: LRS_location_value is used for sorting try: @@ -493,7 +493,7 @@ class GeneralTrait(object): LRS_location_value = ord(str(self.locus_chr).upper()[0])*1000 + float(self.locus_mb) self.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (self.locus_chr, float(self.locus_mb)) - if self.lrs != "": + if self.lrs != "": self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs self.LRS_score_value = LRS_score_value = self.lrs else: @@ -712,7 +712,7 @@ def convert_location_to_value(chromosome, mb): else: location_value = (ord(str(chromosome).upper()[0])*1000 + float(mb)) - + return location_value @app.route("/trait/get_sample_data") @@ -720,11 +720,11 @@ def get_sample_data(): params = request.args trait = params['trait'] dataset = params['dataset'] - + trait_ob = GeneralTrait(name=trait, dataset_name=dataset) - + return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }]) - + #jsonable_sample_data = {} #for sample in trait_ob.data.iteritems(): # jsonable_sample_data[sample] = trait_ob.data[sample].value diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 99a34866..411b0d24 100755 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -48,7 +48,7 @@ class webqtlCaseData(object): if self.num_cases != None: str += " ndata=%d" % self.num_cases return str - + @property def class_outlier(self): """Template helper""" @@ -56,14 +56,14 @@ class webqtlCaseData(object): return "outlier" else: return "" - + @property def display_value(self): if self.value: return "%2.3f" % self.value else: return "x" - + @property def display_variance(self): if self.variance: diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index f6140ac3..f76d8140 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -5,7 +5,7 @@ # scripts. But rather than migrating everything in one go, we'll # take it a step at a time. First the hard coded paths get replaced # with those in utility/tools.py -# +# ######################################### from utility.tools import valid_path, mk_dir, assert_dir, flat_files, TEMPDIR |