diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r--[-rwxr-xr-x] | wqflask/base/trait.py | 243 |
1 files changed, 155 insertions, 88 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index ff80795c..a71d8157 100755..100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -2,7 +2,7 @@ from __future__ import absolute_import, division, print_function import string import resource - +import codecs from htmlgen import HTMLgen2 as HT @@ -31,16 +31,16 @@ class GeneralTrait(object): """ - def __init__(self, get_qtl_info=False, **kw): + def __init__(self, get_qtl_info=False, get_sample_info=True, **kw): # xor assertion assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; if kw.get('dataset_name'): self.dataset = create_dataset(kw.get('dataset_name')) - print(" in GeneralTrait created dataset:", self.dataset) + #print(" in GeneralTrait created dataset:", self.dataset) else: self.dataset = kw.get('dataset') self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. - print("THE NAME IS:", self.name) + #print("THE NAME IS:", self.name) self.cellid = kw.get('cellid') self.identification = kw.get('identification', 'un-named trait') self.haveinfo = kw.get('haveinfo', False) @@ -67,7 +67,8 @@ class GeneralTrait(object): # Todo: These two lines are necessary most of the time, but perhaps not all of the time # So we could add a simple if statement to short-circuit this if necessary self.retrieve_info(get_qtl_info=get_qtl_info) - self.retrieve_sample_data() + if get_sample_info != False: + self.retrieve_sample_data() def jsonable(self): @@ -179,13 +180,15 @@ class GeneralTrait(object): samples = [] vals = [] the_vars = [] + sample_aliases = [] for sample_name, sample_data in self.data.items(): if sample_data.value != None: if not include_variance or sample_data.variance != None: samples.append(sample_name) vals.append(sample_data.value) the_vars.append(sample_data.variance) - return samples, vals, the_vars + sample_aliases.append(sample_data.name2) + return samples, vals, the_vars, sample_aliases # @@ -220,32 +223,6 @@ class GeneralTrait(object): if samplelist == None: samplelist = [] - #assert self.dataset - - #if self.cellid: - # #Probe Data - # query = ''' - # SELECT - # Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id - # FROM - # (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, - # Strain, Probe, ProbeSet) - # left join ProbeSE on - # (ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId) - # WHERE - # Probe.Name = '%s' AND ProbeSet.Name = '%s' AND - # Probe.ProbeSetId = ProbeSet.Id AND - # ProbeXRef.ProbeId = Probe.Id AND - # ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND - # ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND - # ProbeSetFreeze.Name = '%s' AND - # ProbeXRef.DataId = ProbeData.Id AND - # ProbeData.StrainId = Strain.Id - # Order BY - # Strain.Name - # ''' % (self.cellid, self.name, self.dataset.name) - # - #else: results = self.dataset.retrieve_sample_data(self.name) # Todo: is this necessary? If not remove @@ -255,19 +232,10 @@ class GeneralTrait(object): if results: for item in results: - name, value, variance, num_cases = item + name, value, variance, num_cases, name2 = item if not samplelist or (samplelist and name in samplelist): self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) - #def keys(self): - # return self.__dict__.keys() - # - #def has_key(self, key): - # return self.__dict__.has_key(key) - # - #def items(self): - # return self.__dict__.items() - def retrieve_info(self, get_qtl_info=False): assert self.dataset, "Dataset doesn't exist" if self.dataset.type == 'Publish': @@ -290,10 +258,10 @@ class GeneralTrait(object): PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND PublishFreeze.Id = %s """ % (self.name, self.dataset.id) - - print("query is:", query) 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': @@ -328,7 +296,6 @@ class GeneralTrait(object): escape(self.dataset.name), escape(self.name)) trait_info = g.db.execute(query).fetchone() - #print("trait_info is: ", pf(trait_info)) else: #Temp type query = """SELECT %s FROM %s WHERE Name = %s""" trait_info = g.db.execute(query, @@ -339,54 +306,118 @@ class GeneralTrait(object): #XZ: assign SQL query result to trait attributes. for i, field in enumerate(self.dataset.display_fields): - #print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i])) holder = trait_info[i] 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: + self.description_display = "" - self.homologeneid = None - - #print("self.geneid is:", self.geneid) - #print(" type:", type(self.geneid)) - #print("self.dataset.group.name is:", self.dataset.group.name) - if self.dataset.type == 'ProbeSet' and self.dataset.group and self.geneid: - #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. - #XZ: So I have to test if geneid is number before execute the query. - #XZ: The geneid values in database should be cleaned up. - #try: - # float(self.geneid) - # geneidIsNumber = True - #except ValueError: - # geneidIsNumber = False - - #if geneidIsNumber: - - - query = """ - SELECT - HomologeneId - FROM - Homologene, Species, InbredSet - WHERE - Homologene.GeneId =%s AND - InbredSet.Name = '%s' AND - InbredSet.SpeciesId = Species.Id AND - Species.TaxonomyId = Homologene.TaxonomyId - """ % (escape(str(self.geneid)), escape(self.dataset.group.name)) - result = g.db.execute(query).fetchone() - #else: - # result = None + if not self.year.isdigit(): + self.pubmed_text = "N/A" + else: + self.pubmed_text = self.year - if result: - self.homologeneid = result[0] + 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: + #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. + #XZ: So I have to test if geneid is number before execute the query. + #XZ: The geneid values in database should be cleaned up. + #try: + # float(self.geneid) + # geneidIsNumber = True + #except ValueError: + # geneidIsNumber = False + #if geneidIsNumber: + query = """ + SELECT + HomologeneId + FROM + Homologene, Species, InbredSet + WHERE + Homologene.GeneId =%s AND + InbredSet.Name = '%s' AND + InbredSet.SpeciesId = Species.Id AND + Species.TaxonomyId = Homologene.TaxonomyId + """ % (escape(str(self.geneid)), escape(self.dataset.group.name)) + result = g.db.execute(query).fetchone() + #else: + # result = None + + 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') + + if len(description_string) > 1 and description_string != 'None': + description_display = description_string + else: + description_display = self.symbol + + if (len(description_display) > 1 and description_display != 'N/A' and + len(target_string) > 1 and target_string != 'None'): + description_display = description_display + '; ' + target_string.strip() + + # Save it for the jinja2 template + self.description_display = description_display + + #XZ: trait_location_value is used for sorting + trait_location_repr = 'N/A' + trait_location_value = 1000000 + + if self.chr and self.mb: + #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") + #This is so we can convert the location to a number used for sorting + trait_location_value = convert_location_to_value(self.chr, self.mb) + #try: + # trait_location_value = int(self.chr)*1000 + self.mb + #except ValueError: + # if self.chr.upper() == 'X': + # trait_location_value = 20*1000 + self.mb + # else: + # trait_location_value = (ord(str(self.chr).upper()[0])*1000 + + # self.mb) + + #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 + self.LRS_score_repr = "N/A" + self.LRS_score_value = 0 + self.LRS_location_repr = "N/A" + self.LRS_location_value = 1000000 if self.dataset.type == 'ProbeSet' and not self.cellid: query = """ SELECT @@ -399,12 +430,8 @@ class GeneralTrait(object): ProbeSetXRef.ProbeSetFreezeId ={} """.format(self.name, self.dataset.id) trait_qtl = g.db.execute(query).fetchone() - #self.cursor.execute(query) - #trait_qtl = self.cursor.fetchone() if trait_qtl: - print("trait_qtl:", trait_qtl) self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl - print("self.locus:", self.locus) if self.locus: query = """ select Geno.Chr, Geno.Mb from Geno, Species @@ -417,9 +444,9 @@ class GeneralTrait(object): self.locus_chr = result[0] self.locus_mb = result[1] else: - self.locus = self.locus_chr = self.locus_mb = "" + self.locus = self.locus_chr = self.locus_mb = self.additive = "" else: - self.locus = self.locus_chr = self.locus_mb = "" + self.locus = self.locus_chr = self.locus_mb = self.additive = "" else: self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = self.additive = "" @@ -437,8 +464,38 @@ class GeneralTrait(object): """, (self.name, self.dataset.id)).fetchone() if trait_qtl: self.locus, self.lrs, self.additive = trait_qtl + if self.locus: + query = """ + select Geno.Chr, Geno.Mb from Geno, Species + where Species.Name = '{}' and + Geno.Name = '{}' and + Geno.SpeciesId = Species.Id + """.format(self.dataset.group.species, self.locus) + result = g.db.execute(query).fetchone() + if result: + self.locus_chr = result[0] + self.locus_mb = result[1] + else: + self.locus = self.locus_chr = self.locus_mb = self.additive = "" + else: + 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: + LRS_location_value = int(self.locus_chr)*1000 + float(self.locus_mb) + except: + if self.locus_chr.upper() == 'X': + LRS_location_value = 20*1000 + float(self.locus_mb) + else: + 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 != "": + self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs + self.LRS_score_value = LRS_score_value = self.lrs else: raise KeyError, `self.name`+' information is not found in the database.' @@ -646,7 +703,17 @@ class GeneralTrait(object): ZValue = ZValue*sqrt(self.overlap-3) self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue))) - +def convert_location_to_value(chromosome, mb): + try: + location_value = int(chromosome)*1000 + float(mb) + except ValueError: + if chromosome.upper() == 'X': + location_value = 20*1000 + float(mb) + else: + location_value = (ord(str(chromosome).upper()[0])*1000 + + float(mb)) + + return location_value @app.route("/trait/get_sample_data") def get_sample_data(): |