diff options
26 files changed, 102 insertions, 102 deletions
diff --git a/scripts/maintenance/load_genotypes.py b/scripts/maintenance/load_genotypes.py index c235a31f..51278d48 100755 --- a/scripts/maintenance/load_genotypes.py +++ b/scripts/maintenance/load_genotypes.py @@ -19,7 +19,7 @@ def fetch_parameters(config): config_dic['dataid'] = datastructure.get_nextdataid_genotype() config_dic['genofile'] = config.get('config', 'genofile') print("config dictionary:") - for k, v in config_dic.items(): + for k, v in list(config_dic.items()): print(("\t%s: %s" % (k, v))) return config_dic @@ -42,7 +42,7 @@ def parse_genofile(config, config_dic): if line.lower().startswith("chr"): # print("geno file meta dictionary:") - for k, v in meta_dic.items(): + for k, v in list(meta_dic.items()): print(("\t%s: %s" % (k, v))) # print(("geno file head:\n\t%s" % line)) diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py index 0fccaab3..707569db 100644 --- a/wqflask/base/GeneralObject.py +++ b/wqflask/base/GeneralObject.py @@ -33,7 +33,7 @@ class GeneralObject: def __init__(self, *args, **kw): self.contents = list(args) - for name, value in kw.items(): + for name, value in list(kw.items()): setattr(self, name, value) def __setitem__(self, key, value): @@ -50,16 +50,16 @@ class GeneralObject: def __str__(self): s = '' - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): if key != 'contents': s += '%s = %s\n' % (key, self.__dict__[key]) return s def __repr__(self): s = '' - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): s += '%s = %s\n' % (key, self.__dict__[key]) return s def __cmp__(self, other): - return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) + return len(list(self.__dict__.keys())).__cmp__(len(list(other.__dict__.keys()))) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7666348e..e82df226 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -118,7 +118,7 @@ class GeneralTrait(object): vals = [] the_vars = [] sample_aliases = [] - for sample_name, sample_data in self.data.items(): + for sample_name, sample_data in list(self.data.items()): if sample_data.value != None: if not include_variance or sample_data.variance != None: samples.append(sample_name) @@ -260,7 +260,7 @@ def get_sample_data(): trait_dict['pubmed_link'] = trait_ob.pubmed_link trait_dict['pubmed_text'] = trait_ob.pubmed_text - return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) + return json.dumps([trait_dict, {key: value.value for key, value in list(trait_ob.data.items()) }]) else: return None diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 647e58a2..78217587 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -108,7 +108,7 @@ def get_types(groups): """Build types list""" types = {} #print("Groups: ", pf(groups)) - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code @@ -195,9 +195,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index b7b2dc8e..4231cc7c 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -82,7 +82,7 @@ def get_probeset_vals(cursor, dataset_name): def trim_strains(strains, probeset_vals): trimmed_strains = [] #print("probeset_vals is:", pf(probeset_vals)) - first_probeset = list(probeset_vals.itervalues())[0] + first_probeset = list(probeset_vals.values())[0] print("\n**** first_probeset is:", pf(first_probeset)) for strain in strains: print("\n**** strain is:", pf(strain)) diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index d9856eed..204ff59a 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -19,7 +19,7 @@ class Struct(object): ''' def __init__(self, obj): - for k, v in obj.iteritems(): + for k, v in list(obj.items()): if isinstance(v, dict): setattr(self, k, Struct(v)) else: @@ -30,6 +30,6 @@ class Struct(object): def __repr__(self): return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for - (k, v) in self.__dict__.iteritems())) + (k, v) in list(self.__dict__.items()))) diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 8f1c916b..221e5151 100644 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -38,9 +38,9 @@ class Bench(object): @classmethod def report(cls): - total_time = sum((time_taken for time_taken in cls.entries.itervalues())) + total_time = sum((time_taken for time_taken in list(cls.entries.values()))) print("\nTiming report\n") - for name, time_taken in cls.entries.iteritems(): + for name, time_taken in list(cls.entries.items()): percent = int(round((time_taken/total_time) * 100)) print("[{}%] {}: {}".format(percent, name, time_taken)) print() diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 23b0b650..ae42f834 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -175,7 +175,7 @@ class Locus(object): start_pos = 3 for allele in marker_row[start_pos:]: - if allele in geno_table.keys(): + if allele in list(geno_table.keys()): self.genotype.append(geno_table[allele]) else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown self.genotype.append("U") \ No newline at end of file diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 9ce809b6..9a4a235a 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -13,7 +13,7 @@ logger = logging.getLogger(__name__ ) def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" - if "temp_trait" in start_vars.keys(): + if "temp_trait" in list(start_vars.keys()): if start_vars['temp_trait'] == "True": self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) else: diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py index d66c954e..c6a5c260 100644 --- a/wqflask/utility/svg.py +++ b/wqflask/utility/svg.py @@ -133,7 +133,7 @@ def _escape(data, entities={}): # data = data.replace("&", "&") data = data.replace("<", "<") data = data.replace(">", ">") - for chars, entity in entities.items(): + for chars, entity in list(entities.items()): data = data.replace(chars, entity) return data @@ -299,7 +299,7 @@ class SVGelement: self.text = text self.namespace = namespace self.cdata = cdata - for arg in args.keys(): + for arg in list(args.keys()): arg2 = arg.replace("__", ":") arg2 = arg2.replace("_", "-") self.attributes[arg2] = args[arg] @@ -314,7 +314,7 @@ class SVGelement: def toXml(self, level, f): f.write('\t'*level) f.write('<'+self.type) - for attkey in self.attributes.keys(): + for attkey in list(self.attributes.keys()): f.write(' '+_escape(str(attkey))+'=' + _quoteattr(str(self.attributes[attkey]))) if self.namespace: @@ -365,7 +365,7 @@ class tspan(SVGelement): def __repr__(self): s = "<tspan" - for key, value in self.attributes.items(): + for key, value in list(self.attributes.items()): s += ' %s="%s"' % (key, value) s += '>' s += self.text @@ -390,7 +390,7 @@ class tref(SVGelement): def __repr__(self): s = "<tref" - for key, value in self.attributes.items(): + for key, value in list(self.attributes.items()): s += ' %s="%s"' % (key, value) s += '/>' return s @@ -963,7 +963,7 @@ class drawing: xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"") if self.entity: xml.write(" [\n") - for item in self.entity.keys(): + for item in list(self.entity.keys()): xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item])) xml.write("]") xml.write(">\n") @@ -1015,7 +1015,7 @@ class drawing: if element.text: textnode=root.createTextNode(element.text) e.appendChild(textnode) - for attribute in element.attributes.keys(): #in element.attributes is supported from python 2.2 + for attribute in list(element.attributes.keys()): #in element.attributes is supported from python 2.2 e.setAttribute(attribute,str(element.attributes[attribute])) if element.elements: for el in element.elements: diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 5bf700c9..2f2726c6 100644 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -20,6 +20,6 @@ class TempData(object): if __name__ == "__main__": redis = Redis() - for key in redis.keys(): + for key in list(redis.keys()): for field in redis.hkeys(key): print("{}.{}={}".format(key, field, redis.hget(key, field))) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index f790d424..51a87fe1 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -220,7 +220,7 @@ def show_settings(): logger.info(OVERRIDES) logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) - keylist = app.config.keys() + keylist = list(app.config.keys()) print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******") keylist.sort() for k in keylist: diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index 7f5312c1..eb05645e 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -36,7 +36,7 @@ def do_correlation(start_vars): #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) final_results = [] - for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]): + for _trait_counter, trait in enumerate(list(corr_results.keys())[:corr_params['return_count']]): if corr_params['type'] == "tissue": [sample_r, num_overlap, sample_p, symbol] = corr_results[trait] result_dict = { @@ -76,20 +76,20 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): if corr_params['type'] == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params) - sorted_results = collections.OrderedDict(sorted(corr_results.items(), + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature" trait_geneid_dict = this_dataset.retrieve_genes("GeneId") corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params) - sorted_results = collections.OrderedDict(sorted(corr_results.items(), + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][1]))) else: - for target_trait, target_vals in target_dataset.trait_data.iteritems(): + for target_trait, target_vals in list(target_dataset.trait_data.items()): result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type']) if result is not None: corr_results[target_trait] = result - sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) + sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0]))) return sorted_results @@ -100,10 +100,10 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()] - corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values()) + corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=list(trait_symbol_dict.values())) tissue_corr_data = {} - for trait, symbol in trait_symbol_dict.iteritems(): + for trait, symbol in list(trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] @@ -119,7 +119,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid) lit_corr_data = {} - for trait, gene_id in trait_geneid_dict.iteritems(): + for trait, gene_id in list(trait_geneid_dict.items()): mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index cc11e14b..71d9ee03 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -61,7 +61,7 @@ def get_types(groups): """Build types list""" types = {} - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name, _family_name in group_dict: if phenotypes_exist(group_name): @@ -136,9 +136,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 819836b1..57a8d85f 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -36,13 +36,13 @@ class CorrScatterPlot(object): samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data) self.data = [] - self.indIDs = samples_1.keys() + self.indIDs = list(samples_1.keys()) vals_1 = [] - for sample in samples_1.keys(): + for sample in list(samples_1.keys()): vals_1.append(samples_1[sample].value) self.data.append(vals_1) vals_2 = [] - for sample in samples_2.keys(): + for sample in list(samples_2.keys()): vals_2.append(samples_2[sample].value) self.data.append(vals_2) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index de7a1c0c..15a21ee6 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -145,10 +145,10 @@ class CorrelationResults(object): if corr_samples_group == 'samples_other': primary_samples = [x for x in primary_samples if x not in ( self.dataset.group.parlist + self.dataset.group.f1list)] - self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples) + self.process_samples(start_vars, list(self.this_trait.data.keys()), primary_samples) self.target_dataset = data_set.create_dataset(start_vars['corr_dataset']) - self.target_dataset.get_trait_data(self.sample_data.keys()) + self.target_dataset.get_trait_data(list(self.sample_data.keys())) self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method) @@ -168,41 +168,41 @@ class CorrelationResults(object): tissue_corr_data = self.do_tissue_correlation_for_all_traits() if tissue_corr_data != None: - for trait in tissue_corr_data.keys()[:self.return_number]: + for trait in list(tissue_corr_data.keys())[:self.return_number]: self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) else: - for trait, values in self.target_dataset.trait_data.iteritems(): + for trait, values in list(self.target_dataset.trait_data.items()): self.get_sample_r_and_p_values(trait, values) elif self.corr_type == "lit": self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId") lit_corr_data = self.do_lit_correlation_for_all_traits() - for trait in lit_corr_data.keys()[:self.return_number]: + for trait in list(lit_corr_data.keys())[:self.return_number]: self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) elif self.corr_type == "sample": - for trait, values in self.target_dataset.trait_data.iteritems(): + for trait, values in list(self.target_dataset.trait_data.items()): self.get_sample_r_and_p_values(trait, values) - self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(), + self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()), key=lambda t: -abs(t[1][0]))) if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert min/max chromosome to an int for the location range option range_chr_as_int = None - for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): if 'loc_chr' in start_vars: if chr_info.name == self.location_chr: range_chr_as_int = order_id - for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): + for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert trait chromosome to an int for the location range option chr_as_int = 0 - for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): if chr_info.name == trait_object.chr: chr_as_int = order_id @@ -297,14 +297,14 @@ class CorrelationResults(object): #print("trait_gene_symbols: ", pf(trait_gene_symbols.values())) corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=self.trait_symbol_dict.values()) + symbol_list=list(self.trait_symbol_dict.values())) #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict)) #print("trait_gene_symbols: ", pf(trait_gene_symbols)) tissue_corr_data = {} - for trait, symbol in self.trait_symbol_dict.iteritems(): + for trait, symbol in list(self.trait_symbol_dict.items()): if symbol and symbol.lower() in corr_result_tissue_vals_dict: this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()] @@ -314,7 +314,7 @@ class CorrelationResults(object): tissue_corr_data[trait] = [symbol, result[0], result[2]] - tissue_corr_data = collections.OrderedDict(sorted(tissue_corr_data.items(), + tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()), key=lambda t: -abs(t[1][1]))) return tissue_corr_data @@ -359,7 +359,7 @@ class CorrelationResults(object): input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) lit_corr_data = {} - for trait, gene_id in self.trait_geneid_dict.iteritems(): + for trait, gene_id in list(self.trait_geneid_dict.items()): mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id) if mouse_gene_id and str(mouse_gene_id).find(";") == -1: @@ -387,7 +387,7 @@ class CorrelationResults(object): else: lit_corr_data[trait] = [gene_id, 0] - lit_corr_data = collections.OrderedDict(sorted(lit_corr_data.items(), + lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()), key=lambda t: -abs(t[1][1]))) return lit_corr_data diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 35067036..f0be7a98 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -125,7 +125,7 @@ class CTL(object): gt = create_trait(name = ts[0], dataset_name = ts[1]) gt = retrieve_sample_data(gt, dataset, individuals) for ind in individuals: - if ind in gt.data.keys(): + if ind in list(gt.data.keys()): traits.append(gt.data[ind].value) else: traits.append("-999") diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 6646cc36..28c6593d 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -61,7 +61,7 @@ def export_search_results_csv(targs): traits_by_group = sort_traits_by_group(trait_list) file_list = [] - for group in traits_by_group.keys(): + for group in list(traits_by_group.keys()): group_traits = traits_by_group[group] buff = StringIO.StringIO() writer = csv.writer(buff) @@ -135,7 +135,7 @@ def export_search_results_csv(targs): def sort_traits_by_group(trait_list=[]): traits_by_group = {} for trait in trait_list: - if trait.dataset.group.name not in traits_by_group.keys(): + if trait.dataset.group.name not in list(traits_by_group.keys()): traits_by_group[trait.dataset.group.name] = [] traits_by_group[trait.dataset.group.name].append(trait) diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 5098a184..577426b0 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -60,7 +60,7 @@ class Heatmap(object): chrnames = [] self.species = species.TheSpecies(dataset=self.trait_list[0][1]) - for key in self.species.chromosomes.chromosomes.keys(): + for key in list(self.species.chromosomes.chromosomes.keys()): chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) for trait_db in self.trait_list: @@ -93,7 +93,7 @@ class Heatmap(object): pos = [] markernames = [] - for trait in self.trait_results.keys(): + for trait in list(self.trait_results.keys()): lodnames.append(trait) self.dataset.group.get_markers() diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 273168a8..a39e5d0f 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -24,7 +24,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): ##List current Species and other Species speciesId = speciesDict[species] - otherSpecies = [[X, speciesDict[X]] for X in speciesDict.keys()] + otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())] otherSpecies.remove([species, speciesId]) results = g.db.execute(""" diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 7b6e70d2..0328ce85 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -229,7 +229,7 @@ class DisplayMappingResults(object): self.manhattan_plot = start_vars['manhattan_plot'] - if 'permCheck' in start_vars.keys(): + if 'permCheck' in list(start_vars.keys()): self.permChecked = start_vars['permCheck'] else: self.permChecked = False @@ -242,46 +242,46 @@ class DisplayMappingResults(object): else: self.nperm = 0 - if 'bootCheck' in start_vars.keys(): + if 'bootCheck' in list(start_vars.keys()): self.bootChecked = start_vars['bootCheck'] else: self.bootChecked = False - if 'num_bootstrap' in start_vars.keys(): + if 'num_bootstrap' in list(start_vars.keys()): self.nboot = int(start_vars['num_bootstrap']) else: self.nboot = 0 - if 'bootstrap_results' in start_vars.keys(): + if 'bootstrap_results' in list(start_vars.keys()): self.bootResult = start_vars['bootstrap_results'] else: self.bootResult = [] - if 'do_control' in start_vars.keys(): + if 'do_control' in list(start_vars.keys()): self.doControl = start_vars['do_control'] else: self.doControl = "false" - if 'control_marker' in start_vars.keys(): + if 'control_marker' in list(start_vars.keys()): self.controlLocus = start_vars['control_marker'] else: self.controlLocus = "" - if 'covariates' in start_vars.keys(): + if 'covariates' in list(start_vars.keys()): self.covariates = start_vars['covariates'] - if 'maf' in start_vars.keys(): + if 'maf' in list(start_vars.keys()): self.maf = start_vars['maf'] else: self.maf = "" - if 'output_files' in start_vars.keys(): + if 'output_files' in list(start_vars.keys()): self.output_files = start_vars['output_files'] - if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma": + if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] - if 'reaper_version' in start_vars.keys() and self.mapping_method == "reaper": + if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper": self.reaper_version = start_vars['reaper_version'] if 'output_files' in start_vars: self.output_files = ",".join(start_vars['output_files']) self.categorical_vars = "" self.perm_strata = "" - if 'perm_strata' in start_vars.keys() and 'categorical_vars' in start_vars.keys(): + if 'perm_strata' in list(start_vars.keys()) and 'categorical_vars' in list(start_vars.keys()): self.categorical_vars = start_vars['categorical_vars'] self.perm_strata = start_vars['perm_strata'] @@ -323,7 +323,7 @@ class DisplayMappingResults(object): self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH ## BEGIN HaplotypeAnalyst - if 'haplotypeAnalystCheck' in start_vars.keys(): + if 'haplotypeAnalystCheck' in list(start_vars.keys()): self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck'] else: self.haplotypeAnalystChecked = False @@ -331,25 +331,25 @@ class DisplayMappingResults(object): self.graphHeight = self.GRAPH_DEFAULT_HEIGHT self.dominanceChecked = False - if 'LRSCheck' in start_vars.keys(): + if 'LRSCheck' in list(start_vars.keys()): self.LRS_LOD = start_vars['LRSCheck'] else: self.LRS_LOD = start_vars['score_type'] self.intervalAnalystChecked = True self.draw2X = False - if 'additiveCheck' in start_vars.keys(): + if 'additiveCheck' in list(start_vars.keys()): self.additiveChecked = start_vars['additiveCheck'] else: self.additiveChecked = False - if 'viewLegend' in start_vars.keys(): + if 'viewLegend' in list(start_vars.keys()): self.legendChecked = start_vars['viewLegend'] else: self.legendChecked = False - if 'showSNP' in start_vars.keys(): + if 'showSNP' in list(start_vars.keys()): self.SNPChecked = start_vars['showSNP'] else: self.SNPChecked = False - if 'showGenes' in start_vars.keys(): + if 'showGenes' in list(start_vars.keys()): self.geneChecked = start_vars['showGenes'] else: self.geneChecked = False @@ -530,7 +530,7 @@ class DisplayMappingResults(object): showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=showLocusForm, submit=HT.Input(type='hidden')) hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} - for key in hddn.keys(): + for key in list(hddn.keys()): showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) showLocusForm.append(intImg) else: diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index c9d10f7c..145dbc77 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -347,7 +347,7 @@ class RunMapping(object): if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y": if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y": highest_chr = marker['chr1'] - if 'lod_score' in marker.keys(): + if 'lod_score' in list(marker.keys()): self.qtl_results.append(marker) self.trimmed_markers = results @@ -411,7 +411,7 @@ class RunMapping(object): if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y": if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y": highest_chr = marker['chr'] - if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): + if ('lod_score' in list(marker.keys())) or ('lrs_value' in list(marker.keys())): self.qtl_results.append(marker) with Bench("Exporting Results"): @@ -538,28 +538,28 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Mb," + score_type) else: output_file.write("Cm," + score_type) - if "additive" in markers[0].keys(): + if "additive" in list(markers[0].keys()): output_file.write(",Additive") - if "dominance" in markers[0].keys(): + if "dominance" in list(markers[0].keys()): output_file.write(",Dominance") output_file.write("\n") for i, marker in enumerate(markers): output_file.write(marker['name'] + "," + str(marker['chr']) + "," + str(marker['Mb']) + ",") - if "lod_score" in marker.keys(): + if "lod_score" in list(marker.keys()): output_file.write(str(marker['lod_score'])) else: output_file.write(str(marker['lrs_value'])) - if "additive" in marker.keys(): + if "additive" in list(marker.keys()): output_file.write("," + str(marker['additive'])) - if "dominance" in marker.keys(): + if "dominance" in list(marker.keys()): output_file.write("," + str(marker['dominance'])) if i < (len(markers) - 1): output_file.write("\n") def trim_markers_for_figure(markers): - if 'p_wald' in markers[0].keys(): + if 'p_wald' in list(markers[0].keys()): score_type = 'p_wald' - elif 'lod_score' in markers[0].keys(): + elif 'lod_score' in list(markers[0].keys()): score_type = 'lod_score' else: score_type = 'lrs_value' @@ -617,7 +617,7 @@ def trim_markers_for_figure(markers): return filtered_markers def trim_markers_for_table(markers): - if 'lod_score' in markers[0].keys(): + if 'lod_score' in list(markers[0].keys()): sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True) else: sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True) @@ -695,10 +695,10 @@ def get_genofile_samplelist(dataset): def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings = [] for sample in used_samples: - if sample in sample_list.sample_attribute_values.keys(): + if sample in list(sample_list.sample_attribute_values.keys()): combined_string = "" for var in categorical_vars: - if var in sample_list.sample_attribute_values[sample].keys(): + if var in list(sample_list.sample_attribute_values[sample].keys()): combined_string += str(sample_list.sample_attribute_values[sample][var]) else: combined_string += "NA" diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 39a07310..6b3e00fb 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -125,7 +125,7 @@ def add_group_to_resource(): def get_group_names(group_masks): group_masks_with_names = {} - for group_id, group_mask in group_masks.iteritems(): + for group_id, group_mask in list(group_masks.items()): this_mask = group_mask group_name = get_group_info(group_id)['name'] this_mask['name'] = group_name diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 253c887b..68c3ad7d 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -47,7 +47,7 @@ def get_export_metadata(trait_id, dataset_name): def dict_to_sorted_list(dictionary): - sorted_list = [item for item in dictionary.iteritems()] + sorted_list = [item for item in list(dictionary.items())] sorted_list = sorted(sorted_list, cmp=cmp_samples) sorted_values = [item[1] for item in sorted_list] return sorted_values diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index f188fd9d..c156e61b 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -261,7 +261,7 @@ class ShowTrait(object): hddn['export_data'] = "" hddn['export_format'] = "excel" if len(self.scales_in_geno) < 2: - hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0][0] + hddn['mapping_scale'] = self.scales_in_geno[list(self.scales_in_geno.keys())[0]][0][0] # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self self.hddn = hddn @@ -405,7 +405,7 @@ class ShowTrait(object): if not self.temp_trait: other_sample_names = [] - for sample in self.this_trait.data.keys(): + for sample in list(self.this_trait.data.keys()): if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names): primary_sample_names.append(self.this_trait.data[sample].name) primary_sample_names.remove(self.this_trait.data[sample].name2) @@ -558,7 +558,7 @@ def get_table_widths(sample_groups, has_num_cases=False): def has_num_cases(this_trait): has_n = False if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno": - for name, sample in this_trait.data.iteritems(): + for name, sample in list(this_trait.data.items()): if sample.num_cases: has_n = True break @@ -611,7 +611,7 @@ def get_categorical_variables(this_trait, sample_list): if len(sample_list.attributes) > 0: for attribute in sample_list.attributes: attribute_vals = [] - for sample_name in this_trait.data.keys(): + for sample_name in list(this_trait.data.keys()): if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes: attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name]) else: diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index d67f1a2e..394a9e28 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -533,7 +533,7 @@ def heatmap_page(): result = template_vars.__dict__ - for item in template_vars.__dict__.keys(): + for item in list(template_vars.__dict__.keys()): logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) @@ -637,7 +637,7 @@ def loading_page(): if 'wanted_inputs' in initial_start_vars: wanted = initial_start_vars['wanted_inputs'].split(",") start_vars = {} - for key, value in initial_start_vars.iteritems(): + for key, value in list(initial_start_vars.items()): if key in wanted or key.startswith(('value:')): start_vars[key] = value @@ -737,7 +737,7 @@ def mapping_results_page(): 'transform' ) start_vars = {} - for key, value in initial_start_vars.iteritems(): + for key, value in list(initial_start_vars.items()): if key in wanted or key.startswith(('value:')): start_vars[key] = value #logger.debug("Mapping called with start_vars:", start_vars) |