diff options
| author | zsloan | 2018-04-16 21:21:25 +0000 |
|---|---|---|
| committer | zsloan | 2018-04-16 21:21:25 +0000 |
| commit | 2e2698641d0dc8d8315f48b45c170290641d7b0f (patch) | |
| tree | 65932d4841c4903974b384837053d1e0b3c4fb51 | |
| parent | 9750e63d64849d7fa9e1e681f56b73cae96905df (diff) | |
| download | genenetwork2-2e2698641d0dc8d8315f48b45c170290641d7b0f.tar.gz | |
Removed a bunch of unused code from the following files:
marker_regression_gn1.py
marker_regression.py
do_search.py
export_traits.py
heatmap.py
GeneUtil.py
heatmap.html
| -rw-r--r-- | wqflask/wqflask/do_search.py | 88 | ||||
| -rw-r--r-- | wqflask/wqflask/export_traits.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/heatmap/heatmap.py | 173 | ||||
| -rw-r--r-- | wqflask/wqflask/interval_analyst/GeneUtil.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 59 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 886 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 67 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/heatmap.html | 1 |
8 files changed, 81 insertions, 1196 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 07c67384..e2a0a479 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -79,38 +79,6 @@ class DoSearch(object): else: return None -class QuickMrnaAssaySearch(DoSearch): - """A general search for mRNA assays""" - - 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.name_num as ProbeSet_name_num - FROM ProbeSet """ - - header_fields = ['Index', - 'Record', - 'Symbol', - 'Location'] - - def run(self): - """Generates and runs a search for assays across all mRNA expression datasets""" - - logger.debug("Running ProbeSetSearch") - query = self.base_query + """WHERE (MATCH (ProbeSet.Name, - ProbeSet.description, - ProbeSet.symbol, - ProbeSet.alias) - AGAINST ('%s' IN BOOLEAN MODE)) - """ % (escape(self.search_term[0])) - - return self.execute(query) - - class MrnaAssaySearch(DoSearch): """A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites""" @@ -311,54 +279,6 @@ class PhenotypeSearch(DoSearch): 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) - - return query - - def run(self): - """Generates and runs a search across all phenotype datasets""" - - query = self.compile_final_query(where_clause = self.get_where_clause()) - - return self.execute(query) - class GenotypeSearch(DoSearch): """A search within a genotype dataset""" @@ -767,14 +687,6 @@ class MeanSearch(MrnaAssaySearch): return where_clause - def get_final_query(self): - self.where_clause = self.get_where_clause() - logger.debug("where_clause is:", pf(self.where_clause)) - - self.query = self.compile_final_query(where_clause = self.where_clause) - - return self.query - def run(self): self.where_clause = self.get_where_clause() logger.debug("where_clause is:", pf(self.where_clause)) diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index f8fce929..ab4c0d7c 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -1,6 +1,5 @@ from __future__ import print_function, division -import operator import csv import xlsxwriter import StringIO diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 56ff11cd..af75d441 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -3,7 +3,6 @@ from __future__ import absolute_import, print_function, division import sys # sys.path.append(".") Never in a running webserver -import gc import string import cPickle import os @@ -16,7 +15,6 @@ import resource import scipy import numpy as np -from scipy import linalg from pprint import pformat as pf @@ -82,21 +80,16 @@ class Heatmap(object): this_trait = trait_db[0] this_sample_data = this_trait.data - #self.sample_data[this_trait.name] = [] this_trait_vals = [] for sample in self.all_sample_list: if sample in this_sample_data: this_trait_vals.append(this_sample_data[sample].value) - #self.sample_data[this_trait.name].append(this_sample_data[sample].value) else: this_trait_vals.append('') - #self.sample_data[this_trait.name].append('') self.sample_data.append(this_trait_vals) self.gen_reaper_results() - #self.gen_pylmm_results() - #chrnames = [] lodnames = [] chr_pos = [] pos = [] @@ -106,9 +99,6 @@ class Heatmap(object): lodnames.append(trait) for marker in self.dataset.group.markers.markers: - #if marker['chr'] not in chrnames: - # chr_ob = [marker['chr'], "filler"] - # chrnames.append(chr_ob) chr_pos.append(marker['chr']) pos.append(marker['Mb']) markernames.append(marker['name']) @@ -126,9 +116,6 @@ class Heatmap(object): json_data = self.json_data ) - print("self.js_data:", self.js_data) - - def gen_reaper_results(self): self.trait_results = {} for trait_db in self.trait_list: @@ -145,172 +132,14 @@ class Heatmap(object): trimmed_samples.append(samples[i]) trimmed_values.append(values[i]) - self.lrs_array = genotype.permutation(strains = trimmed_samples, - trait = trimmed_values, - nperm= self.num_permutations) - - #self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)] - #self.significant = self.lrs_array[int(self.num_permutations*0.95-1)] - reaper_results = genotype.regression(strains = trimmed_samples, trait = trimmed_values) - lrs_values = [float(qtl.lrs) for qtl in reaper_results] - print("lrs_values:", lrs_values) - #self.dataset.group.markers.add_pvalues(p_values) self.trait_results[this_trait.name] = [] for qtl in reaper_results: if qtl.additive > 0: self.trait_results[this_trait.name].append(-float(qtl.lrs)) else: - self.trait_results[this_trait.name].append(float(qtl.lrs)) - #for lrs in lrs_values: - # if - # self.trait_results[this_trait.name].append(lrs) - - - #this_db_samples = self.dataset.group.samplelist - #this_sample_data = this_trait.data - ##print("this_sample_data", this_sample_data) - #this_trait_vals = [] - #for index, sample in enumerate(this_db_samples): - # if sample in this_sample_data: - # sample_value = this_sample_data[sample].value - # this_trait_vals.append(sample_value) - # else: - # this_trait_vals.append("x") - - #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals]) - - #key = "pylmm:input:" + str(self.temp_uuid) - #print("key is:", pf(key)) - - #genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] - - #no_val_samples = self.identify_empty_samples(this_trait_vals) - #trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) - - #genotype_matrix = np.array(trimmed_genotype_data).T - - #print("genotype_matrix:", str(genotype_matrix.tolist())) - #print("pheno_vector:", str(pheno_vector.tolist())) - - #params = dict(pheno_vector = pheno_vector.tolist(), - # genotype_matrix = genotype_matrix.tolist(), - # restricted_max_likelihood = True, - # refit = False, - # temp_uuid = str(self.temp_uuid), - # - # # meta data - # timestamp = datetime.datetime.now().isoformat(), - # ) - # - #json_params = json.dumps(params) - ##print("json_params:", json_params) - #Redis.set(key, json_params) - #Redis.expire(key, 60*60) - #print("before printing command") - # - #command = 'python lmm.py --key {} --species {}'.format(key, - # "other") - #print("command is:", command) - #print("after printing command") - # - #os.system(command) - # - #json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60) - - def gen_pylmm_results(self): - # This function is NOT used. If it is, we should use a shared function with marker_regression.py - self.trait_results = {} - for trait_db in self.trait_list: - this_trait = trait_db[0] - #this_db = trait_db[1] - self.dataset.group.get_markers() - - this_db_samples = self.dataset.group.samplelist - this_sample_data = this_trait.data - #print("this_sample_data", this_sample_data) - this_trait_vals = [] - for index, sample in enumerate(this_db_samples): - if sample in this_sample_data: - sample_value = this_sample_data[sample].value - this_trait_vals.append(sample_value) - else: - this_trait_vals.append("x") - - pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals]) - - key = "pylmm:input:" + str(self.temp_uuid) - #print("key is:", pf(key)) - - genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] - - no_val_samples = self.identify_empty_samples(this_trait_vals) - trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) - - genotype_matrix = np.array(trimmed_genotype_data).T - - #print("genotype_matrix:", str(genotype_matrix.tolist())) - #print("pheno_vector:", str(pheno_vector.tolist())) - - params = dict(pheno_vector = pheno_vector.tolist(), - genotype_matrix = genotype_matrix.tolist(), - restricted_max_likelihood = True, - refit = False, - temp_uuid = str(self.temp_uuid), - - # meta data - timestamp = datetime.datetime.now().isoformat(), - ) - - json_params = json.dumps(params) - #print("json_params:", json_params) - Redis.set(key, json_params) - Redis.expire(key, 60*60) - print("before printing command") - - command = PYLMM_COMMAND+' --key {} --species {}'.format(key, - "other") - print("command is:", command) - print("after printing command") - - os.system(command) - - json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60) - results = json.loads(json_results[1]) - p_values = [float(result) for result in results['p_values']] - #print("p_values:", p_values) - self.dataset.group.markers.add_pvalues(p_values) - - self.trait_results[this_trait.name] = [] - for marker in self.dataset.group.markers.markers: - self.trait_results[this_trait.name].append(marker['lod_score']) - - - def identify_empty_samples(self, values): - no_val_samples = [] - for sample_count, val in enumerate(values): - if val == "x": - no_val_samples.append(sample_count) - return no_val_samples - - def trim_genotypes(self, genotype_data, no_value_samples): - trimmed_genotype_data = [] - for marker in genotype_data: - new_genotypes = [] - for item_count, genotype in enumerate(marker): - if item_count in no_value_samples: - continue - try: - genotype = float(genotype) - except ValueError: - genotype = np.nan - pass - new_genotypes.append(genotype) - trimmed_genotype_data.append(new_genotypes) - return trimmed_genotype_data - - + self.trait_results[this_trait.name].append(float(qtl.lrs))
\ No newline at end of file diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index fda7773f..2c60dd70 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -6,7 +6,7 @@ from flask import Flask, g #Just return a list of dictionaries #each dictionary contains sub-dictionary -def loadGenes(chrName, diffCol, startMb, endMb, webqtlDb =None, species='mouse'): +def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd'] diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 3ec61e55..bfb63995 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -16,7 +16,6 @@ import uuid import rpy2.robjects as ro import numpy as np -from scipy import linalg import cPickle as pickle import itertools @@ -84,7 +83,6 @@ class MarkerRegression(object): self.geno_db_exists = start_vars['geno_db_exists'] else: try: - geno_dataset = data_set.create_dataset(self.dataset.group.name + "Geno") self.geno_db_exists = "True" except: self.geno_db_exists = "False" @@ -278,7 +276,6 @@ class MarkerRegression(object): ) else: - self.cutoff = 2 self.qtl_results = [] highest_chr = 1 #This is needed in order to convert the highest chr to X/Y for marker in results: @@ -426,7 +423,6 @@ class MarkerRegression(object): if self.dataset.group.species == "human": p_values, t_stats = self.gen_human_results(pheno_vector, key, temp_uuid) - #p_values = self.trim_results(p_values) else: logger.debug("NOW CWD IS:", os.getcwd()) @@ -478,8 +474,6 @@ class MarkerRegression(object): json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60) results = json.loads(json_results[1]) p_values = [float(result) for result in results['p_values']] - #logger.debug("p_values:", p_values[:10]) - #p_values = self.trim_results(p_values) t_stats = results['t_stats'] #t_stats, p_values = lmm.run( @@ -493,19 +487,8 @@ class MarkerRegression(object): self.dataset.group.markers.add_pvalues(p_values) - #self.get_lod_score_cutoff() - return self.dataset.group.markers.markers - def trim_results(self, p_values): - logger.debug("len_p_values:", len(p_values)) - if len(p_values) > 500: - p_values.sort(reverse=True) - trimmed_values = p_values[:500] - - return trimmed_values - - #def gen_human_results(self, pheno_vector, tempdata): def gen_human_results(self, pheno_vector, key, temp_uuid): file_base = locate(self.dataset.group.name,"mapping") @@ -562,18 +545,6 @@ class MarkerRegression(object): return p_values, t_stats - def get_lod_score_cutoff(self): - logger.debug("INSIDE GET LOD CUTOFF") - high_qtl_count = 0 - for marker in self.dataset.group.markers.markers: - if marker['lod_score'] > 1: - high_qtl_count += 1 - - if high_qtl_count > 1000: - return 1 - else: - return 0 - def identify_empty_samples(self): no_val_samples = [] for sample_count, val in enumerate(self.vals): @@ -597,28 +568,6 @@ class MarkerRegression(object): trimmed_genotype_data.append(new_genotypes) return trimmed_genotype_data -def create_snp_iterator_file(group): - """ - This function is only called by main below - """ - raise Exception("Paths are undefined here") - plink_file_base = os.path.join(TMPDIR, group) - plink_input = input.plink(plink_file_base, type='b') - - data = dict(plink_input = list(plink_input), - numSNPs = plink_input.numSNPs) - - #input_dict = {} - # - #input_dict['plink_input'] = list(plink_input) - #input_dict['numSNPs'] = plink_input.numSNPs - # - - snp_file_base = os.path.join(webqtlConfig.SNP_PATH, group + ".snps.gz") - - with gzip.open(snp_file_base, "wb") as fh: - pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL) - def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type): with open(results_path, "w+") as output_file: output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") @@ -652,8 +601,6 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("\n") def trim_markers_for_table(markers): - num_markers = len(markers) - if 'lod_score' in markers[0].keys(): sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True) else: @@ -664,8 +611,4 @@ def trim_markers_for_table(markers): trimmed_sorted_markers = sorted_markers[:200] return trimmed_sorted_markers else: - return sorted_markers - - -if __name__ == '__main__': - import cPickle as pickle + return sorted_markers
\ No newline at end of file diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 81da8976..da713325 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -30,7 +30,7 @@ from math import * import piddle as pid import sys,os import cPickle -import httplib, urllib +import httplib from flask import Flask, g @@ -52,7 +52,6 @@ logger = utility.logger.getLogger(__name__ ) ######################################### class MarkerRegression(object): cMGraphInterval = 5 - maxBootStrap = 50 GRAPH_MIN_WIDTH = 900 GRAPH_MAX_WIDTH = 10000 # Don't set this too high GRAPH_DEFAULT_WIDTH = 1280 @@ -81,8 +80,6 @@ class MarkerRegression(object): DRAW_DETAIL_MB = 4 DRAW_UTR_LABELS_MB = 4 - MIN_PIXELS_BETWEEN_LABELS = 50 - qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary') # Note that "qmark.gif" is a similar, smaller, rounded-edges question mark. It doesn't look # like the ones on the image, though, which is why we don't use it here. @@ -93,11 +90,8 @@ class MarkerRegression(object): NR_INDIVIDUALS = 0 ## END HaplotypeAnalyst - ALEX_DEBUG_BOOL_COLORIZE_GENES = 1 # 0=don't colorize, 1=colorize ALEX_DEBUG_BOOL_PRINT_GENE_LIST = 1 - kWIDTH_DEFAULT=1 - kONE_MILLION = 1000000 LODFACTOR = 4.61 @@ -105,18 +99,14 @@ class MarkerRegression(object): SNP_COLOR = pid.orange # Color for the SNP "seismograph" TRANSCRIPT_LOCATION_COLOR = pid.mediumpurple - GENE_FILL_COLOR = pid.HexColor(0x6666FF) - GENE_OUTLINE_COLOR = pid.HexColor(0x000077) BOOTSTRAP_BOX_COLOR = pid.yellow LRS_COLOR = pid.HexColor(0x0000FF) - LRS_LINE_WIDTH = 2 SIGNIFICANT_COLOR = pid.HexColor(0xEBC7C7) SUGGESTIVE_COLOR = pid.gainsboro SIGNIFICANT_WIDTH = 5 SUGGESTIVE_WIDTH = 5 ADDITIVE_COLOR_POSITIVE = pid.green ADDITIVE_COLOR_NEGATIVE = pid.orange - ADDITIVE_COLOR = ADDITIVE_COLOR_POSITIVE DOMINANCE_COLOR_POSITIVE = pid.darkviolet DOMINANCE_COLOR_NEGATIVE = pid.red @@ -127,15 +117,7 @@ class MarkerRegression(object): HAPLOTYPE_RECOMBINATION = pid.darkgray ## END HaplotypeAnalyst - QMARK_EDGE_COLOR = pid.HexColor(0x718118) - QMARK_FILL_COLOR = pid.HexColor(0xDEE3BB) - TOP_RIGHT_INFO_COLOR = pid.black - X_AXIS_LABEL_COLOR = pid.black #HexColor(0x505050) - - MINI_VIEW_MAGNIFIED_REGION_COLOR = pid.HexColor(0xCC0000) - MINI_VIEW_OUTSIDE_REGION_COLOR = pid.HexColor(0xEEEEEE) - MINI_VIEW_BORDER_COLOR = pid.black CLICKABLE_WEBQTL_REGION_COLOR = pid.HexColor(0xF5D3D3) CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = pid.HexColor(0xFCE9E9) @@ -154,18 +136,9 @@ class MarkerRegression(object): HELP_PAGE_REF = '/glossary.html' - DRAW_UTR_LABELS=0 - def __init__(self, start_vars): - - #templatePage.__init__(self, fd) - - #if not self.openMysql(): - # return logger.info("Running qtlreaper") - #helper_functions.get_species_dataset_trait(self, start_vars) - self.temp_uuid = start_vars['temp_uuid'] self.dataset = start_vars['dataset'] @@ -249,17 +222,7 @@ class MarkerRegression(object): if 'use_loco' in start_vars.keys(): self.use_loco = start_vars['use_loco'] - #try: self.selectedChr = int(start_vars['selected_chr']) - #except: - # self.selectedChr = -1 - - #whether include parents and F1 for InbredSet - #fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression') - #if ((fd.parentsf14regression == 'on') and fd.genotype_2): - # fd.genotype = fd.genotype_2 - #else: - # fd.genotype = fd.genotype_1 self.strainlist = self.dataset.group.samplelist self.genotype = self.dataset.group.read_genotype_file() @@ -279,7 +242,6 @@ class MarkerRegression(object): self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH ## BEGIN HaplotypeAnalyst - #self.haplotypeAnalystChecked = fd.formdata.getvalue('haplotypeAnalystCheck') if 'haplotypeAnalystCheck' in start_vars.keys(): self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck'] else: @@ -292,7 +254,6 @@ class MarkerRegression(object): self.LRS_LOD = start_vars['LRSCheck'] else: self.LRS_LOD = start_vars['score_type'] - self.cutoff = start_vars['cutoff'] self.intervalAnalystChecked = True self.draw2X = False if 'additiveCheck' in start_vars.keys(): @@ -324,34 +285,8 @@ class MarkerRegression(object): except: self.lrsMax = 0 - #self.additiveChecked = fd.formdata.getvalue('additiveCheck') - #self.dominanceChecked = fd.formdata.getvalue('dominanceCheck') - #self.LRS_LOD = fd.formdata.getvalue('LRSCheck', 'LRS') - #self.intervalAnalystChecked = fd.formdata.getvalue('intervalAnalystCheck') - #self.legendChecked = fd.formdata.getvalue('viewLegend') - #self.geneChecked = fd.formdata.getvalue('showGenes') - #self.SNPChecked = fd.formdata.getvalue('showSNP') - #self.draw2X = fd.formdata.getvalue('draw2X') - #self.lrsMax = float(fd.formdata.getvalue('lrsMax', 0)) - #self.startMb = fd.formdata.getvalue('startMb', "-1") - #self.endMb = fd.formdata.getvalue('endMb', "-1") - - #try: - # self.startMb = float(self.startMb) - # self.endMb = float(self.endMb) - # if self.startMb > self.endMb: - # temp = self.startMb - # self.startMb = self.endMb - # self.endMb = temp - # #minimal distance 10bp - # if self.endMb - self.startMb < 0.00001: - # self.endMb = self.startMb + 0.00001 - #except: - # self.startMb = self.endMb = -1 - #Trait Infos self.identification = "" - #self.identification = fd.formdata.getvalue('identification', "") ################################################################ # Generate Chr list and Retrieve Length Information @@ -390,7 +325,6 @@ class MarkerRegression(object): else: self.GraphInterval = self.cMGraphInterval #cM - self.dataSource = 'editingPage' self.traitList = [] thisTrait = start_vars['this_trait'] self.traitList.append(thisTrait) @@ -412,8 +346,6 @@ class MarkerRegression(object): self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1 # default: self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT -## for paper: - # #self.graphHeight = self.graphHeight + 1 * self.NR_INDIVIDUALS * self.EACH_GENE_HEIGHT - 180 ## END HaplotypeAnalyst ################################################################ @@ -421,12 +353,6 @@ class MarkerRegression(object): ################################################################ self.multipleInterval = len(self.traitList) > 1 self.qtlresults = start_vars['qtl_results'] - #errorMessage = self.calculateAllResult(fd) - #if errorMessage: - # heading = "Mapping" - # detail = ['%s' % errorMessage] - # self.error(heading=heading,detail=detail) - # return if self.multipleInterval: self.colorCollection = Plot.colorSpectrum(len(self.qtlresults)) @@ -455,9 +381,6 @@ class MarkerRegression(object): for i, strain in enumerate(self.diffCol): self.diffCol[i] = g.db.execute("select Id from Strain where Symbol = %s", strain).fetchone()[0] - #self.cursor.execute("select Id from Strain where Symbol = %s", strain) - #self.diffCol[i] = self.cursor.fetchone()[0] - #print self.diffCol ################################################################ # GeneCollection goes here @@ -480,13 +403,13 @@ class MarkerRegression(object): chrName = "X" else: chrName = self.selectedChr - self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse") + self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "mouse") elif self.dataset.group.species == "rat": if self.selectedChr == 21: chrName = "X" else: chrName = self.selectedChr - self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat") + self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "rat") if self.geneCol and self.intervalAnalystChecked: ####################################################################### @@ -495,26 +418,13 @@ class MarkerRegression(object): #through set GENEID is None # ####################################################################### - #GENEID = fd.formdata.getvalue('GeneId') or None GENEID = None - geneTableContainer = HT.Div(Id="sortable") #Div to hold table self.geneTable(self.geneCol, GENEID) - #geneTable = self.geneTable(self.geneCol, GENEID) - #geneTableContainer.append(geneTable) - - #mainfmName = webqtlUtil.genRandStr("fm_") - #tableForm = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=mainfmName, submit=HT.Input(type='hidden')) - #tableForm.append(HT.Input(name='FormID', value='', type='hidden')) - #tableForm.append(geneTableContainer) - ################################################################ # Plots goes here ################################################################ - #if self.plotScale != 'physic' or self.multipleInterval: - # showLocusForm = webqtlUtil.genRandStr("fm_") - #else: showLocusForm = "" intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight)) gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm) @@ -530,23 +440,6 @@ class MarkerRegression(object): intCanvasX2 = pid.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2)) gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2) intCanvasX2.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename+"X2"), format='png') - #DLintImgX2=HT.Href(text='Download',url = '/image/'+self.filename+'X2.png', Class='smallsize', target='_blank') - - #textUrl = self.writeQTL2Text(fd, self.filename) - - ################################################################ - # Info tables goes here - ################################################################ - #traitInfoTD = self.traitInfoTD(fd) - - #if self.draw2X: - # traitInfoTD.append(HT.P(), DLintImgX2, ' a higher resolution 2X image. ') - #else: - # traitInfoTD.append(HT.P()) - #if textUrl: - # traitInfoTD.append(HT.BR(), textUrl, ' results in tab-delimited text format.') - #traitRemapTD = self.traitRemapTD(self.cursor, fd) - #topTable = HT.TableLite(HT.TR(traitInfoTD, HT.TD(" ", width=25), traitRemapTD), border=0, cellspacing=0, cellpadding=0) ################################################################ # Outputs goes here @@ -564,158 +457,15 @@ class MarkerRegression(object): if (self.permChecked and self.nperm > 0) and not (self.multipleInterval and 0 < self.nperm): self.perm_filename = self.drawPermutationHistogram() - #perm_text_file = self.permutationTextFile() ################################################################ # footnote goes here ################################################################ btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.') - #if (self.additiveChecked): - # btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar) - if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno': btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.') - #if self.permChecked and not self.multipleInterval and 0 < self.nperm: - # TD_LR = HT.TD(HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200) - # #TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200) - #else: - TD_LR = HT.TD(HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo), bgColor='#eeeeee', height = 200) - #TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200) - - - if geneTable: - iaForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=intervalAnalyst"), enctype='multipart/form-data', - name="iaForm", submit=HT.Input(type='hidden')) - hddn = {'chromosome':self.genotype[0].name, 'species':self.species,'startMb':self.startMb,'endMb':self.endMb} - if self.diffCol: - hddn['s1'] = self.diffCol[0] - hddn['s2'] = self.diffCol[1] - for key in hddn.keys(): - iaForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) - iaForm.append(HT.Paragraph("Interval Analyst : Chr %s from %2.6f to %2.6f Mb" % (self.genotype[0].name, self.startMb, self.endMb), - HT.Input(name='customize', value='Customize', onClick= "formInNewWindow(this.form);", type='button', Class="button"), Class="subtitle")) - TD_LR.append(HT.Blockquote(iaForm)) - # optionsTable - selectall = HT.Href(url="#redirect", onClick="checkAll(document.getElementsByName('%s')[0]);" % mainfmName) - selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;") - selectall.append(selectall_img) - reset = HT.Href(url="#redirect", onClick="checkNone(document.getElementsByName('%s')[0]); return false;" % mainfmName) - reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;") - reset.append(reset_img) - selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('%s')[0]);" % mainfmName) - selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;") - selectinvert.append(selectinvert_img) - addselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (RISet, mainfmName)) - addselect_img = HT.Image("/images/add_collection1_final.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;") - addselect.append(addselect_img) - geneweaver = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'ODEIM');" % mainfmName) - geneweaver_img = HT.Image("/images/ODE_logo_final.jpg", name="GeneWeaver", alt="Gene Weaver", title="Gene Weaver", style="border:none") - geneweaver.append(geneweaver_img) - optionsTable = HT.TableLite() - optionsTable.append(HT.TR( - HT.TD(selectall, width="77", style="text-align:center"), - HT.TD(reset, width="77", style="text-align:center"), - HT.TD(selectinvert, width="77", style="text-align:center"), - HT.TD(geneweaver, width="77", style="text-align:center"), - )) - optionsTable.append(HT.TR( - HT.TD("Select", style="text-align:center"), - HT.TD("Deselect", style="text-align:center"), - HT.TD("Invert", style="text-align:center"), - HT.TD("Gene Weaver", style="text-align:center"), - )) - TD_LR.append(HT.Blockquote(optionsTable)) - # geneTableContainer - TD_LR.append(HT.Blockquote(tableForm)) - - self.body = TD_LR - - #self.dict['body'] = TD_LR - #self.dict['title'] = "Mapping" - - - def writeQTL2Text(self, filename): - if self.multipleInterval: - return "" - #_dominance = (self.genotype.type == 'intercross') - _Mb = self.genotype.Mbmap - - ###Write to text file - fpText = open(os.path.join(webqtlConfig.TMPDIR, filename) + '.txt','wb') - - fpText.write("Source: WebQTL, The GeneNetwork (%s)\n" % webqtlConfig.PORTADDR) - # - fpText.write("Site: GN\n") - fpText.write("Page: Map Viewer\n") - fpText.write(time.strftime("Date and Time (US Center): %b %d, %Y at %I.%M %p\n", time.localtime())) - fpText.write("Trait ID: %s\n" % self.this_trait.name) - fpText.write("Suggestive LRS = %0.2f\n" % self.suggestive) - fpText.write("Significant LRS = %0.2f\n" % self.significant) - """ - if self.this_trait.symbol and self.this_trait.chr and self.this_trait.mb: - writeSymbol, writeChromosome, writeMb = self.this_trait.symbol, self.this_trait.chr, self.this_trait.mb - else: - writeSymbol, writeChromosome, writeMb = (" ", " ", " ") - fpText.write("Gene Symbol: %s\n" % writeSymbol) - fpText.write("Location: Chr %s @ %s Mb\n" % (writeChromosome, writeMb)) - #selectedChr = self.indexToChrName(int(fd.formdata.getvalue('chromosomes', -1))) - #fpText.write("Chromosome: %s\n" % selectedChr) - fpText.write("Region: %0.6f-%0.6f Mb\n\n" % (self.startMb, self.endMb)) - """ - - if hasattr(self, 'LRSArray'): - if _dominance: - fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\tDominance\n') - else: - fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\n') - else: - if _dominance: - fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\tDominance\n') - else: - fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\n') - - i = 0 - for marker in self.qtlresults: - if _Mb: - locusMb = '%2.3f' % marker['Mb'] - else: - locusMb = 'N/A' - - if hasattr(self, 'LRSArray'): - if start_vars['score_type'] == "LRS": - lrs_lod = marker['lrs_value'] - else: - lrs_lod = marker['lod_score'] - - P_value = self.calculatePValue(lrs_lod, self.perm_output) - - #if _dominance: - # fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \ - # qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, P_value, qtlresult.additive, qtlresult.dominance)) - #else: - if P_value: - fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\n" %(marker['chr'], \ - marker['name'], marker['cM'], locusMb, lrs_lod, P_value)) - else: - fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%s\n" %(marker['chr'], \ - marker['name'], marker['cM'], locusMb , lrs_lod, '-')) - else: - #if _dominance: - # fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \ - # qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, qtlresult.additive, qtlresult.dominance)) - #else: - fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\n" %(marker['chr'], \ - marker['name'], marker['cM'], locusMb , lrs_lod)) - - i += 1 - - fpText.close() - textUrl = '/tmp/'+filename+'.txt' - #textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='smallsize') - return textUrl - def plotIntMapping(self, canvas, offset= (80, 120, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""): #calculating margins xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset @@ -742,8 +492,6 @@ class MarkerRegression(object): cHeight = canvas.size[1] plotWidth = cWidth - xLeftOffset - xRightOffset plotHeight = cHeight - yTopOffset - yBottomOffset - startPixelX = xLeftOffset - endPixelX = (xLeftOffset + plotWidth) #Drawing Area Height drawAreaHeight = plotHeight @@ -767,7 +515,6 @@ class MarkerRegression(object): #Image map gifmap = HT.Map(name = "WebQTLImageMap") - #gifmap = None newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset) # Draw the alternating-color background first and get plotXScale @@ -946,15 +693,6 @@ class MarkerRegression(object): this_chr = str(self.ChrList[self.selectedChr][0]) else: this_chr = str(self.ChrList[self.selectedChr][1]+1) - # for i, qtlresult in enumerate(self.qtlresults): - # if Chr == this_chr: - # if Mb < self.startMb or Mb > self.endMb: - # return - # else: - # locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale - # break - # elif self.selectedChr == -1: - # if str(qtlresult['chr']) != Chr: if self.plotScale == 'physic': if self.selectedChr > -1: @@ -1012,7 +750,6 @@ class MarkerRegression(object): canvas.drawPolygon(((leftOffset+6, startPosY-6), (leftOffset, startPosY+6), (leftOffset+12, startPosY+6)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR) - def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol: return @@ -1052,7 +789,7 @@ class MarkerRegression(object): snpDensity = float(SNPCounts[i-xLeftOffset]*SNP_HEIGHT_MODIFIER/maxCount) canvas.drawLine(i, drawSNPLocationY+(snpDensity)*zoom, i, drawSNPLocationY-(snpDensity)*zoom, color=self.SNP_COLOR, width=1) - def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, locLocation= None): + def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1): nameWidths = [] yPaddingTop = 10 colorFont=pid.Font(ttf="trebuc",size=12,bold=1) @@ -1080,14 +817,12 @@ class MarkerRegression(object): canvas.drawRect(rightShift,yPaddingTop+kstep*15, rectWidth+rightShift,yPaddingTop+10+kstep*15, fillColor=thisLRSColor) canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=pid.black) if thisTrait.db: - COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,) HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) Areas = HT.Area(shape='rect',coords=COORDS,href=HREF) gifmap.areas.append(Areas) - - def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1, locLocation= None): + def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1): xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset plotWidth = canvas.size[0] - xLeftOffset - xRightOffset plotHeight = canvas.size[1] - yTopOffset - yBottomOffset @@ -1131,9 +866,6 @@ class MarkerRegression(object): startPosX = xLeftOffset canvas.drawLine(startPosX, startPosY, startPosX + 32, startPosY, color=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH) canvas.drawLine(startPosX, startPosY + stepPosY, startPosX + 32, startPosY + stepPosY, color=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH) - lod = 1 - if self.LRS_LOD == 'LOD': - lod = self.LODFACTOR canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black) canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black) @@ -1156,7 +888,6 @@ class MarkerRegression(object): string3 = cofactor_names else: string2 += 'no cofactors' - string3 = '' elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": string2 = 'Using R/qtl mapping method with ' if self.controlLocus and self.doControl != "false": @@ -1198,9 +929,6 @@ class MarkerRegression(object): yPaddingTop = yTopOffset - displayStartInBases = startMb*self.kONE_MILLION - displayEndInBases = endMb*self.kONE_MILLION - for gIndex, theGO in enumerate(self.geneCol): geneNCBILink = 'http://www.ncbi.nlm.nih.gov/gene?term=%s' if self.dataset.group.species == "mouse": @@ -1215,7 +943,6 @@ class MarkerRegression(object): cdsStart = theGO['cdsStart'] cdsEnd = theGO['cdsEnd'] accession = theGO['NM_ID'] - geneId = theGO['GeneID'] geneSymbol = theGO["GeneSymbol"] strand = theGO["Strand"] exonCount = theGO["exonCount"] @@ -1233,10 +960,7 @@ class MarkerRegression(object): geneStartPix = xLeftOffset; # clip the first in-range gene #color the gene based on SNP density - - #found earlier, needs to be recomputed as snps are added - #always apply colors now, even if SNP Track not checked - Zach 11/24/2010 densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] @@ -1269,7 +993,6 @@ class MarkerRegression(object): txEnd = theGO["TxEnd"] cdsStart = theGO["TxStart"] cdsEnd = theGO["TxEnd"] - geneId = theGO["GeneID"] geneSymbol = theGO["GeneSymbol"] strand = theGO["Strand"] exonCount = 0 @@ -1298,11 +1021,7 @@ class MarkerRegression(object): #Draw Genes geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom - - if 1:#drawClickableRegions: - geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING - else: - geneYLocation += self.BAND_SPACING + geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING #draw the detail view if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3: @@ -1310,7 +1029,6 @@ class MarkerRegression(object): arrowColor = pid.Color(0.7, 0.7, 0.7) #draw the line that runs the entire length of the gene - #canvas.drawString(str(geneStartPix), 300, 400) canvas.drawLine(geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, color=outlineColor, width=1) #draw the arrows @@ -1360,7 +1078,6 @@ class MarkerRegression(object): utrStartPix = xLeftOffset + plotWidth #canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor) - #if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB: if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB: if strand == "-": labelText = "3'" @@ -1382,7 +1099,6 @@ class MarkerRegression(object): utrStartPix = xLeftOffset + plotWidth #canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor) - #if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB: if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB: if strand == "-": labelText = "5'" @@ -1403,8 +1119,6 @@ class MarkerRegression(object): if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol: return - fpText = open(os.path.join(webqtlConfig.TMPDIR, "hallo") + '.txt','wb') - clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0) xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset @@ -1412,13 +1126,9 @@ class MarkerRegression(object): plotHeight = canvas.size[1] - yTopOffset - yBottomOffset yZero = canvas.size[1] - yBottomOffset fontZoom = zoom - widthMultiplier = 1 yPaddingTop = yTopOffset - exprdrawn = 0 - - #thisTrait = self.traitList[0] thisTrait = self.this_trait _strains, _vals, _vars, _aliases = thisTrait.export_informative() @@ -1428,7 +1138,6 @@ class MarkerRegression(object): temp = GeneralObject(name=_strains[ii], value=_val) smd.append(temp) - smd.sort(lambda A, B: cmp(A.value, B.value)) smd.reverse() @@ -1453,13 +1162,9 @@ class MarkerRegression(object): drawit = 0; if drawit == 1: - if self.genotype[0][i].name != " - " : - plotRight = geneEndPix + 4 - - #### end find out PlotRight firstGene = 1 @@ -1514,11 +1219,7 @@ class MarkerRegression(object): #Draw Genes geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom - - if 1:#drawClickableRegions: - geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING - else: - geneYLocation += self.BAND_SPACING + geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING if self.genotype[0][i].name != " - " : @@ -1605,8 +1306,6 @@ class MarkerRegression(object): canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black) canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black) - fpText.close() - ## END HaplotypeAnalyst def drawClickBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -1650,7 +1349,6 @@ class MarkerRegression(object): xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1)) WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT)) - bandWidth = xBrowse2 - xBrowse1 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" @@ -1688,7 +1386,6 @@ class MarkerRegression(object): traitFont = pid.Font(ttf="verdana", size=14, bold=0) chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont) canvas.drawString("Chr %s" % self.ChrList[self.selectedChr][0], chrX, ensemblPaddingTop-5, font=chrFont, color=pid.gray) - traitX = chrX - 28 - canvas.stringWidth("database", font=traitFont) # end of drawBrowserClickableRegions else: #draw the gray text @@ -1696,7 +1393,6 @@ class MarkerRegression(object): traitFont = pid.Font(ttf="verdana", size=14, bold=0) chrX = xLeftOffset + (plotWidth - canvas.stringWidth("Chr %s" % currentChromosome, font=chrFont))/2 canvas.drawString("Chr %s" % currentChromosome, chrX, 32, font=chrFont, color=pid.gray) - traitX = chrX - 28 - canvas.stringWidth("database", font=traitFont) # end of drawBrowserClickableRegions pass @@ -1723,13 +1419,11 @@ class MarkerRegression(object): xAxisLabelColor = pid.black fontHeight = 12*fontZoom # How tall the font that we're using is spacingFromLabelToAxis = 5 - spacingFromLineToLabel = 3 if self.plotScale == 'physic': strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont) ###Physical single chromosome view if self.selectedChr > -1: - graphMbWidth = endMb - startMb XScale = Plot.detScale(startMb, endMb) XStart, XEnd, XStep = XScale if XStep < 8: @@ -1755,7 +1449,6 @@ class MarkerRegression(object): canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0) else: canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark - # end else ###Physical genome wide view else: @@ -1785,7 +1478,6 @@ class MarkerRegression(object): preLpos = -1 distinctCount = 0.0 - #if len(self.genotype) > 1: if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes for i, _chr in enumerate(self.genotype): thisChr = [] @@ -1894,12 +1586,6 @@ class MarkerRegression(object): #LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment. #if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter. - #ZS: I'm not sure what this if statement is supposed to do. It appears to work correctly for both LOD and LRS if I just set lodm to 1.0 - # if self.LRS_LOD == 'LRS': - # lodm = self.LODFACTOR - # else: - # lodm = 1.0 - #ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD if self.lrsMax <= 0: #sliding scale if "lrs_value" in self.qtlresults[0]: @@ -2016,10 +1702,6 @@ class MarkerRegression(object): else: if self.additiveChecked: additiveMax = max(map(lambda X : abs(X['additive']), self.qtlresults)) - #if INTERCROSS: - # dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0])) - #else: - # dominanceMax = -1 lrsEdgeWidth = 2 if zoom == 2: @@ -2038,7 +1720,6 @@ class MarkerRegression(object): startPosX = xLeftOffset for i, qtlresult in enumerate(self.qtlresults): m = 0 - #startPosX = xLeftOffset thisLRSColor = self.colorCollection[0] if qtlresult['chr'] != previous_chr and self.selectedChr == -1: @@ -2085,25 +1766,13 @@ class MarkerRegression(object): startPosX += newStartPosX oldStartPosX = newStartPosX - #startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale - - #for j, _chr in enumerate(self.genotype): #ZS: This is beause the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used if self.plotScale == "physic": this_chr = str(self.ChrList[self.selectedChr][0]) else: this_chr = str(self.ChrList[self.selectedChr][1]+1) if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr: - #AdditiveCoordXY = [] - #DominanceCoordXY = [] - #for k, _locus in enumerate(_chr): Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale - #if self.plotScale == 'physic': - #Xc = startPosX + (_locus.Mb-startMb)*plotXScale - #Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale - #else: - #Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale - #Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale # updated by NL 06-18-2011: # fix the over limit LRS graph issue since genotype trait may give infinite LRS; @@ -2127,11 +1796,6 @@ class MarkerRegression(object): Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max else: Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max - #if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': - #if self.qtlresults[j]['lrs_value'] > 460 or self.qtlresults[j]['lrs_value']=='inf': - # Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max - #else: - # Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max if self.manhattan_plot == True: point_color = pid.black @@ -2144,11 +1808,8 @@ class MarkerRegression(object): additiveMax = 0.000001 Yc = yZero - qtlresult['additive']*AdditiveHeightThresh/additiveMax AdditiveCoordXY.append((Xc, Yc)) - # if not self.multipleInterval and INTERCROSS and self.additiveChecked: - # Yc = yZero - qtlresult['dominance']*DominanceHeightThresh/dominanceMax - # DominanceCoordXY.append((Xc, Yc)) + m += 1 - #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) if self.manhattan_plot != True: canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) @@ -2220,7 +1881,6 @@ class MarkerRegression(object): additiveScale = Plot.detScaleOld(0,additiveMax) additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2] additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) - maxAdd = additiveScale[1] addPlotScale = AdditiveHeightThresh/additiveMax additiveAxisList.append(additiveScale[1]) @@ -2312,298 +1972,6 @@ class MarkerRegression(object): return plotXScale - def calculateAllResult(self, fd): - - weightedRegression = fd.formdata.getvalue('applyVarianceSE') - - self.genotype = self.genotype.addinterval() - resultSlice = [] - controlGeno = [] - - if self.multipleInterval: - self.suggestive = 0 - self.significant = 0 - if self.selectedChr > -1: - self.genotype.chromosome = [self.genotype[self.selectedChr]] - else: - #single interval mapping - try: - self.suggestive = float(fd.formdata.getvalue('permSuggestive')) - self.significant = float(fd.formdata.getvalue('permSignificance')) - except: - self.suggestive = None - self.significant = None - - _strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression) - - if webqtlUtil.ListNotNull(_vars): - pass - else: - weightedRegression = 0 - _strains, _vals, _vars = self.traitList[0].exportInformative() - - ##locate genotype of control Locus - if self.controlLocus: - controlGeno2 = [] - _FIND = 0 - for _chr in self.genotype: - for _locus in _chr: - if _locus.name == self.controlLocus: - controlGeno2 = _locus.genotype - _FIND = 1 - break - if _FIND: - break - if controlGeno2: - _prgy = list(self.genotype.prgy) - for _strain in _strains: - _idx = _prgy.index(_strain) - controlGeno.append(controlGeno2[_idx]) - else: - return "The control marker you selected is not in the genofile." - - if weightedRegression: - self.perm_output = self.genotype.permutation(strains = _strains, trait = _vals, - variance = _vars, nperm=self.nperm) - else: - self.perm_output = self.genotype.permutation(strains = _strains, trait = _vals, - nperm=self.nperm) - - if self.significant and self.suggestive: - pass - else: - if self.nperm < 100: - self.suggestive = 0 - self.significant = 0 - else: - self.suggestive = self.perm_output[int(self.nperm*0.37-1)] - self.significant = self.perm_output[int(self.nperm*0.95-1)] - - #calculating bootstrap - #from now on, genotype could only contain a single chromosome - #permutation need to be performed genome wide, this is not the case for bootstrap - - #due to the design of qtlreaper, composite regression need to be performed genome wide - if not self.controlLocus and self.selectedChr > -1: - self.genotype.chromosome = [self.genotype[self.selectedChr]] - elif self.selectedChr > -1: #self.controlLocus and self.selectedChr > -1 - lociPerChr = map(len, self.genotype) - resultSlice = reduce(lambda X, Y: X+Y, lociPerChr[:self.selectedChr], 0) - resultSlice = [resultSlice,resultSlice+lociPerChr[self.selectedChr]] - else: - pass - - #calculate QTL for each trait - self.qtlresults = [] - - for thisTrait in self.traitList: - _strains, _vals, _vars = thisTrait.exportInformative(weightedRegression) - if self.controlLocus: - if weightedRegression: - qtlresult = self.genotype.regression(strains = _strains, trait = _vals, - variance = _vars, control = self.controlLocus) - else: - qtlresult = self.genotype.regression(strains = _strains, trait = _vals, - control = self.controlLocus) - if resultSlice: - qtlresult = qtlresult[resultSlice[0]:resultSlice[1]] - else: - if weightedRegression: - qtlresult = self.genotype.regression(strains = _strains, trait = _vals, - variance = _vars) - else: - qtlresult = self.genotype.regression(strains = _strains, trait = _vals) - - self.qtlresults.append(qtlresult) - - if not self.multipleInterval: - if self.controlLocus and self.selectedChr > -1: - self.genotype.chromosome = [self.genotype[self.selectedChr]] - - if self.bootChecked: - if controlGeno: - self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, - control = controlGeno, nboot=fd.nboot) - elif weightedRegression: - self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, - variance = _vars, nboot=fd.nboot) - else: - self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, - nboot=fd.nboot) - else: - self.bootResult = [] - - def calculatePValue (self, query_LRS, permutation_LRS_array): - query_index = len(permutation_LRS_array) - for i, one_permutation_LRS in enumerate(permutation_LRS_array): - if one_permutation_LRS >= query_LRS: - query_index = i - break - try: - P_value = float(len(permutation_LRS_array) - query_index) / len(permutation_LRS_array) - except: - P_value = '' - return P_value - - def helpButton(self, anchor): - return HT.Href(self.HELP_PAGE_REF + '#%s' % anchor, self.qmarkImg, target=self.HELP_WINDOW_NAME) - - - def traitRemapTD(self, cursor, fd): - chrList = HT.Select(name="chromosomes", data=self.ChrList, selected=[self.selectedChr], - onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);") - - physicOnly = HT.Span(' *', Class="cr") - - showSNPCheck = HT.Input(type='checkbox', Class='checkbox', name='showSNP', value='ON', checked=self.SNPChecked) - showSNPText = HT.Span('SNP Track ', self.helpButton("snpSeismograph"), Class="fs12 fwn") - - showGenesCheck = HT.Input(type='checkbox', Class='checkbox', name='showGenes', value='ON', checked=self.geneChecked) - showGenesText = HT.Span('Gene Track', Class="fs12 fwn") - - showIntervalAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='intervalAnalystCheck', value='ON', checked=self.intervalAnalystChecked) - showIntervalAnalystText = HT.Span('Interval Analyst', Class="fs12 fwn") -## BEGIN HaplotypeAnalyst - - showHaplotypeAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='haplotypeAnalystCheck', value='ON', checked=self.haplotypeAnalystChecked) - showHaplotypeAnalystText = HT.Span('Haplotype Analyst', Class="fs12 fwn") -## END HaplotypeAnalyst - - leftBox = HT.Input(type="text", name="startMb", size=10) - rightBox = HT.Input(type="text", name="endMb", size=10) - if self.selectedChr > -1 and self.plotScale=='physic': - leftBox.value = self.startMb - rightBox.value = self.endMb - - scaleBox = HT.Select(name="scale", onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);") - scaleBox.append(("Genetic", "morgan")) - if fd.genotype.Mbmap: - scaleBox.append(("Physical", "physic")) - scaleBox.selected.append(self.plotScale) - - permBox = HT.Input(type="checkbox", name="permCheck", value='ON', checked=self.permChecked, Class="checkbox") - permText = HT.Span("Permutation Test ", self.helpButton("Permutation"), Class="fs12 fwn") - bootBox = HT.Input(type="checkbox", name="bootCheck", value='ON', checked=self.bootChecked, Class="checkbox") - bootText = HT.Span("Bootstrap Test ", self.helpButton("bootstrap"), Class="fs12 fwn") - additiveBox = HT.Input(type="checkbox", name="additiveCheck", value='ON', checked=self.additiveChecked, Class="checkbox") - additiveText = HT.Span("Allele Effects ", self.helpButton("additive"), Class="fs12 fwn") - dominanceBox = HT.Input(type="checkbox", name="dominanceCheck", value='ON', checked=self.dominanceChecked, Class="checkbox") - dominanceText = HT.Span("Dominance Effects ", self.helpButton("Dominance"), Class="fs12 fwn") - - lrsRadio = HT.Input(type="radio", name="LRSCheck", value='LRS', checked = (self.LRS_LOD == "LRS")) - lodRadio = HT.Input(type="radio", name="LRSCheck", value='LOD', checked = (self.LRS_LOD != "LRS")) - lrsMaxBox = HT.Input(type="text", name="lrsMax", value=self.lrsMax, size=3) - widthBox = HT.Input(type="text", name="graphWidth", size=5, value=str(self.graphWidth)) - legendBox = HT.Input(type="checkbox", name="viewLegend", value='ON', checked=self.legendChecked, Class="checkbox") - legendText = HT.Span("Legend", Class="fs12 fwn") - - draw2XBox = HT.Input(type="checkbox", name="draw2X", value='ON', Class="checkbox") - draw2XText = HT.Span("2X Plot", Class="fs12 fwn") - - regraphButton = HT.Input(type="button", Class="button", onClick="javascript:databaseFunc(this.form,'showIntMap');", value="Remap") - controlsForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype="multipart/form-data", name="changeViewForm", submit=HT.Input(type='hidden')) - controlsTable = HT.TableLite(border=0) - innerControlsTable = HT.TableLite(border=0) - if self.selectedChr == -1: - minimumGraphWidth = self.MULT_GRAPH_MIN_WIDTH - else: - minimumGraphWidth = self.GRAPH_MIN_WIDTH - innerControlsTable.append( - HT.TR(HT.TD("Chr: ", Class="fs12 fwb ffl"),HT.TD(chrList, scaleBox, regraphButton)), - HT.TR(HT.TD("View: ", Class="fs12 fwb ffl"),HT.TD(leftBox, " to ", rightBox, "Mb", physicOnly, NOWRAP="on")), - HT.TR(HT.TD("Units: ", Class="fs12 fwb ffl"), HT.TD(lrsRadio, "LRS ", lodRadio, "LOD ", self.helpButton("LOD"))), - HT.TR(HT.TD(" ", Class="fs12 fwb ffl"), HT.TD(lrsMaxBox, "units on Y-axis (0 for default)", Class="fs11 fwn")), - HT.TR(HT.TD("Width: ", Class="fs12 fwb ffl"), HT.TD(widthBox, "pixels (minimum=%d)" % minimumGraphWidth, Class="fs11 fwn ")) - ) - #whether SNP - # comment this, because this will make caculation very slow. - #cursor.execute("Select Species.Id from SnpAll, Species where SnpAll.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species) - #SNPorNot = cursor.fetchall() - SNPorNot = True - #Whether Gene - cursor.execute("Select Species.Id from GeneList, Species where GeneList.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species) - GeneorNot = cursor.fetchall() - - if self.multipleInterval: - optionPanel = HT.TD(valign="top", NOWRAP="on") - else: - optionPanel = HT.TD(permBox, permText, HT.BR(), bootBox, bootText, HT.BR(), additiveBox, additiveText, HT.BR(), valign="top", NOWRAP="on") - #whether dominance - if self.genotype.type == 'intercross': - optionPanel.append(dominanceBox, dominanceText, HT.BR()) - if SNPorNot: - optionPanel.append(showSNPCheck, showSNPText, physicOnly, HT.BR()) - if GeneorNot: - optionPanel.append(showGenesCheck, showGenesText, physicOnly, HT.BR(), - showIntervalAnalystCheck, showIntervalAnalystText, physicOnly, HT.BR()) -## BEGIN HaplotypeAnalyst - optionPanel.append(showHaplotypeAnalystCheck, showHaplotypeAnalystText, physicOnly, HT.BR()) -## END HaplotypeAnalyst - optionPanel.append(legendBox, legendText, HT.BR(),draw2XBox, draw2XText) - controlsTable.append( - HT.TR(HT.TD(innerControlsTable, valign="top"), - HT.TD(" ", width=15), optionPanel), - HT.TR(HT.TD(physicOnly, " only apply to single chromosome physical mapping", align="Center", colspan=3, Class="fs11 fwn")) - ) - controlsForm.append(controlsTable) - - controlsForm.append(HT.Input(name="permSuggestive", value=self.suggestive, type="hidden")) - controlsForm.append(HT.Input(name="permSignificance", value=self.significant, type="hidden")) - -## BEGIN HaplotypeAnalyst #### haplotypeAnalystCheck added below -## END HaplotypeAnalyst - - for key in fd.formdata.keys(): - if key == "searchResult" and type([]) == type(fd.formdata.getvalue(key)): - controlsForm.append(HT.Input(name=key, value=string.join(fd.formdata.getvalue(key), "\t"), type="hidden")) - elif key not in ("endMb", "startMb", "chromosomes", "scale", "permCheck", "bootCheck", "additiveCheck", "dominanceCheck", - "LRSCheck", "intervalAnalystCheck", "haplotypeAnalystCheck", "lrsMax", "graphWidth", "viewLegend", 'showGenes', 'showSNP', 'draw2X', - 'permSuggestive', "permSignificance"): - controlsForm.append(HT.Input(name=key, value=fd.formdata.getvalue(key), type="hidden")) - else: - pass - - # updated by NL, move function changeView(i) to webqtl.js and change it to function changeView(i, Chr_Mb_list) - # move function chrLength(a, b, c) to webqtl.js and change it to function chrLength(a, b, c, Chr_Mb_list) - self.dict['js1'] = '<script src="/javascript/sorttable.js"></script>' - return HT.TD(controlsForm, Class="doubleBorder", width=400) - - def traitInfoTD(self, fd): - if self.selectedChr == -1: - intMapHeading = HT.Paragraph('Map Viewer: Whole Genome', Class="title") - else: - intMapHeading = HT.Paragraph('Map Viewer: Chr %s' % self.genotype[0].name, Class="title") - - heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (self.species.title(), fd.RISet) , HT.BR()) - #Trait is from an database - if self.traitList and self.traitList[0] and self.traitList[0].db: - #single trait - if len(self.traitList) == 1: - thisTrait = self.traitList[0] - trait_url = HT.Href(text=thisTrait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \ - "?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (thisTrait.db.name, thisTrait.name), \ - target='_blank', Class="normalsize") - heading2.append(HT.Strong("Database: "), HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name ,\ - target='_blank',Class="normalsize"),HT.BR()) - if thisTrait.db.type == 'ProbeSet': - heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(), - HT.Strong("Gene Symbol: "), HT.Italic('%s' % thisTrait.symbol,id="green"),HT.BR()) - if thisTrait.chr and thisTrait.mb: - heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb)) - elif thisTrait.db.type == 'Geno': - heading2.append(HT.Strong('Locus : '), trait_url, HT.BR()) - if thisTrait.chr and thisTrait.mb: - heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb)) - elif thisTrait.db.type == 'Publish': - heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR()) - else: - pass - else: - heading2.append(HT.Strong("Traits: "), "Multiple Traits") - else: - heading2.append(HT.Strong("Trait Name: "), fd.identification) - return HT.TD(intMapHeading, heading2, valign="top") - def drawPermutationHistogram(self): ######################################### # Permutation Graph @@ -2622,78 +1990,18 @@ class MarkerRegression(object): return filename - # img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test') - - # self.suggestive = self.perm_output[int(self.nperm*0.37-1)] - # self.significant = self.perm_output[int(self.nperm*0.95-1)] - # self.highlysignificant = self.perm_output[int(self.nperm*0.99-1)] - - # permutationHeading = HT.Paragraph('Histogram of Permutation Test') - # permutationHeading.__setattr__("class","title") - - # permutation = HT.TableLite() - # permutation.append(HT.TR(HT.TD(img)), - # HT.TR(HT.TD('')), - # HT.TR(HT.TD('Total of %d permutations'%self.nperm))) - - # return permutation - - def permutationTextFile(self): - filename= webqtlUtil.genRandStr("Reg_") - fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb') - fpText.write('Suggestive LRS (p = 0.63) = %3.2f\n'%self.suggestive) - fpText.write('Significant LRS (p = 0.05) = %3.2f\n'%self.significant) - fpText.write('Highly Significant LRS (p = 0.01) = %3.2f\n\n'%self.highlysignificant) - fpText.write('%s Permutations\n\n' % str(len(self.perm_output))) - LRSInfo =HT.Paragraph(' Suggestive LRS = %3.2f\n'%self.suggestive, - HT.BR(), - ' Significant LRS =%3.2f\n'%self.significant, - HT.BR(), - ' Highly Significant LRS =%3.2f\n' % self.highlysignificant) - - for lrs_value in self.perm_output: - fpText.write(str(lrs_value) + "\n") - - textUrl = HT.Href(text = 'Download Permutation Results', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn') - - return textUrl - def geneTable(self, geneCol, refGene=None): - #SNPLink = 0 #Not sure what this is used for - if self.dataset.group.species == 'mouse' or self.dataset.group.species == 'rat': - #gene_tblobj = {} - self.gene_table_header = self.getGeneTableHeader(refGene=None) + self.gene_table_header = self.getGeneTableHeaderList(refGene=None) self.gene_table_body = self.getGeneTableBody(geneCol, refGene=None) - #gene_tblobj["header"] = self.getGeneTableHeader(refGene=None) - #gene_tblobj["body"] = self.getGeneTableBody(geneCol, refGene=None) - - #sortby = self.getSortByValue() - - #filename= webqtlUtil.genRandStr("Mapping_") - - #objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') - #cPickle.dump(gene_tblobj, objfile) - #objfile.close() - - #gene_table = webqtlUtil.genTableObj(tblobj=gene_tblobj, file=filename, sortby=sortby, tableID="sortable", addIndex="0") else: self.gene_table_header = None self.gene_table_body = None - #gene_table = "" - - #return gene_table - - def getGeneTableHeader(self, refGene=None): - gene_tblobj_header = [] + def getGeneTableHeaderList(self, refGene=None): gene_table_header_list = [] - - col_class = "fs14 fwb ffl b1 cw cbrb" - if self.dataset.group.species == "mouse": - if refGene: gene_table_header_list = ["Index", "Symbol", @@ -2706,25 +2014,6 @@ class MarkerRegression(object): "Mb Start (hg19)", "Literature Correlation", "Gene Description"] - #"PolymiRTS Database" + HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank").__str__(), - #"Gene Weaver Info Content" + HT.Href(url='http://geneweaver.org/', text='>>', target="_blank").__str__()] - - # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), - # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), - # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=2), - # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), - # THCell(HT.TD('SNP',HT.BR(),'Count', align='left', width=47, Class=col_class), text="snp_count", idx=4), - # THCell(HT.TD('SNP',HT.BR(),'Density', align='left', width=78, Class=col_class), text="snp_density", idx=5), - # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=6), - # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), - # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), - # THCell(HT.TD('Literature',HT.BR(),'Correlation', align='left', width=100, Class=col_class), text="lit_corr", idx=9), - # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', width=290, Class=col_class), text="description", idx=10), - # THCell(HT.TD('PolymiRTS',HT.BR(),'Database', HT.BR(), HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"), - # align='left', width=100, Class=col_class), sort=0, idx=11), - # THCell(HT.TD('Gene Weaver', HT.BR(), 'Info Content', HT.BR(), HT.Href(url='http://geneweaver.org/', text='>>', target="_blank", Class="normalsize"), - # align='left', width=110, Class=col_class), sort=0, idx=12), - # ]] else: gene_table_header_list = ["", "Index", @@ -2737,27 +2026,7 @@ class MarkerRegression(object): "Human Chr", "Mb Start (hg19)", "Gene Description"] - #"PolymiRTS Database" + HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank").__str__(), - #"Gene Weaver Info Content" + HT.Href(url='http://geneweaver.org/', text='>>', target="_blank").__str__()] - - # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), - # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), - # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=2), - # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), - # THCell(HT.TD('SNP',HT.BR(),'Count', align='left', width=47, Class=col_class), text="snp_count", idx=4), - # THCell(HT.TD('SNP',HT.BR(),'Density', align='left', width=78, Class=col_class), text="snp_density", idx=5), - # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=6), - # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), - # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), - # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', width=290, Class=col_class), text="description", idx=9), - # THCell(HT.TD('PolymiRTS',HT.BR(),'Database', HT.BR(), HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"), - # align='left', width=100, Class=col_class), sort=0, idx=10), - # THCell(HT.TD('Gene Weaver', HT.BR(), 'Info Content', HT.BR(), HT.Href(url='http://geneweaver.org/', text='>>', target="_blank", Class="normalsize"), - # align='left', width=110, Class=col_class), sort=0, idx=11), - # ]] - elif self.dataset.group.species == "rat": - gene_table_header_list = ["", "Index", "Symbol", @@ -2770,52 +2039,13 @@ class MarkerRegression(object): "Mb Start (hg19)", "Gene Description"] - # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0), - # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1), - # THCell(HT.TD('Mb Start',HT.BR(),'(rn3)', align='left', width=100, Class=col_class), text="mb_start_rn3", idx=2), - # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3), - # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=4), - # THCell(HT.TD('Mouse',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="mouse_chr", idx=5), - # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=6), - # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7), - # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8), - # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', Class=col_class), text="description", idx=9)]] - - else: - pass - return gene_table_header_list - #return gene_tblobj_header def getGeneTableBody(self, geneCol, refGene=None): - - tblobj_body = [] #contains table rows - className = "fs13 b1 c222" - gene_table_body = [] tableIterationsCnt = 0 if self.dataset.group.species == "mouse": - - # polymiRTS - # http://lily.uthsc.edu:8080/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=2&chrom_from=115&chrom_to=125 - #XZ: We can NOT assume their web service is always on. We must put this block of code in try except. - try: - conn = httplib.HTTPConnection("lily.uthsc.edu:8080") - conn.request("GET", "/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=%s&chrom_from=%s&chrom_to=%s" % (self.genotype[0].name, self.startMb, self.endMb)) - response = conn.getresponse() - data = response.read() - data = data.split() - conn.close() - dic = {} - index = 0 - for i in data: - if index%3==0: - dic[data[index]] = HT.Href(url=data[index+2], text=data[index+1], target="_blank", Class="normalsize") - index = index+1 - except Exception: - dic={} - for gIndex, theGO in enumerate(geneCol): tableIterationsCnt = tableIterationsCnt + 1 @@ -2829,7 +2059,6 @@ class MarkerRegression(object): txEnd = theGO["TxEnd"] theGO["snpDensity"] = theGO["snpCount"]/geneLength if self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST: - #accessionString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Display&DB=gene&term=%s' % theGO["NM_ID"] geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"] allProbeString = '%s?cmd=sch&gene=%s&alias=1' % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), theGO["GeneSymbol"]) @@ -2842,10 +2071,6 @@ class MarkerRegression(object): mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"]*1000000.0)) +"&pix=620&Submit=submit" - #Used for sorting - mouseStartValue = int(theGO["TxStart"]) - - #the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: if theGO['humanGene']["TxStart"] == '': @@ -2854,20 +2079,11 @@ class MarkerRegression(object): humanStartDisplay = "%0.6f" % theGO['humanGene']["TxStart"] humanChr = theGO['humanGene']["Chromosome"] - if humanChr.find('q'): - humanChrSort = humanChr[:humanChr.find("q")].join(humanChr[(humanChr.find("q")+1):]) #value used when sorting table - elif humanChr.find('p'): - humanChrSort = humanChr[:humanChr.find("p")].join(humanChr[(humanChr.find("p")+1):]) #value used when sorting table - else: - humanChrSort = humanChr humanTxStart = theGO['humanGene']["TxStart"] - #Used for sorting - humanStartValue = float(theGO['humanGene']["TxStart"]) - humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000*theGO['humanGene']["TxStart"]), int(1000000*theGO['humanGene']["TxEnd"])) else: - humanStartString = humanChr = humanChrSort = humanStartDisplay = humanStartValue = "--" + humanStartString = humanChr = humanStartDisplay = "--" geneDescription = theGO["GeneDescription"] if len(geneDescription) > 26: @@ -2885,22 +2101,12 @@ class MarkerRegression(object): else: avgExpr = "%0.6f" % avgExpr - # polymiRTS - polymiRTS = ' ' - if dic.has_key(theGO["GeneID"]): - polymiRTS = dic[theGO["GeneID"]] - # If we have a referenceGene then we will show the Literature Correlation if theGO["Chromosome"] == "X": chr_as_int = 19 else: chr_as_int = int(theGO["Chromosome"]) - 1 if refGene: - try: - literatureCorrelation = self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) - except: - literatureCorrelation = "N/A" - literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A") this_row = [selectCheck.__str__(), @@ -2915,25 +2121,7 @@ class MarkerRegression(object): HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(), literatureCorrelationString, geneDescription] - #polymiRTS, - - - # this_row.append(TDCell(HT.TD(tableIterationsCnt, selectCheck, width=30, align='right', Class=className), tableIterationsCnt, tableIterationsCnt)) - # this_row.append(TDCell(HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank"), " ", probeSetSearch, align='right', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) - # this_row.append(TDCell(HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank"), align='right', Class=className), str(mouseStartValue), mouseStartValue)) - # this_row.append(TDCell(HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength), align='right', Class=className), "%0.3f" % geneLength, geneLength)) - # this_row.append(TDCell(HT.TD(snpString, align='right', Class=className), str(theGO["snpCount"]), theGO["snpCount"])) - # this_row.append(TDCell(HT.TD(snpDensityStr, align='right', Class=className), snpDensityStr, theGO["snpDensity"])) - # this_row.append(TDCell(HT.TD(avgExpr, align='right', Class=className), "--", "--")) - # this_row.append(TDCell(HT.TD(humanChr, align='right', Class=className), humanChr, humanChrSort)) - # this_row.append(TDCell(HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank"), align='right', Class=className), humanStartDisplay, humanStartValue)) - # this_row.append(TDCell(HT.TD(literatureCorrelationString, align='right', Class=className), literatureCorrelationString, literatureCorrelation)) - # this_row.append(TDCell(HT.TD(geneDescription, align='right', Class=className), geneDescription, geneDescription)) - # this_row.append(TDCell(HT.TD(polymiRTS, align='right', Class=className), "", "")) - # this_row.append(TDCell(HT.TD("", align='right', Class=className), "", "")) - else: - this_row = [selectCheck.__str__(), str(tableIterationsCnt), HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__() + " " + probeSetSearch.__str__(), @@ -2945,29 +2133,11 @@ class MarkerRegression(object): humanChr, HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(), geneDescription] - #polymiRTS, - - - # this_row.append(TDCell(HT.TD(tableIterationsCnt, selectCheck, width=30, align='right', Class=className), tableIterationsCnt, tableIterationsCnt)) - # this_row.append(TDCell(HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank"), " ", probeSetSearch, align='right', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) - # this_row.append(TDCell(HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank"), align='right', Class=className), str(mouseStartValue), mouseStartValue)) - # this_row.append(TDCell(HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength), align='right', Class=className), "%0.3f" % geneLength, geneLength)) - # this_row.append(TDCell(HT.TD(snpString, align='right', Class=className), str(theGO["snpCount"]), theGO["snpCount"])) - # this_row.append(TDCell(HT.TD(snpDensityStr, align='right', Class=className), snpDensityStr, theGO["snpDensity"])) - # this_row.append(TDCell(HT.TD(avgExpr, align='right', Class=className), "--", "--")) - # this_row.append(TDCell(HT.TD(humanChr, align='right', Class=className), humanChr, humanChrSort)) - # this_row.append(TDCell(HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank"), align='right', Class=className), humanStartDisplay, humanStartValue)) - # this_row.append(TDCell(HT.TD(geneDescription, align='right', Class=className), geneDescription, geneDescription)) - # this_row.append(TDCell(HT.TD(polymiRTS, align='right', Class=className), "", "")) - # this_row.append(TDCell(HT.TD("", align='right', Class=className), "", "")) gene_table_body.append(this_row) - #tblobj_body.append(this_row) elif self.dataset.group.species == 'rat': - for gIndex, theGO in enumerate(geneCol): - this_row = [] #container for the cells of each row selectCheck = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)").__str__() #checkbox for each row @@ -2984,7 +2154,6 @@ class MarkerRegression(object): chr_as_int = int(theGO["Chromosome"]) - 1 geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"])) - #geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1)) geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1)) avgExprVal = [] @@ -3003,15 +2172,9 @@ class MarkerRegression(object): #the chromosomes for human 1 are 1qXX.XX if theGO['humanGene']: humanChr = theGO['humanGene']["Chromosome"] - if 'q' in humanChr: - humanChrSort = humanChr[:humanChr.find("q")].join(humanChr[(humanChr.find("q")+1):]) #value used when sorting table - elif 'p' in humanChr: - humanChrSort = humanChr[:humanChr.find("p")].join(humanChr[(humanChr.find("p")+1):]) #value used when sorting table - else: - humanChrSort = humanChr humanTxStart = theGO['humanGene']["TxStart"] else: - humanChr = humanTxStart = humanChrSort = "" + humanChr = humanTxStart = "" geneDesc = theGO["GeneDescription"] if geneDesc == "---": @@ -3029,26 +2192,9 @@ class MarkerRegression(object): humanTxStart, geneDesc] - - #this_row.append(TDCell(HT.TD(gIndex + 1, selectCheck, align='left', Class=className), str(gIndex+1), gIndex+1)) - #this_row.append(TDCell(HT.TD(webqtlSearch, geneSymbolNCBI, align='left', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"])) - #this_row.append(TDCell(HT.TD(theGO["TxStart"], align='left', Class=className), theGO["TxStart"], theGO["TxStart"])) - #this_row.append(TDCell(HT.TD(HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)), align='left', Class=className), "%0.3f" % (geneLength*1000.0), (geneLength*1000.0))) - #this_row.append(TDCell(HT.TD(avgExprVal, align='left', Class=className), "", "")) - #this_row.append(TDCell(HT.TD(mouseChr, align='left', Class=className), mouseChr, mouseChr)) - #this_row.append(TDCell(HT.TD(mouseTxStart, align='left', Class=className), mouseTxStart, mouseTxStart)) - #this_row.append(TDCell(HT.TD(humanChr, align='left', Class=className), humanChr, humanChrSort)) - #this_row.append(TDCell(HT.TD(humanTxStart, align='left', Class=className), humanTxStart, humanTxStart)) - #this_row.append(TDCell(HT.TD(geneDesc, align='left', Class=className), geneDesc, geneDesc)) - gene_table_body.append(this_row) - #tblobj_body.append(this_row) - - else: - pass return gene_table_body - #return tblobj_body def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None): if not geneId1 or not geneId2: @@ -3067,10 +2213,4 @@ class MarkerRegression(object): lCorr = lCorr[0] break except: raise #lCorr = None - return lCorr - - def getSortByValue(self): - - sortby = ("", "") - - return sortby + return lCorr
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index b7ebb9ed..d00b52b8 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1527,6 +1527,36 @@ } }, "mouse": { + "AIL": { + "Hippocampus mRNA": [ + [ + "844", + "UCSD_AIL_HIP_RNA-Seq_0418", + "UCSD AIL Hippocampus (Apr18) RNA-Seq" + ] + ], + "Phenotypes": [ + [ + "None", + "AILPublish", + "AIL Published Phenotypes" + ] + ], + "Prefrontal Cortex mRNA": [ + [ + "846", + "UCSD_AIL_PFC_RNA-Seq_0418", + "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq" + ] + ], + "Striatum mRNA": [ + [ + "845", + "UCSD_AIL_STR_RNA-Seq_0418", + "UCSD AIL Striatum (Apr18) RNA-Seq" + ] + ] + }, "AKXD": { "Genotypes": [ [ @@ -2968,7 +2998,7 @@ "BXD-Bone": { "Phenotypes": [ [ - "None", + "650", "BXD-BonePublish", "BXD-Bone Published Phenotypes" ] @@ -3156,6 +3186,13 @@ ] }, "CIE-RMA": { + "Hippocampus mRNA": [ + [ + "831", + "INIA_UTHSC_Hip_AffyMTA1_May17", + "INIA-UTHSC Hippocampus CIE Affy MTA 1.0 GeneLevel (Mar18) RMA" + ] + ], "Midbrain mRNA": [ [ "830", @@ -3826,6 +3863,10 @@ ], "mouse": [ [ + "AIL", + "AIL Advanced Intercross Line" + ], + [ "AKXD", "AKXD" ], @@ -3875,7 +3916,7 @@ ], [ "BXD-Bone", - "BXD Bone" + "BXD Bone Individual Data" ], [ "BXD-Harvested", @@ -4727,6 +4768,24 @@ ] }, "mouse": { + "AIL": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA" + ], + [ + "Striatum mRNA", + "Striatum mRNA" + ] + ], "AKXD": [ [ "Genotypes", @@ -5111,6 +5170,10 @@ "Phenotypes" ], [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ "Midbrain mRNA", "Midbrain mRNA" ] diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html index 49d7f962..68880829 100644 --- a/wqflask/wqflask/templates/heatmap.html +++ b/wqflask/wqflask/templates/heatmap.html @@ -39,7 +39,6 @@ <script language="javascript" type="text/javascript" src="/static/new/javascript/lodheatmap.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/curvechart.js"></script> -<!-- <script language="javascript" type="text/javascript" src="/static/new/javascript/create_heatmap.js"></script>--> <script language="javascript" type="text/javascript" src="/static/new/javascript/iplotMScanone_noeff.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> |