diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 147 | ||||
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 66 | ||||
| -rw-r--r-- | wqflask/base/species.py | 80 | ||||
| -rw-r--r-- | wqflask/base/template.py | 123 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 206 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 28 | ||||
| -rw-r--r-- | wqflask/base/webqtlFormData.py | 352 |
7 files changed, 6 insertions, 996 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index a4eaaa2e..9ca880d0 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -29,7 +29,6 @@ import json import gzip import cPickle as pickle import itertools -from operator import itemgetter from redis import Redis Redis = Redis() @@ -316,9 +315,6 @@ class DatasetGroup(object): return mapping_id, mapping_names - def get_specified_markers(self, markers = []): - self.markers = HumanMarkers(self.name, markers) - def get_markers(self): logger.debug("self.species is:", self.species) @@ -449,7 +445,6 @@ def datasets(group_name, this_group = None): group_name, webqtlConfig.PUBLICTHRESH, "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) - #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)): for dataset_item in the_results: tissue_name = dataset_item[0] dataset = dataset_item[1] @@ -457,14 +452,10 @@ def datasets(group_name, this_group = None): if tissue_name in ['#PublishFreeze', '#GenoFreeze']: dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) else: - dataset_sub_menu = [item[1:] for item in dataset] - tissue_already_exists = False - tissue_position = None for i, tissue_dict in enumerate(dataset_menu): if tissue_dict['tissue'] == tissue_name: tissue_already_exists = True - tissue_position = i break if tissue_already_exists: @@ -719,20 +710,6 @@ class PhenotypeDataSet(DataSet): # (Urgently?) Need to write this pass - def get_trait_list(self): - query = """ - select PublishXRef.Id - from PublishXRef, PublishFreeze - where PublishFreeze.InbredSetId=PublishXRef.InbredSetId - and PublishFreeze.Id = {} - """.format(escape(str(self.id))) - logger.sql(query) - results = g.db.execute(query).fetchall() - trait_data = {} - for trait in results: - trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) - return trait_data - def get_trait_info(self, trait_list, species = ''): for this_trait in trait_list: @@ -746,7 +723,7 @@ class PhenotypeDataSet(DataSet): #of the post-publication description if this_trait.confidential: this_trait.description_display = "" - continue # for now + continue # for now, because no authorization features if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( privilege=self.privilege, @@ -770,9 +747,7 @@ class PhenotypeDataSet(DataSet): #LRS and its location this_trait.LRS_score_repr = "N/A" - this_trait.LRS_score_value = 0 this_trait.LRS_location_repr = "N/A" - this_trait.LRS_location_value = 1000000 if this_trait.lrs: query = """ @@ -789,17 +764,7 @@ class PhenotypeDataSet(DataSet): LRS_Chr = result[0] LRS_Mb = result[1] - #XZ: LRS_location_value is used for sorting - try: - LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb) - except: - if LRS_Chr.upper() == 'X': - LRS_location_value = 20*1000 + float(LRS_Mb) - else: - LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb) - this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs - this_trait.LRS_score_value = LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb)) def retrieve_sample_data(self, trait): @@ -861,40 +826,13 @@ class GenotypeDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - def get_trait_list(self): - query = """ - select Geno.Name - from Geno, GenoXRef - where GenoXRef.GenoId = Geno.Id - and GenoFreezeId = {} - """.format(escape(str(self.id))) - logger.sql(query) - results = g.db.execute(query).fetchall() - trait_data = {} - for trait in results: - trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) - return trait_data - def get_trait_info(self, trait_list, species=None): for this_trait in trait_list: if not this_trait.haveinfo: this_trait.retrieveInfo() - #XZ: trait_location_value is used for sorting - trait_location_repr = 'N/A' - trait_location_value = 1000000 - if this_trait.chr and this_trait.mb: - try: - trait_location_value = int(this_trait.chr)*1000 + this_trait.mb - except: - if this_trait.chr.upper() == 'X': - trait_location_value = 20*1000 + this_trait.mb - else: - trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb - this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) ) - this_trait.location_value = trait_location_value def retrieve_sample_data(self, trait): query = """ @@ -989,20 +927,6 @@ class MrnaAssayDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - def get_trait_list_1(self): - query = """ - select ProbeSet.Name - from ProbeSet, ProbeSetXRef - where ProbeSetXRef.ProbeSetId = ProbeSet.Id - and ProbeSetFreezeId = {} - """.format(escape(str(self.id))) - logger.sql(query) - results = g.db.execute(query).fetchall() - trait_data = {} - for trait in results: - trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) - return trait_data - def get_trait_info(self, trait_list=None, species=''): # Note: setting trait_list to [] is probably not a great idea. @@ -1034,27 +958,8 @@ class MrnaAssayDataSet(DataSet): # Save it for the jinja2 template this_trait.description_display = description_display - #XZ: trait_location_value is used for sorting - trait_location_repr = 'N/A' - trait_location_value = 1000000 - if this_trait.chr and this_trait.mb: - #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") - #This is so we can convert the location to a number used for sorting - trait_location_value = self.convert_location_to_value(this_trait.chr, this_trait.mb) - #try: - # trait_location_value = int(this_trait.chr)*1000 + this_trait.mb - #except ValueError: - # if this_trait.chr.upper() == 'X': - # trait_location_value = 20*1000 + this_trait.mb - # else: - # trait_location_value = (ord(str(this_trait.chr).upper()[0])*1000 + - # this_trait.mb) - - #ZS: Put this in function currently called "convert_location_to_value" - this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, - float(this_trait.mb)) - this_trait.location_value = trait_location_value + this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb)) #Get mean expression value query = ( @@ -1076,9 +981,7 @@ class MrnaAssayDataSet(DataSet): #LRS and its location this_trait.LRS_score_repr = 'N/A' - this_trait.LRS_score_value = 0 this_trait.LRS_location_repr = 'N/A' - this_trait.LRS_location_value = 1000000 #Max LRS and its Locus location if this_trait.lrs and this_trait.locus: @@ -1093,40 +996,10 @@ class MrnaAssayDataSet(DataSet): if result: lrs_chr, lrs_mb = result - #XZ: LRS_location_value is used for sorting - lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb) this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs - this_trait.LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb)) - - def convert_location_to_value(self, chromosome, mb): - try: - location_value = int(chromosome)*1000 + float(mb) - except ValueError: - if chromosome.upper() == 'X': - location_value = 20*1000 + float(mb) - else: - location_value = (ord(str(chromosome).upper()[0])*1000 + - float(mb)) - - return location_value - - def get_sequence(self): - query = """ - SELECT - ProbeSet.BlatSeq - FROM - ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSet.Id=ProbeSetXRef.ProbeSetId and - ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and - ProbeSet.Name = %s - ProbeSetFreeze.Name = %s - """ % (escape(self.name), escape(self.dataset.name)) - logger.sql(query) - results = g.db.execute(query).fetchone() - return results[0] + return trait_list def retrieve_sample_data(self, trait): query = """ @@ -1150,7 +1023,6 @@ class MrnaAssayDataSet(DataSet): #logger.debug("RETRIEVED RESULTS HERE:", results) return results - def retrieve_genes(self, column_name): query = """ select ProbeSet.Name, ProbeSet.%s @@ -1204,19 +1076,6 @@ class TempDataSet(DataSet): desc = self.handle_pca(desc) return desc - def get_group(self): - query = """ - SELECT - InbredSet.Name, InbredSet.Id - FROM - InbredSet, Temp - WHERE - Temp.InbredSetId = InbredSet.Id AND - Temp.Name = "%s" - """ % self.name - logger.sql(query) - self.group, self.group_id = g.db.execute(query).fetchone() - def retrieve_sample_data(self, trait): query = """ SELECT diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index eb836e6c..6fec5dcd 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -18,21 +18,11 @@ class MrnaAssayTissueData(object): def __init__(self, gene_symbols=None): self.gene_symbols = gene_symbols - self.have_data = False if self.gene_symbols == None: self.gene_symbols = [] - #print("self.gene_symbols:", self.gene_symbols) - self.data = collections.defaultdict(Bunch) - #self.gene_id_dict ={} - #self.data_id_dict = {} - #self.chr_dict = {} - #self.mb_dict = {} - #self.desc_dict = {} - #self.probe_target_desc_dict = {} - query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description from ( select Symbol, max(Mean) as maxmean @@ -52,7 +42,6 @@ class MrnaAssayTissueData(object): in_clause = db_tools.create_in_clause(gene_symbols) #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower - query += ''' Symbol in {} group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean; @@ -67,9 +56,7 @@ class MrnaAssayTissueData(object): for result in results: symbol = result[0] - #if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]: if symbol.lower() in lower_symbols: - #gene_symbols.append(symbol) symbol = symbol.lower() self.data[symbol].gene_id = result.GeneId @@ -79,8 +66,6 @@ class MrnaAssayTissueData(object): self.data[symbol].description = result.description self.data[symbol].probe_target_description = result.Probe_Target_Description - print("self.data: ", pf(self.data)) - ########################################################################### #Input: cursor, symbolList (list), dataIdDict(Dict) #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair, @@ -107,53 +92,4 @@ class MrnaAssayTissueData(object): else: symbol_values_dict[result.Symbol.lower()].append(result.value) - #for symbol in self.data: - # data_id = self.data[symbol].data_id - # symbol_values_dict[symbol] = self.get_tissue_values(data_id) - - - return symbol_values_dict - - - #def get_tissue_values(self, data_id): - # """Gets the tissue values for a particular gene""" - # - # tissue_values=[] - # - # query = """SELECT value, id - # FROM TissueProbeSetData - # WHERE Id IN {}""".format(db_tools.create_in_clause(data_id)) - # - # #try : - # results = g.db.execute(query).fetchall() - # for result in results: - # tissue_values.append(result.value) - # #symbol_values_dict[symbol] = value_list - # #except: - # # symbol_values_pairs[symbol] = None - # - # return tissue_values - -######################################################################################################## -#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol -#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair. -# key is symbol, value is one list of expression values of one probeSet. -#function: wrapper function for getSymbolValuePairDict function -# build gene symbol list if necessary, cut it into small lists if necessary, -# then call getSymbolValuePairDict function and merge the results. -######################################################################################################## - -#def get_trait_symbol_and_tissue_values(symbol_list=None): -# tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list) -# -# #symbolList, -# #geneIdDict, -# #dataIdDict, -# #ChrDict, -# #MbDict, -# #descDict, -# #pTargetDescDict = getTissueProbeSetXRefInfo( -# # GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId) -# -# if len(tissue_data.gene_symbols): -# return get_symbol_values_pairs(tissue_data) + return symbol_values_dict
\ No newline at end of file diff --git a/wqflask/base/species.py b/wqflask/base/species.py index ce763fc3..4ac2213c 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -18,19 +18,6 @@ class TheSpecies(object): self.dataset = dataset #print("self.dataset is:", pf(self.dataset.__dict__)) self.chromosomes = Chromosomes(self.dataset) - self.genome_mb_length = self.chromosomes.get_genome_mb_length() - - #@property - #def chromosomes(self): - # chromosomes = [("All", -1)] - # - # for counter, genotype in enumerate(self.dataset.group.genotype): - # if len(genotype) > 1: - # chromosomes.append((genotype.name, counter)) - # - # print("chromosomes is: ", pf(chromosomes)) - # - # return chromosomes class IndChromosome(object): def __init__(self, name, length): @@ -42,16 +29,11 @@ class IndChromosome(object): """Chromosome length in megabases""" return self.length / 1000000 - def set_cm_length(self, genofile_chr): - self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM - - class Chromosomes(object): def __init__(self, dataset): self.dataset = dataset self.chromosomes = collections.OrderedDict() - query = """ Select Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet @@ -64,64 +46,4 @@ class Chromosomes(object): results = g.db.execute(query).fetchall() for item in results: - self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) - - self.set_mb_graph_interval() - #self.get_cm_length_list() - - - def set_mb_graph_interval(self): - """Empirical megabase interval""" - - if self.chromosomes: - self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) - else: - self.mb_graph_interval = 1 - - #if self.chromosomes: - #assert self.chromosomes, "Have to add some code back in apparently to set it to 1" - #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12) - #else: - #self.mb_graph_interval = 1 - - - def get_genome_mb_length(self): - """Gets the sum of each chromosome's length in megabases""" - - return sum([ind_chromosome.mb_length for ind_chromosome in self.chromosomes.values()]) - - - def get_genome_cm_length(self): - """Gets the sum of each chromosome's length in centimorgans""" - - return sum([ind_chromosome.cm_length for ind_chromosome in self.chromosomes.values()]) - - def get_cm_length_list(self): - """Chromosome length in centimorgans - - Calculates the length in centimorgans by subtracting the centimorgan position - of the last marker in a chromosome by the position of the first marker - - """ - - self.dataset.group.read_genotype_file() - - self.cm_length_list = [] - - for chromosome in self.dataset.group.genotype: - self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM) - - print("self.cm_length_list:", pf(self.cm_length_list)) - - assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!" - for counter, chromosome in enumerate(self.chromosomes.values()): - chromosome.cm_length = self.cm_length_list[counter] - #self.chromosomes[counter].cm_length = item - - for key, value in self.chromosomes.items(): - print("bread - %s: %s" % (key, pf(vars(value)))) - - -# Testing -#if __name__ == '__main__': -# foo = dict(bar=dict(length)) + self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
\ No newline at end of file diff --git a/wqflask/base/template.py b/wqflask/base/template.py deleted file mode 100644 index aa8f90dc..00000000 --- a/wqflask/base/template.py +++ /dev/null @@ -1,123 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -template = """ -<?XML VERSION="1.0" ENCODING="UTF-8"> -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> -<HTML> -<HEAD> -<TITLE>%s</TITLE> - -<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> -<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine"> -<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." > -<META NAME="author" CONTENT ="GeneNetwork developers" > -<META NAME="geo.placename" CONTENT ="Memphis, TN" > -<META NAME="geo.region" CONTENT="US-TN"> -%s -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> -<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" /> -<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" /> -<link type="text/css" href='/css/custom-theme/jquery-ui-1.8.12.custom.css' rel='Stylesheet' /> -<link type="text/css" href='/css/tab_style.css' rel='Stylesheet' /> - -<script type="text/javascript" src="/javascript/jquery-1.5.2.min.js"></script> -<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> -<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT> -<SCRIPT SRC="/javascript/tablesorter.js"></SCRIPT> -<SCRIPT SRC="/javascript/jqueryFunction.js"></SCRIPT> -<script src="/javascript/tabbed_pages.js" type="text/javascript"></script> -<script src="/javascript/jquery-ui-1.8.12.custom.min.js" type="text/javascript"></script> -%s - -<script type="text/javascript"> - var _gaq = _gaq || []; - _gaq.push(['_setAccount', 'UA-3782271-1']); - _gaq.push(['_trackPageview']); - (function() { - var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; - ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; - var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); - })(); -</script> -</HEAD> -<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff %s> -%s -<TABLE cellSpacing=5 cellPadding=4 width="100%%" border=0> - <TBODY> - <!-- Start of header --> - <TR> - %s - </TR> - <!-- End of header --> - - <!-- Start of body --> - <TR> - <TD bgColor=#eeeeee class="solidBorder"> - <Table width= "100%%" cellSpacing=0 cellPadding=5> - <TR> - %s - </TR> - </TABLE> - </TD> - </TR> - <!-- End of body --> - - <!-- Start of footer --> - <TR> - <TD align=center bgColor=#ddddff class="solidBorder"> - <TABLE width="90%%">%s</table> - </td> - </TR> - <!-- End of footer --> -</TABLE> - -<!-- menu script itself. you should not modify this file --> -<script language="JavaScript" src="/javascript/menu_new.js"></script> -<!-- items structure. menu hierarchy and links are stored there --> -<script language="JavaScript" src="/javascript/menu_items.js"></script> -<!-- files with geometry and styles structures --> -<script language="JavaScript" src="/javascript/menu_tpl.js"></script> -<script language="JavaScript"> - <!--// - // Note where menu initialization block is located in HTML document. - // Don't try to position menu locating menu initialization block in - // some table cell or other HTML element. Always put it before </body> - // each menu gets two parameters (see demo files) - // 1. items structure - // 2. geometry structure - new menu (MENU_ITEMS, MENU_POS); - // make sure files containing definitions for these variables are linked to the document - // if you got some javascript error like "MENU_POS is not defined", then you've made syntax - // error in menu_tpl.js file or that file isn't linked properly. - - // also take a look at stylesheets loaded in header in order to set styles - //--> -</script> -</BODY> -</HTML> -""" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index acc055d8..b71dacf6 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -25,10 +25,6 @@ logger = getLogger(__name__ ) from wqflask import user_manager -def print_mem(stage=""): - mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss - print("{}: {}".format(stage, mem/1024)) - class GeneralTrait(object): """ Trait class defines a trait in webqtl, can be either Microarray, @@ -63,9 +59,7 @@ class GeneralTrait(object): self.symbol = None self.LRS_score_repr = "N/A" - self.LRS_score_value = 0 self.LRS_location_repr = "N/A" - self.LRS_location_value = 1000000 if kw.get('fullname'): name2 = value.split("::") @@ -82,90 +76,6 @@ class GeneralTrait(object): if get_sample_info != False: self = retrieve_sample_data(self, self.dataset) - - def get_name(self): - stringy = "" - if self.dataset and self.name: - stringy = "%s::%s" % (self.dataset, self.name) - if self.cellid: - stringy += "::" + self.cellid - else: - stringy = self.description - return stringy - - - def get_given_name(self): - """ - when user enter a trait or GN generate a trait, user want show the name - not the name that generated by GN randomly, the two follow function are - used to give the real name and the database. displayName() will show the - database also, getGivenName() just show the name. - For other trait, displayName() as same as getName(), getGivenName() as - same as self.name - - Hongqiang 11/29/07 - - """ - stringy = self.name - if self.dataset and self.name: - desc = self.dataset.get_desc() - if desc: - #desc = self.handle_pca(desc) - stringy = desc - return stringy - - - def display_name(self): - stringy = "" - if self.dataset and self.name: - desc = self.dataset.get_desc() - #desc = self.handle_pca(desc) - if desc: - #desc = self.handle_pca(desc) - #stringy = desc - #if desc.__contains__('PCA'): - # desc = desc[desc.rindex(':')+1:].strip() - #else: - # desc = desc[:desc.index('entered')].strip() - #desc = self.handle_pca(desc) - stringy = "%s::%s" % (self.dataset, desc) - else: - stringy = "%s::%s" % (self.dataset, self.name) - if self.cellid: - stringy += "::" + self.cellid - else: - stringy = self.description - - return stringy - - - #def __str__(self): - # #return "%s %s" % (self.getName(), self.group) - # return self.getName() - #__str__ = getName - #__repr__ = __str__ - - def export_data(self, samplelist, the_type="val"): - """ - export data according to samplelist - mostly used in calculating correlation - - """ - result = [] - for sample in samplelist: - if self.data.has_key(sample): - if the_type=='val': - result.append(self.data[sample].val) - elif the_type=='var': - result.append(self.data[sample].var) - elif the_type=='N': - result.append(self.data[sample].N) - else: - raise KeyError, `the_type`+' the_type is incorrect.' - else: - result.append(None) - return result - def export_informative(self, include_variance=0): """ export informative sample @@ -185,19 +95,6 @@ class GeneralTrait(object): sample_aliases.append(sample_data.name2) return samples, vals, the_vars, sample_aliases - - @property - def name_header_fmt(self): - '''Return a human-readable name for use in page header''' - if self.dataset.type == 'ProbeSet': - return self.symbol - elif self.dataset.type == 'Geno': - return self.name - elif self.dataset.type == 'Publish': - return self.post_publication_abbreviation - else: - return "unnamed" - @property def description_fmt(self): '''Return a text formated description''' @@ -252,29 +149,6 @@ class GeneralTrait(object): fmt += (' on the minus strand ') return fmt - -# In ProbeSet, there are maybe several annotations match one sequence -# so we need use sequence(BlatSeq) as the identification, when we update -# one annotation, we update the others who match the sequence also. -# -# Hongqiang Li, 3/3/2008 -def getSequence(trait, dataset_name): - dataset = create_dataset(dataset_name) - - if dataset.type == 'ProbeSet': - results = g.db.execute(''' - SELECT - ProbeSet.BlatSeq - FROM - ProbeSet, ProbeSetFreeze, ProbeSetXRef - WHERE - ProbeSet.Id=ProbeSetXRef.ProbeSetId and - ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and - ProbeSet.Name = %s - ProbeSetFreeze.Name = %s - ''', trait.name, dataset.name).fetchone() - - return results[0] def retrieve_sample_data(trait, dataset, samplelist=None): if samplelist == None: @@ -293,18 +167,6 @@ def retrieve_sample_data(trait, dataset, samplelist=None): if not samplelist or (samplelist and name in samplelist): trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) return trait - -def convert_location_to_value(chromosome, mb): - try: - location_value = int(chromosome)*1000 + float(mb) - except ValueError: - if chromosome.upper() == 'X': - location_value = 20*1000 + float(mb) - else: - location_value = (ord(str(chromosome).upper()[0])*1000 + - float(mb)) - - return location_value @app.route("/trait/get_sample_data") def get_sample_data(): @@ -542,38 +404,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait.pubmed_id: trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id - - trait.homologeneid = None if dataset.type == 'ProbeSet' and dataset.group: - if trait.geneid: - #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. - #XZ: So I have to test if geneid is number before execute the query. - #XZ: The geneid values in database should be cleaned up. - #try: - # float(self.geneid) - # geneidIsNumber = True - #except ValueError: - # geneidIsNumber = False - #if geneidIsNumber: - query = """ - SELECT - HomologeneId - FROM - Homologene, Species, InbredSet - WHERE - Homologene.GeneId ='%s' AND - InbredSet.Name = '%s' AND - InbredSet.SpeciesId = Species.Id AND - Species.TaxonomyId = Homologene.TaxonomyId - """ % (escape(str(trait.geneid)), escape(dataset.group.name)) - logger.sql(query) - result = g.db.execute(query).fetchone() - #else: - # result = None - - if result: - trait.homologeneid = result[0] - description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') @@ -589,46 +420,19 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): # Save it for the jinja2 template trait.description_display = description_display - #XZ: trait_location_value is used for sorting trait.location_repr = 'N/A' - trait.location_value = 1000000 - if trait.chr and trait.mb: - #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") - #This is so we can convert the location to a number used for sorting - trait_location_value = convert_location_to_value(trait.chr, trait.mb) - #try: - # trait_location_value = int(self.chr)*1000 + self.mb - #except ValueError: - # if self.chr.upper() == 'X': - # trait_location_value = 20*1000 + self.mb - # else: - # trait_location_value = (ord(str(self.chr).upper()[0])*1000 + - # self.mb) - - #ZS: Put this in function currently called "convert_location_to_value" trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) - trait.location_value = trait_location_value elif dataset.type == "Geno": trait.location_repr = 'N/A' - trait.location_value = 1000000 - if trait.chr and trait.mb: - #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") - #This is so we can convert the location to a number used for sorting - trait_location_value = convert_location_to_value(trait.chr, trait.mb) - - #ZS: Put this in function currently called "convert_location_to_value" trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb)) - trait.location_value = trait_location_value if get_qtl_info: #LRS and its location trait.LRS_score_repr = "N/A" - trait.LRS_score_value = 0 trait.LRS_location_repr = "N/A" - trait.LRS_location_value = 1000000 if dataset.type == 'ProbeSet' and not trait.cellid: query = """ SELECT @@ -699,19 +503,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.locus = trait.lrs = trait.additive = "" if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "": - #XZ: LRS_location_value is used for sorting - try: - LRS_location_value = int(trait.locus_chr)*1000 + float(trait.locus_mb) - except: - if trait.locus_chr.upper() == 'X': - LRS_location_value = 20*1000 + float(trait.locus_mb) - else: - LRS_location_value = ord(str(trait.locus_chr).upper()[0])*1000 + float(trait.locus_mb) - trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb)) if trait.lrs != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs - trait.LRS_score_value = LRS_score_value = trait.lrs else: raise KeyError, `trait.name`+' information is not found in the database.' diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 1e66e957..4708bf0a 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -20,46 +20,20 @@ USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4} #minimum number of informative strains KMININFORMATIVE = 5 -#maximum number of traits for interval mapping -MULTIPLEMAPPINGLIMIT = 11 - -#maximum number of traits for correlation -MAXCORR = 100 - #Daily download limit from one IP DAILYMAXIMUM = 1000 #maximum LRS value MAXLRS = 460.0 -#temporary data life span -MAXLIFE = 86400 - #MINIMUM Database public value PUBLICTHRESH = 0 -#NBCI address -NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" -UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s" -GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s" -OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s" -UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"; -HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s" +#EXTERNAL LINK ADDRESSES PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" -UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit" UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s' -UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s" -ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s' -DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s' -UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s" -GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit" -ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" - -# The following paths are no longer in use! -# HTMLPATH is replaced by GENODIR -# IMGDIR is replaced by GENERATED_IMAGE_DIR # Temporary storage (note that this TMPDIR can be set as an # environment variable - use utility.tools.TEMPDIR when you diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py deleted file mode 100644 index 10251756..00000000 --- a/wqflask/base/webqtlFormData.py +++ /dev/null @@ -1,352 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by GeneNetwork Core Team 2010/10/20 - -#from mod_python import Cookie - -from __future__ import print_function -from pprint import pformat as pf - -import string -import os - -import reaper - -import webqtlConfig -from webqtlCaseData import webqtlCaseData -from utility import webqtlUtil - -class webqtlFormData(object): - 'Represents data from a WebQTL form page, needed to generate the next page' - - attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance' - 'suggestive','significance','submitID','identification', 'enablevariance', - 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') - - #XZ: Attention! All attribute values must be picklable! - - def __init__(self, - start_vars = None, - req = None, - mod_python_session=None, - FieldStorage_formdata=None): - # Todo: rework this whole thing - print("in webqtlFormData start_vars are:", pf(start_vars)) - for item in webqtlFormData.attrs: - self.__dict__[item] = None - - #ZS: This is only used in DataEditingPage.py (as far as I know) - self.varianceDispName = None - - for item in start_vars: - self.__dict__[item] = start_vars[item] - print(" Now self.dict is:", pf(self.__dict__)) - - #Todo: This can't be good below...rework - try: - self.remote_ip = req.connection.remote_ip - except: - self.remote_ip = '1.2.3.4' - - if req and req.headers_in.has_key('referer'): - self.refURL = req.headers_in['referer'] - else: - self.refURL = None - - # For now let's just comment all this out - Sam - - #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie. - # - ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable. - #self.input_session_data = sessionData.sessionData( mod_python_session ) - # - ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data. - #self.formdata = cgiData( FieldStorage_formdata ) - # - ##get Form ID - #self.formID = self.formdata.getfirst('FormID') - # - ##get rest of the attributes - #if self.formID: - # for item in self.attrs: - # value = self.formdata.getfirst(item) - # if value != None: - # setattr(self,item,string.strip(value)) - - self.ppolar = None - self.mpolar = None - - print("[yellow] self.group is:", self.group) - if self.group: - #try: - # # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group] - #except: - # f1 = f12 = self.mpolar = self.ppolar = None - - - def set_number(stringy): - return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000 - - self.nperm = set_number(self.nperm) - self.nboot = set_number(self.nboot) - - - #if self.allsamplelist: - # self.allsamplelist = map(string.strip, string.split(self.allsamplelist)) - print("self.allsamplelist is:", self.allsamplelist) - if self.allsamplelist: - self.allsamplelist = self.allsamplelist.split() - print("now self.allsamplelist is:", self.allsamplelist) - #self.readGenotype() - #self.readData() - - if self.group == 'BXD300': - self.group = 'BXD' - - - def __getitem__(self, key): - print("in __getitem__") - return self.__dict__[key] - - def get(self, key, default=None): - if key in self.__dict__: - return self.__dict__[key] - else: - return default - - def __str__(self): - rstr = '' - for item in self.attrs: - if item != 'genotype': - rstr += '%s:%s\n' % (item,str(getattr(self,item))) - return rstr - - - def readGenotype(self): - '''read genotype from .geno file''' - if self.group == 'BXD300': - self.group = 'BXD' - - assert self.group, "self.group needs to be set" - - #genotype_1 is Dataset Object without parents and f1 - #genotype_2 is Dataset Object with parents and f1 (not for intercross) - - self.genotype_1 = reaper.Dataset() - - full_filename = locate(self.group + '.geno','genotype') - - # reaper barfs on unicode filenames, so here we ensure it's a string - full_filename = str(full_filename) - self.genotype_1.read(full_filename) - - print("Got to after read") - - try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.group] - except KeyError: - _f1 = _f12 = _mat = _pat = None - - self.genotype_2 = self.genotype_1 - if self.genotype_1.type == "group" and _mat and _pat: - self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1) - - #determine default genotype object - if self.incparentsf1 and self.genotype_1.type != "intercross": - self.genotype = self.genotype_2 - else: - self.incparentsf1 = 0 - self.genotype = self.genotype_1 - - self.samplelist = list(self.genotype.prgy) - self.f1list = [] - self.parlist = [] - - if _f1 and _f12: - self.f1list = [_f1, _f12] - if _mat and _pat: - self.parlist = [_mat, _pat] - - - def readData(self, samplelist, incf1=None): - '''read user input data or from trait data and analysis form''' - - if incf1 == None: - incf1 = [] - - if not self.genotype: - self.readGenotype() - if not samplelist: - if incf1: - samplelist = self.f1list + self.samplelist - else: - samplelist = self.samplelist - - #print("before traitfiledata self.traitfile is:", pf(self.traitfile)) - - traitfiledata = getattr(self, "traitfile", None) - traitpastedata = getattr(self, "traitpaste", None) - variancefiledata = getattr(self, "variancefile", None) - variancepastedata = getattr(self, "variancepaste", None) - Nfiledata = getattr(self, "Nfile", None) - - #### Todo: Rewrite below when we get to someone submitting their own trait ##### - - def to_float(item): - try: - return float(item) - except ValueError: - return None - - print("bottle samplelist is:", samplelist) - if traitfiledata: - tt = traitfiledata.split() - values = map(webqtlUtil.StringAsFloat, tt) - elif traitpastedata: - tt = traitpastedata.split() - values = map(webqtlUtil.StringAsFloat, tt) - else: - print("mapping formdataasfloat") - #values = map(self.FormDataAsFloat, samplelist) - values = [to_float(getattr(self, key)) for key in samplelist] - print("rocket values is:", values) - - - if len(values) < len(samplelist): - values += [None] * (len(samplelist) - len(values)) - elif len(values) > len(samplelist): - values = values[:len(samplelist)] - print("now values is:", values) - - - if variancefiledata: - tt = variancefiledata.split() - variances = map(webqtlUtil.StringAsFloat, tt) - elif variancepastedata: - tt = variancepastedata.split() - variances = map(webqtlUtil.StringAsFloat, tt) - else: - variances = map(self.FormVarianceAsFloat, samplelist) - - if len(variances) < len(samplelist): - variances += [None]*(len(samplelist) - len(variances)) - elif len(variances) > len(samplelist): - variances = variances[:len(samplelist)] - - if Nfiledata: - tt = string.split(Nfiledata) - nsamples = map(webqtlUtil.IntAsFloat, tt) - if len(nsamples) < len(samplelist): - nsamples += [None]*(len(samplelist) - len(nsamples)) - else: - nsamples = map(self.FormNAsFloat, samplelist) - - ##values, variances, nsamples is obsolete - self.allTraitData = {} - for i, _sample in enumerate(samplelist): - if values[i] != None: - self.allTraitData[_sample] = webqtlCaseData( - _sample, values[i], variances[i], nsamples[i]) - print("allTraitData is:", pf(self.allTraitData)) - - - - def informativeStrains(self, samplelist=None, include_variances = None): - '''if readData was called, use this to output informative samples (sample with values)''' - - if not samplelist: - samplelist = self.samplelist - - samples = [] - values = [] - variances = [] - - #print("self.allTraitData is:", pf(self.allTraitData)) - - for sample in samplelist: - if sample in self.allTraitData: - _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance - if _val != None: - if include_variances: - if _var != None: - samples.append(sample) - values.append(_val) - variances.append(_var) - else: - samples.append(sample) - values.append(_val) - variances.append(None) - - return samples, values, variances, len(samples) - - - - #def FormDataAsFloat(self, key): - # - # #try: - # # return float(self.key) - # #except: - # # return None - - - def FormVarianceAsFloat(self, key): - try: - return float(self.formdata.getfirst('V' + key)) - except: - return None - - def FormNAsFloat(self, key): - try: - return int(self.formdata.getfirst('N' + key)) - except: - return None - - def Sample(self): - 'Create some dummy data for testing' - self.group = 'BXD' - self.incparentsf1 = 'on' - #self.display = 9.2 - #self.significance = 16.1 - self.readGenotype() - self.identification = 'BXD : Coat color example by Lu Lu, et al' - #self.readGenotype() - #self.genotype.ReadMM('AXBXAforQTL') - #self.samplelist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy) - #self.samplelist.sort() - self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2), - 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2), - 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4), - 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2), - 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3), - 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3), - 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2), - 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4), - 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4), - 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1), - 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4), - 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4), - 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)} |