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Diffstat (limited to 'web/webqtl/search/TextSearchPage.py')
| -rwxr-xr-x | web/webqtl/search/TextSearchPage.py | 536 |
1 files changed, 536 insertions, 0 deletions
diff --git a/web/webqtl/search/TextSearchPage.py b/web/webqtl/search/TextSearchPage.py new file mode 100755 index 00000000..42ff72c4 --- /dev/null +++ b/web/webqtl/search/TextSearchPage.py @@ -0,0 +1,536 @@ +# 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 + +import string +import os +import cPickle +from math import * + +import reaper +from htmlgen import HTMLgen2 as HT + +from base import admin +from base import webqtlConfig +from base.templatePage import templatePage +from utility import webqtlUtil +from base.webqtlDataset import webqtlDataset +from base.webqtlTrait import webqtlTrait +from utility.THCell import THCell +from utility.TDCell import TDCell +from utility import webqtlUtil + + + +class TextSearchPage(templatePage): + maxReturn = 200 + + def __init__(self, fd): + + templatePage.__init__(self, fd) + + if not self.openMysql(): + return + + # updated by NL, deleted jquery here, move it to dhtml.js + self.dict['js1'] = '' + + species_list = [] #List of species (mouse, rat, human), with the selected species listed first + + input_species = string.strip(string.lower(fd.formdata.getfirst('species', "mouse"))) #XZ, Oct 28, 2009: I changed the default species to mouse. + species_list.append(input_species) + #Create list of species (mouse, rat, human) with the species the user selected first + for species in ["mouse","rat","human"]: + if species not in species_list: + species_list.append(species) + + ADMIN_tissue_alias = admin.ADMIN_tissue_alias + + tissue = string.strip(string.lower(fd.formdata.getfirst('tissue', ""))) + if tissue: + try: + rev_ADMIN_tissue_alias = {} + for key in ADMIN_tissue_alias.keys(): + rev_ADMIN_tissue_alias[key] = key + for alias in ADMIN_tissue_alias[key]: + rev_ADMIN_tissue_alias[alias.upper()] = key + tissue = rev_ADMIN_tissue_alias[tissue.upper()] + except: + tissue = "UNKNOWN" + + #possibly text output + txtOutput = [] #ZS: if format=text + all_species_dataset_count = 0 #XZ: count of datasets across all species; used in the opening text of the page + all_species_trait_count = 0 #XZ: count of records across all species; used in opening text of the page and text file (if format = text) + + #div containing the tabs (species_container), the tabs themselves (species_tab_list, which is inserted into species_tabs), and the table (species_table) containing both the tissue and results tables for each tab + species_container = HT.Div(id="species_tabs", Class="tab_container") #Div that will contain tabs for mouse/rat/human species; each tab contains a table with the result count for each tissue group + species_tab_list = [HT.Href(text="%s" % species_list[0].capitalize(), url="#species1"), HT.Href(text="%s" % species_list[1].capitalize(), url="#species2"), HT.Href(text="%s" % species_list[2].capitalize(), url="#species3")] + species_tabs = HT.List(species_tab_list, Class="tabs") + species_table = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") + + for i in range(len(species_list)): + species_container_table = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") #ZS: Table containing both the tissue record count and trait record tables as cells; this fixes a display issue in some browsers that places the tables side by side instead of top/bottom + + species = species_list[i] + ADMIN_search_dbs = admin.ADMIN_search_dbs[species] + this_species_dataset_count = 0 #XZ: count of the datasets containing results for this species + this_species_trait_count = 0 #XZ: count of the trait records for this species + + div = HT.Div(id="species%s" % (i+1), Class="tab_content") + tab_container = HT.Span() #ZS: Contains species_container_table within the species' tab + + tissuePageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") + tissue_tblobj = {} # object used to create the table listing the results for each tissue + tissue_tblobj['header'] = self.getTissueTableHeader() # creates header for table listing results for selected tissue + + traitPageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") + trait_tblobj = {} # object used to create the table listing the trait results for each tissue + trait_tblobj['header'] = self.getTraitTableHeader() # creates header for table listing trait results for selected tissue + + tissue_tblobj['body'], trait_tblobj['body'], this_species_dataset_count, this_species_trait_count, this_species_txtOutput = self.createTableBodies(fd, species, tissue, ADMIN_search_dbs) + + if species == input_species: + txtOutput = this_species_txtOutput + + filename1 = webqtlUtil.genRandStr("Search_") #filename for tissue table object + tissue_objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename1), 'wb') + cPickle.dump(tissue_tblobj, tissue_objfile) + tissue_objfile.close() + + tissue_sortby = self.getTissueSortByValue() # sets how the tissue table should be sorted by default + tissue_div = HT.Div(webqtlUtil.genTableObj(tblobj=tissue_tblobj, file=filename1, sortby=tissue_sortby, tableID = "tissue_sort%s" % (i+1), addIndex = "1"), Id="tissue_sort%s" % (i+1)) + + tissuePageTable.append(HT.TR(HT.TD(" "))) + tissuePageTable.append(HT.TR(HT.TD(tissue_div))) + tissuePageTable.append(HT.TR(HT.TD(" "))) + species_container_table.append(HT.TR(HT.TD(tissuePageTable)), HT.TR(HT.TD(" "))) + + + filename2 = webqtlUtil.genRandStr("Search_") #filename for trait table object + trait_objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename2), 'wb') + cPickle.dump(trait_tblobj, trait_objfile) + trait_objfile.close() + + trait_sortby = self.getTraitSortByValue() # sets how the trait table should be sorted by default + trait_div = HT.Div(webqtlUtil.genTableObj(tblobj=trait_tblobj, file=filename2, sortby=trait_sortby, tableID = "results_sort%s" % (i+1), addIndex = "0"), Id="results_sort%s" % (i+1)) + + traitPageTable.append(HT.TR(HT.TD(" "))) + traitPageTable.append(HT.TR(HT.TD(trait_div))) + traitPageTable.append(HT.TR(HT.TD(" "))) + species_container_table.append(HT.TR(HT.TD(traitPageTable)), HT.TR(HT.TD(" "))) + + if this_species_trait_count == 0: + tab_container.append(HT.Div("No records retrieved for this species.", align="left", valign="top", style="font-size:42")) + else: + tab_container.append(species_container_table) + + all_species_dataset_count += this_species_dataset_count + all_species_trait_count += this_species_trait_count + + div.append(tab_container) + species_table.append(HT.TR(HT.TD(div))) + + species_container.append(species_table) + + + + + if fd.returnFmt != 'text': #if the format is not 'text' + self.dict['title'] = 'Search Results' + TD_LR = HT.TD(height=100,width="100%",bgColor='#fafafa',valign="top") + pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") # Table containing all of the page's elements (opening text, form); in some browers the elements arrange themselves horizontally if you don't put them into a table, so this fixes that problem + + formTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="100%",border=0) # Table containing all of the form's elements (tabs, option buttons); used to correct the same issue mentioned in pageTable's comment + + mainForm = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden')) + hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet} + hddn['incparentsf1']='ON' + for key in hddn.keys(): + mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) + + #Add to collection, select all, invert selection, and deselect all ("reset") buttons + addselect = HT.Href(url="#redirect", Class="add_traits") + 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) + selectall = HT.Href(url="#redirect", onClick="checkAll(document.getElementsByName('showDatabase')[0]);") + selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;") + selectall.append(selectall_img) + selectinvert = HT.Href(url="#redirect", onClick="checkInvert(document.getElementsByName('showDatabase')[0];") + selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;") + selectinvert.append(selectinvert_img) + reset = HT.Href(url="#redirect", onClick="checkNone(document.getElementsByName('showDatabase')[0]); return false;") + reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;") + reset.append(reset_img) + + #Table with select, deselect, invert, etc. It is used for the results table. + optionsTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="20%",border=0) + optionsRow = HT.TR(HT.TD(selectall, width="25%"), HT.TD(reset, width="25%"), HT.TD(selectinvert, width="25%"), HT.TD(addselect, width="25%")) + labelsRow = HT.TR(HT.TD(" "*2,"Select", width="25%"), HT.TD(" ","Deselect", width="25%"), HT.TD(" "*3,"Invert", width="25%"), HT.TD(" "*4,"Add", width="25%")) + optionsTable.append(HT.TR(HT.TD(" ")), optionsRow, labelsRow) + + if fd.geneName: + searchType = "gene name " + fd.geneName + elif fd.refseq: + searchType = "RefSeq accession number " + fd.refseq + elif fd.genbankid: + searchType = "Genbank ID " + fd.genbankid + elif fd.geneid: + searchType = "Gene ID " + fd.geneid + else: + searchType = "" + + SearchText = HT.Span("You searched for the %s in GeneNetwork." % searchType, HT.BR(), + "We queried %s expression datasets across %s species and listed the results" % (all_species_dataset_count, len(species_list)), HT.BR(), + "below. A total of %s records that may be of interest to you were found. The" % all_species_trait_count, HT.BR(), + "top table lists the number of results found for each relevant tissue, and the", HT.BR(), + "bottom gives a basic summary of each result. To study one of the results, click", HT.BR(), + "its Record ID. More detailed information is also available for each result's group", HT.BR() , + "and dataset. To switch between species, click the tab with the corresponding", HT.BR(), + "label.", HT.BR(), HT.BR(), + "Please visit the links to the right to learn more about the variety of features", HT.BR(), + "available within GeneNetwork.") + + LinkText = HT.Span() + + mainLink = HT.Href(url="/webqtl/main.py", text = "Main Search Page", target="_blank") + homeLink = HT.Href(url="/home.html", text = "What is GeneNetwork?", target="_blank") + tourLink = HT.Href(url="/tutorial/WebQTLTour/", text = "Tour of GeneNetwork (20-40 min)", target="_blank") + faqLink = HT.Href(url="/faq.html", text = "Frequently Asked Questions", target="_blank") + glossaryLink = HT.Href(url="/glossary.html", text = "Glossary of terms used throughout GeneNetwork", target="_blank") + + LinkText.append(mainLink, HT.BR(), homeLink, HT.BR(), tourLink, HT.BR(), faqLink, HT.BR(), glossaryLink) + + formTable.append(HT.TR(HT.TD(species_tabs, species_container)), HT.TR(HT.TD(optionsTable))) + mainForm.append(formTable) + + + if fd.geneName: + SearchHeading = HT.Paragraph('Search Results for gene name ', fd.geneName) + elif fd.refseq: + SearchHeading = HT.Paragraph('Search Results for RefSeq accession number ', fd.refseq) + elif fd.genbankid: + SearchHeading = HT.Paragraph('Search Results for Genbank ID ', fd.genbankid) + elif fd.geneid: + SearchHeading = HT.Paragraph('Search Results for Gene ID ', fd.geneid) + else: + SearchHeading = HT.Paragraph('') + + SearchHeading.__setattr__("class","title") + + pageTable.append(HT.TR(HT.TD(SearchText, width=600), HT.TD(LinkText, align="left", valign="top")), HT.TR(HT.TD(" ", colspan=2)), HT.TR(HT.TD(mainForm, colspan=2))) + TD_LR.append(SearchHeading, pageTable) + self.dict['body'] = TD_LR + else: + if len(txtOutput) == 0: + self.output = "##No records were found for this species. \n" + else: + self.output = "##A total of %d records were returned. \n" % all_species_trait_count + newOutput = [] + strainLists = {} + for item in txtOutput: + tissueGrp, thisTrait = item + RISet = thisTrait.riset + if strainLists.has_key(RISet): + thisStrainlist = strainLists[RISet] + else: + thisGenotype = reaper.Dataset() + thisGenotype.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno')) + if thisGenotype.type == "riset": + _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[RISet] + thisGenotype = thisGenotype.add(Mat=_mat, Pat=_pat, F1=_f1) + thisStrainlist = list(thisGenotype.prgy) + strainLists[RISet] = thisStrainlist + thisTrait.retrieveData(strainlist=thisStrainlist) + thisData = [] + for item in thisStrainlist: + if thisTrait.data.has_key(item): thisData.append(thisTrait.data[item].val) + else: thisData.append(None) + newOutput.append(["Structure", "Database", "ProbeSetID", "Cross"] + thisStrainlist) + newOutput.append([tissueGrp, '"%s"' % thisTrait.db.fullname, thisTrait.name, RISet]+map(str,thisData)) + newOutput = webqtlUtil.asymTranspose(newOutput) + for item in newOutput: + self.output += string.join(item, "\t") + "\n" + + + def createTableBodies(self, fd, species, tissue, ADMIN_search_dbs): + + this_species_txtOutput = [] + + #priority GeneName > refseq > genbankid + this_species_trait_count = 0 #count of all traits in this species + this_species_dataset_count = 0 #Number of datasets in this species + row_count = 0 #Index number used in the first row of the trait table + trait_tblobj_body = [] #body of table with the results themselves; + tissue_tblobj_body = [] #body of table with the number of results for each tissue group + className = "fs12 fwn b1 c222" + + for i, tissueGrp in enumerate(ADMIN_search_dbs.keys()): + if tissue and tissue.upper() != tissueGrp.upper(): + continue + dbNames = ADMIN_search_dbs[tissueGrp] + + tissue_tr = [] #Table row for tissue group + tissue_tr.append(TDCell(HT.TD('', Class=className))) + tissue_tr.append(TDCell(HT.TD(tissueGrp.capitalize(), Class=className), tissueGrp, tissueGrp)) #Append cell with tissue name to row + + this_tissue_record_count = 0 #Count of the results for each tissue + for dbName in dbNames: + this_species_dataset_count += 1 + thisDB = webqtlDataset(dbName, self.cursor) + + if fd.geneName: + if fd.searchAlias: + self.cursor.execute("""SELECT ProbeSet.Name + FROM + ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetFreeze.Name = "%s" AND + ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND + MATCH (ProbeSet.symbol, alias) AGAINST ("+%s" IN BOOLEAN MODE) AND + ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneName)) + else: + self.cursor.execute("""SELECT ProbeSet.Name + FROM + ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetFreeze.Name = "%s" AND + ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND + ProbeSet.symbol = "%s" AND + ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneName)) + elif fd.refseq: + + # XZ, Oct/08/2009: Search for RefSeq ID is kind of tricky. One probeset can have multiple RefseqIDs that are delimited by ' /// ' (currently). + # So I have to use 'like' instead of '=' in SQL query. But user search with one short string, for example 'NM_1', it will return thousands of results. + # To prevent this, I set the restriction that the length of input Refseq ID must be at least 9 characters. Otherwise, do NOT start searching. + # Even with the restriction of input RefSeqID, I'm still worried about the 'like' in SQL query. My concern is in future, there might be RefSeqIDs with + # 10 characters whose first 9 characters are the same as the existing ones. So I decide to further check the result. We should also consider that the + # RefSeqID in database may have version number such as "NM_177938.2". If the input RefSeqID is 'NM_177938', it should be matched. I think we should get rid of the version number in database. + + if len(fd.refseq) < 9: + if fd.returnFmt != 'text': + heading = "Search Result" + detail = ["The RefSeq ID that you inputed is less than 9 characters. GeneNetwork thinks it is not a legitimate RefSeq ID and did not do the search. Please try to use a RefSeq ID with at least 9 characters."] + self.error(heading=heading,detail=detail,error="Not Found") + else: + self.output = "#The gene name or IDs you submitted did not match any record in the databases available. You may try different gene names or tissue type." + return + else: + sqlString = """SELECT ProbeSet.Id, ProbeSet.RefSeq_TranscriptId + FROM + ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetFreeze.Name = "%s" AND + ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND + MATCH(ProbeSet.RefSeq_TranscriptId) AGAINST ("+%s" IN BOOLEAN MODE) AND + ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.refseq) + + self.cursor.execute(sqlString) + + results = self.cursor.fetchall() + if results: + Id_of_really_matched_probeset = [] + + for one_result in results: + ProbeSet_Id, ProbeSet_RefSeq_TranscriptId = one_result + multiple_RefSeqId = string.split(string.strip(ProbeSet_RefSeq_TranscriptId), '///') + for one_RefSeqId in multiple_RefSeqId: + tokens = string.split( one_RefSeqId, '.' ) + one_RefSeqId_without_versionNum = string.strip(tokens[0]) + if one_RefSeqId_without_versionNum == fd.refseq: + Id_of_really_matched_probeset.append( ProbeSet_Id ) + break + + if Id_of_really_matched_probeset: + condition_string = " or ".join(["Id = %s" % one_ID for one_ID in Id_of_really_matched_probeset]) + sqlString = """SELECT ProbeSet.Name from ProbeSet where (%s)""" % condition_string + + self.cursor.execute(sqlString) + else: + pass + + elif fd.genbankid: + self.cursor.execute("""SELECT ProbeSet.Name + FROM + ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetFreeze.Name = "%s" AND + ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND + ProbeSet.GenbankId = "%s" AND + ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.genbankid)) + elif fd.geneid: + self.cursor.execute("""SELECT ProbeSet.Name + FROM + ProbeSet, ProbeSetFreeze, ProbeSetXRef + WHERE + ProbeSetFreeze.Name = "%s" AND + ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND + ProbeSet.GeneId = "%s" AND + ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneid)) + else: + continue + + results = self.cursor.fetchall() + if len(results) > 0: + this_tissue_record_count += len(results) + this_species_trait_count += this_tissue_record_count + + for result in results: + _ProbeSetID = result[0] + thisTrait = webqtlTrait(db=thisDB, name=_ProbeSetID, cursor=self.cursor) + results_tr = [] + trId = str(thisTrait) + _traitUrl = thisTrait.genHTML(dispFromDatabase=1) + _traitName = str(thisTrait) + + #ZS: check box column + results_tr.append(TDCell(HT.TD(str(row_count+1), HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", align="right", Class=className), str(row_count+1), row_count+1)) + row_count += 1 + + #ZS: Tissue column + results_tr.append(TDCell(HT.TD(tissueGrp.capitalize(), Class=className), tissueGrp, tissueGrp)) + + #ZS: Group column + risetUrl = HT.Href(text=thisTrait.riset, url="http://www.genenetwork.org/%sCross.html#%s" % (species, thisTrait.riset), target="_blank", Class=className) + results_tr.append(TDCell(HT.TD(risetUrl, Class=className), thisTrait.riset, thisTrait.riset)) + + #ZS: Dataset column + results_tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name, + target='_blank', Class="fs13 fwn non_bold"), Class=className), thisTrait.db.name.upper(), thisTrait.db.name.upper())) + + #ZS: Trait ID column + results_tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % ('showDatabase', thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name)) + + #ZS: Symbol column and Description column + description_string = str(thisTrait.description).strip() + if (thisTrait.db.type == "ProbeSet"): + target_string = str(thisTrait.probe_target_description).strip() + + description_display = '' + + if len(description_string) > 1 and description_string != 'None': + description_display = description_string + else: + description_display = thisTrait.symbol + + if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None': + description_display = description_display + '; ' + target_string.strip() + + description_string = description_display + else: + results_tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz")) + + results_tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string)) + + #XZ: trait_location_value is used for sorting + trait_location_repr = "--" + trait_location_value = 1000000 + + if hasattr(thisTrait, 'chr') and hasattr(thisTrait, 'mb') and thisTrait.chr and thisTrait.mb: + try: + trait_location_value = int(thisTrait.chr)*1000 + thisTrait.mb + except: + if thisTrait.chr.upper() == "X": + trait_location_value = 20*1000 + thisTrait.mb + else: + trait_location_value = ord(str(thisTrait.chr).upper()[0])*1000 + thisTrait.mb + + trait_location_repr = "Chr%s: %.6f" % (thisTrait.chr, float(thisTrait.mb) ) + + results_tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value)) + + #ZS: Mean column + self.cursor.execute(""" + select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet + where ProbeSetXRef.ProbeSetFreezeId = %d and + ProbeSet.Id = ProbeSetXRef.ProbeSetId and + ProbeSet.Name = '%s' + """ % (thisTrait.db.id, thisTrait.name)) + result = self.cursor.fetchone() + if result: + if result[0]: + mean = result[0] + else: + mean=0 + else: + mean = 0 + + repr = "%2.3f" % mean + results_tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean)) + trait_tblobj_body.append(results_tr) + + this_species_txtOutput.append([tissueGrp, thisTrait]) + + + tissue_tr.append(TDCell(HT.TD(str(this_tissue_record_count), Class=className), str(this_tissue_record_count), this_tissue_record_count)) + tissue_tblobj_body.append(tissue_tr) + + self.output = "self.output" + + return tissue_tblobj_body, trait_tblobj_body, this_species_dataset_count, this_species_trait_count, this_species_txtOutput + + + def getTissueSortByValue(self): + + sortby = ("tissue_group", "up") + + return sortby + + + def getTraitSortByValue(self): + + sortby = ("tissue", "up") + + return sortby + + + def getTissueTableHeader(self): + + tblobj_header = [] + + className = "fs13 fwb ffl b1 cw cbrb" + + tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0), + THCell(HT.TD('Tissue',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="tissue_group", idx=1), + THCell(HT.TD('Results', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="results", idx=2)]] + + return tblobj_header + + def getTraitTableHeader(self): + + tblobj_header = [] + + className = "fs13 fwb ffl b1 cw cbrb" + + tblobj_header = [[THCell(HT.TD('Index',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="index", idx=0), + THCell(HT.TD('Tissue',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="tissue", idx=1), + THCell(HT.TD('Group',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="group", idx=2), + THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=3), + THCell(HT.TD('Record ID', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=4), + THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=5), + THCell(HT.TD('Location', HT.BR(), 'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=6), + THCell(HT.TD('Mean', HT.BR(), 'Expr', HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=7)]] + + return tblobj_header |