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Diffstat (limited to 'web/webqtl/search/TextSearchPage.py')
| -rwxr-xr-x | web/webqtl/search/TextSearchPage.py | 536 |
1 files changed, 0 insertions, 536 deletions
diff --git a/web/webqtl/search/TextSearchPage.py b/web/webqtl/search/TextSearchPage.py deleted file mode 100755 index 42ff72c4..00000000 --- a/web/webqtl/search/TextSearchPage.py +++ /dev/null @@ -1,536 +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 - -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 |