aboutsummaryrefslogtreecommitdiff
path: root/web/webqtl/collection/AddToSelectionPage.py
diff options
context:
space:
mode:
Diffstat (limited to 'web/webqtl/collection/AddToSelectionPage.py')
-rw-r--r--web/webqtl/collection/AddToSelectionPage.py695
1 files changed, 0 insertions, 695 deletions
diff --git a/web/webqtl/collection/AddToSelectionPage.py b/web/webqtl/collection/AddToSelectionPage.py
deleted file mode 100644
index 2a99e8c1..00000000
--- a/web/webqtl/collection/AddToSelectionPage.py
+++ /dev/null
@@ -1,695 +0,0 @@
-#AddToSelectionPage.py
-
-import string
-from htmlgen import HTMLgen2 as HT
-import os
-import cPickle
-import reaper
-
-from base import webqtlConfig
-from base.templatePage import templatePage
-from utility.THCell import THCell
-from utility.TDCell import TDCell
-from utility import webqtlUtil
-from showTrait import ShowProbeInfoPage
-# NL, 07/27/2010: add 'import webqtlDatabaseFunction' for retrieveSpecies function
-from dbFunction import webqtlDatabaseFunction
-from base.webqtlTrait import webqtlTrait
-
-
-#########################################
-# Add to Selection Page
-#########################################
-class AddToSelectionPage(templatePage):
-
- def __init__(self,fd):
-
- templatePage.__init__(self, fd)
-
- if not self.openMysql():
- return
-
- if not fd.genotype:
- fd.readGenotype()
-
- self.searchResult = fd.formdata.getvalue('searchResult', [])
- if type("1") == type(self.searchResult):
- self.searchResult = [self.searchResult]
- if fd.formdata.getvalue('fromDataEditingPage'):
- searchResult2 = fd.formdata.getvalue('fullname')
- if searchResult2:
- self.searchResult.append(searchResult2)
-
- if self.searchResult:
- pass
- else:
- templatePage.__init__(self, fd)
- heading = 'Add Collections'
- detail = ['You need to select at least one trait to add to your selection.']
- self.error(heading=heading,detail=detail)
- return
-
- if self.genSelection(fd=fd):
- self.writeHTML(fd)
-
-
-
- def genSelection(self, fd=None, checkPreSelection = 1):
- collectionName = '%s_Select' % fd.RISet
-
- if checkPreSelection:
- try:
- preSelection = fd.input_session_data[collectionName]
- preSelection = list(string.split(preSelection,','))
- except:
- preSelection = []
- else:
- preSelection = []
-
- if preSelection:
- for item in preSelection:
- if item not in self.searchResult:
- self.searchResult.append(item)
-
- self.searchResult = map(self.transfer2NewName, self.searchResult)
-
- for item in self.searchResult:
- if not item:
- self.searchResult.remove(item)
-
- if len(self.searchResult) > 3000:
- heading = 'Add Collections'
- detail = ['You are adding over 3000 traits to selections, please reduce your number of traits.']
- self.error(heading=heading,detail=detail)
- return 0
-
- searchResult2 = []
- self.theseTraits = []
- for item in self.searchResult:
- try:
- thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
- thisTrait.retrieveInfo(QTL=1)
- self.theseTraits.append(thisTrait)
- searchResult2.append(item)
- except:
- pass
-
- allTraitStr = string.join(searchResult2,',')
-
- self.session_data_changed[collectionName] = allTraitStr
-
- return 1
-
-
-
- def writeHTML(self,fd):
- TD_LR = HT.TD(height=100,width="100%",bgColor='#eeeeee',valign="top")
- pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
- tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0, align="Left")
- seq = 1
- SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
-
- mintmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'showIntMap');}")
- mintmap_img = HT.Image("/images/multiple_interval_mapping1_final.jpg", name='mintmap', alt="Multiple Interval Mapping", title="Multiple Interval Mapping", style="border:none;")
- mintmap.append(mintmap_img)
- mcorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'compCorr');}")
- mcorr_img = HT.Image("/images/compare_correlates2_final.jpg", name='comparecorr', alt="Compare Correlates", title="Compare Correlates", style="border:none;")
- mcorr.append(mcorr_img)
- cormatrix = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');}")
- cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", name='corrmatrix', alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;")
- cormatrix.append(cormatrix_img)
- networkGraph = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'networkGraph');}")
- networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='networkgraph', alt="Network Graphs", title="Network Graphs", style="border:none;")
- networkGraph.append(networkGraph_img)
- heatmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');}")
- heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='heatmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;")
- heatmap.append(heatmap_img)
- partialCorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'partialCorrInput');}")
- partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;")
- partialCorr.append(partialCorr_img)
-
- BN = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'BNInput');}")
- networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='BayesianNetwork', alt="Bayesian Network", title="Bayesian Network", style="border:none;")
- BN.append(networkGraph_img)
-
- removeselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('showDatabase')[0], 'removeSelection');" % fd.RISet)
- removeselect_img = HT.Image("/images/remove_selection1_final.jpg", name="removeselect", alt="Remove Selection", title="Remove Selection", style="border:none;")
- removeselect.append(removeselect_img)
- selectall = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', true);")
- selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
- selectall.append(selectall_img)
- reset = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', false);")
- reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
- reset.append(reset_img)
- exportSelect = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'exportSelectionDetailInfo');")
- exportSelect_img = HT.Image("/images/export2_final.jpg", name="exportSelection", alt="Export Selection", title="Export Selection", style="border:none;")
- exportSelect.append(exportSelect_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)
-
- chrMenu = HT.Input(type='hidden',name='chromosomes',value='all')
-
- importFile = HT.Input(type='file', name='importfile', size=15)
- importButton = HT.Input(type='button',name='importSelection',value='Load Collection', onClick="addRmvSelection('%s', this.form, 'importSelect');" % fd.RISet,Class="button")
- exportButton = HT.Input(type='button' ,name='exportSelection',value='Save Collection', onClick="databaseFunc(this.form,'exportSelect');", Class="button")
- importMenu = HT.Select(name='importmethod')
- importMenu.append(('append','append'))
- importMenu.append(('replace','replace'))
-
- ODE = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'ODE');")
- ODE_img = HT.Image("/images/ODE_logo_final.jpg", name="ode", alt="ODE", title="ODE", style="border:none")
- ODE.append(ODE_img)
-
- GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'GCAT');")
- GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none")
- GCATButton.append(GCATButton_img)
-
- GeneSet = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0],'GOTree');")
- GeneSet_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
- GeneSet.append(GeneSet_img)
-
- #need to be refined
- if fd.genotype.Mbmap:
- scale = HT.Input(name="scale", value="physic", type="hidden")
- else:
- scale = ""
-
- formMain = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
-
- #XZ, July 22, 2011: I add parameters for interval mapping
- hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet,'incparentsf1':'ON','showHideOptions':'more','scale':'physic','additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'intervalAnalystCheck':'ON','bootCheck':None, 'permCheck':None, 'applyVarianceSE':None}
- for key in hddn.keys():
- formMain.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-
- if not self.searchResult:
- SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
- formMain.append(HT.HR(width="70%", color = "blue"),importFile, ' ', importMenu, ' ', importButton)
- TD_LR.append(SelectionHeading,HT.Blockquote('No trait has been added to this selection.'), HT.Center(HT.BR(), HT.BR(), HT.BR(), HT.BR(), formMain))
- self.dict['body'] = str(TD_LR)
- self.dict['title'] = "%s Trait Collection" % fd.RISet
- return
-
- #########################################
- # Creating table object for AJAX table #
- #########################################
- tblobj = {}
- mainfmName = 'showDatabase'
- # NL, 07/27/2010. retrieveSpecies function has been moved from webqtlTrait.py to webqtlDatabaseFunction.py;
- species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
- if species == 'human':
- chrMenu = scale = mintmap = heatmap = ""
-
- tblobj['header'] = self.getCollectionTableHeader()
-
- sortby = self.getSortByValue()
-
- thisRISet = fd.RISet
- tblobj['body'] = self.getCollectionTableBody(RISet=thisRISet, traitList=self.theseTraits, formName=mainfmName, species=species)
-
- filename= webqtlUtil.genRandStr("Search_")
-
- objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
- cPickle.dump(tblobj, objfile)
- objfile.close()
-
-
- div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), Id="sortable")
-
-
- containerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
- postContainerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
-
- optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="400", border=0, align="Left")
- optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(removeselect), HT.TD(exportSelect)))
- optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*1,"Remove"), HT.TD(" "*1,"Export")))
- postContainerTable.append(HT.TR(HT.TD(optionsTable)))
- containerTable.append(HT.TR(HT.TD(optionsTable)))
-
- functionTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="480",border=0, align="Left")
- functionRow = HT.TR(HT.TD(networkGraph, width="16.7%"), HT.TD(cormatrix, width="16.7%"), HT.TD(partialCorr, width="16.7%"), HT.TD(mcorr, width="16.7%"), HT.TD(mintmap, width="16.7%"), HT.TD(heatmap))
- if species == "human":
- labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")))
- else:
- labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")), HT.TD(HT.Text("QTL Map")), HT.TD(HT.Text(text="Heat Map")))
- functionTable.append(functionRow, labelRow)
- postContainerTable.append(HT.TR(HT.TD(functionTable)))
- containerTable.append(HT.TR(HT.TD(functionTable)))
-
- moreOptions = HT.Input(type='button',name='options',value='More Options', onClick="",Class="toggle")
- fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle")
-
-
-
- if (fd.formdata.getvalue('showHideOptions') == 'less'):
- postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
- containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
- else:
- postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
- containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
-
-
- LinkOutTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="320",border=0, align="Left")
- LinkOutRow = HT.TR(HT.TD(GeneSet, width="33%"), HT.TD(GCATButton, width="33%"), HT.TD(ODE, width="33%"), style="display:none;", Class="extra_options")
- LinkOutLabels = HT.TR(HT.TD(HT.Text("Gene Set")), HT.TD(" "*2, HT.Text("GCAT")), HT.TD(" "*3, HT.Text("ODE")), style="display:none;", Class="extra_options")
- LinkOutTable.append(LinkOutRow,LinkOutLabels)
- postContainerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable)))
- containerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable)))
-
- pageTable.append(HT.TR(HT.TD(containerTable)))
- chrMenu = scale = ""
-
- pageTable.append(HT.TR(HT.TD(div)))
- pageTable.append(HT.TR(HT.TD(" ")))
- if len(self.theseTraits) > 20:
- pageTable.append(HT.TR(HT.TD(postContainerTable)))
- pageTable.append(HT.TR(HT.TD(importFile, ' ', importMenu, ' ', importButton, ' '*10, exportButton)))
- #Took out scaleMenu since it will be replaced with a jquery popup in the future - Zach 5/10/2010
- formMain.append(chrMenu,scale,pageTable)
-
- #Updated by NL, deleted showHideJS, moved jquery to jqueryFunction.js
- self.dict['js1'] = ''
- TD_LR.append(SelectionHeading,formMain)
-
- self.dict['body'] = str(TD_LR)
- self.dict['js2'] = 'onLoad="pageOffset()"'
- self.dict['layer'] = self.generateWarningLayer()
- self.dict['title'] = "%s Trait Collection" % thisRISet
-
- def transfer2NewName(self, str):
- "this is temporary"
- if str.find("::") < 0:
- return str.replace(":", "::")
- else:
- return str
-
- def generateWarningLayer(self):
-
- layerString = """
- <!-- BEGIN FLOATING LAYER CODE //-->
- <div id="warningLayer" style="padding:3px; border: 1px solid #222;
- background-color: #fff; position:absolute;width:250px;left:100;top:100;visibility:hidden">
- <table border="0" width="250" class="cbrb" cellspacing="0" cellpadding="5">
- <tr>
- <td width="100%">
- <table border="0" width="100%" cellspacing="0" cellpadding="0" height="36">
- <tr>
- <td class="cbrb cw ff15 fwb" align="Center" width="100%" style="padding:4px">
- Sort Table
- </td>
- </tr>
- <tr>
- <td width="100%" bgcolor="#eeeeee" align="Center" style="padding:4px">
- <!-- PLACE YOUR CONTENT HERE //-->
- Resorting this table <br>
- <!-- END OF CONTENT AREA //-->
- </td>
- </tr>
- </table>
- </td>
- </tr>
- </table>
- </div>
- <!-- END FLOATING LAYER CODE //-->
-
- """
-
- return layerString
-
- def getCollectionTableHeader(self):
-
- tblobj_header = []
-
- className = "fs13 fwb ffl b1 cw cbrb"
-
- tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0),
- THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=1),
- THCell(HT.TD('Trait', HT.BR(), 'ID', HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=2),
- THCell(HT.TD('Symbol', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="symbol", idx=3),
- THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=4),
- THCell(HT.TD('Location', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=5),
- THCell(HT.TD('Mean', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=6),
- THCell(HT.TD('N', HT.BR(), 'Cases', HT.BR(), valign="top", Class=className, nowrap="on"), text="samples", idx=7),
- THCell(HT.TD('Max LRS', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs", idx=8),
- THCell(HT.TD('Max LRS Location',HT.BR(),'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs_location", idx=9)]]
-
- return tblobj_header
-
- def getCollectionTableBody(self, RISet=None, traitList=None, formName=None, species=''):
-
- tblobj_body = []
-
- className = "fs12 fwn b1 c222"
-
- for thisTrait in traitList:
- tr = []
-
- if not thisTrait.haveinfo:
- thisTrait.retrieveInfo(QTL=1)
-
- if thisTrait.riset != RISet:
- continue
-
- trId = str(thisTrait)
-
- #XZ: check box column
- tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className)))
-
- #XZ: Dataset column
- tr.append(TDCell(HT.TD(thisTrait.db.name, Class="fs12 fwn b1 c222"), thisTrait.db.name, thisTrait.db.name.upper()))
-
- #XZ: Trait ID column
- if thisTrait.cellid:
- tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.cellid,url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, thisTrait.db.name, thisTrait.name, thisTrait.cellid), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.cellid), thisTrait.cellid))
- else:
- tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name))
-
- #XZ: Symbol column and Description column
- if (thisTrait.db.type == "Publish"):
- AbbreviationString = "--"
- if (thisTrait.post_publication_abbreviation != None):
- AbbreviationString = thisTrait.post_publication_abbreviation
- PhenotypeString = thisTrait.post_publication_description
- if thisTrait.confidential:
- if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
- if thisTrait.pre_publication_abbreviation:
- AbbreviationString = thisTrait.pre_publication_abbreviation
- else:
- AbbreviationString = "--"
- PhenotypeString = thisTrait.pre_publication_description
-
- if AbbreviationString == "--":
- tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
- else:
- tr.append(TDCell(HT.TD(AbbreviationString, Class=className), AbbreviationString, AbbreviationString.upper()))
-
- tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper()))
-
-
- elif (thisTrait.db.type == "ProbeSet" or thisTrait.db.type == "Temp"):
- description_string = str(thisTrait.description).strip()
- if (thisTrait.db.type == "ProbeSet"):
- if (thisTrait.symbol != None):
- if thisTrait.geneid:
- symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % thisTrait.geneid, Class="font_black fs12 fwn")
- else:
- symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % thisTrait.symbol, Class="font_black fs12 fwn")
- tr.append(TDCell(HT.TD(symbolurl, align="left", Class="fs12 fwn b1 c222 fsI"), thisTrait.symbol, thisTrait.symbol))
- else:
- tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
- 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:
- tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
- tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string))
- else:
- if (thisTrait.name != None):
- tr.append(TDCell(HT.TD(thisTrait.name, Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name))
- else:
- tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
- tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
-
- #XZ: Location column
- if (thisTrait.db.type == "Publish"):
- tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
- else:
- if thisTrait.db.type == "ProbeSet" and thisTrait.cellid:
- EnsemblProbeSetID = thisTrait.name
- if '_at' in thisTrait.name:
- EnsemblProbeSetID = thisTrait.name[0:thisTrait.name.index('_at')+3]
-
- #These tables (Ensembl) were created by Xusheng Wang in 2010 and are mm9 (so they'll need to be changed at some point to be mm10.
- self.cursor.execute('''
- SELECT EnsemblProbeLocation.*
- FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze, ProbeSetFreeze
- WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
- GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
- ProbeSetFreeze.Id=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id group by Chr, Start, End'''
- ,(thisTrait.cellid, EnsemblProbeSetID, thisTrait.db.id))
- LocationFields = self.cursor.fetchall()
-
- Chr=''
- Mb=''
- Start=''
- End=''
- if (len(LocationFields)>=1):
- Chr,Start,End,Strand,MisMatch,ProbeId = map(self.nullRecord,LocationFields[0])
- Start /= 1000000.0
- End /= 1000000.0
- Mb = Start
- if (len(LocationFields)>1):
- self.cursor.execute('''
- SELECT ProbeSet.Chr, ProbeSet.Mb FROM ProbeSet, ProbeFreeze, ProbeSetFreeze
- WHERE ProbeSet.ChipId=ProbeFreeze.ChipId and ProbeSet.Name=%s and ProbeSetFreeze.Id=%s and
- ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id'''
- ,(thisTrait.name, thisTrait.db.id))
- ProbeSetChr, ProbeSetMb = map(self.nullRecord,self.cursor.fetchall()[0])
-
- self.cursor.execute('''
- SELECT EnsemblProbeLocation.*, ABS(EnsemblProbeLocation.Start/1000000-%s) as Mb
- FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze
- WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
- GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
- EnsemblProbeLocation.Chr=%s and ProbeSetFreezeId=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id order by Mb limit 1'''
- ,(ProbeSetMb, thisTrait.cellid, EnsemblProbeSetID, ProbeSetChr, thisTrait.db.id))
- NewLocationFields = self.cursor.fetchall()
- if (len(NewLocationFields)>0):
- Chr,Start,End,Strand,MisMatch,ProbeId,Mb = map(self.nullRecord,NewLocationFields[0])
- Start /= 1000000.0
- End /= 1000000.0
- Mb = Start
-
- #ZS: trait_location_value is used for sorting
- trait_location_repr = "--"
- trait_location_value = 1000000
-
- if Chr and Mb:
- try:
- trait_location_value = int(Chr)*1000 + Mb
- except:
- if Chr.upper() == "X":
- trait_location_value = 20*1000 + Mb
- else:
- trait_location_value = ord(str(Chr).upper()[0])*1000 + Mb
-
- trait_location_repr = "Chr%s: %.6f" % (Chr, float(Mb) )
-
- tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
-
- else:
-
- #ZS: 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) )
-
- tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
-
- #XZ: Mean column
- if (thisTrait.db.type == "ProbeSet"):
- if thisTrait.cellid:
- mean = -10000.0
- try:
- thisTrait.retrieveData()
- mean, median, var, stdev, sem, N = reaper.anova(thisTrait.exportInformative()[1])
- except:
- pass
- repr = '%2.3f' % mean
- mean = '%2.2f' % mean
- tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))
- else:
- 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
-
- #XZ, 06/05/2009: It is neccessary to turn on nowrap
- repr = "%2.3f" % mean
- tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))
-
- elif (thisTrait.db.type == "Publish"):
- self.cursor.execute("""
- select count(PublishData.value), sum(PublishData.value) from PublishData, PublishXRef, PublishFreeze
- where PublishData.Id = PublishXRef.DataId and
- PublishXRef.Id = %s and
- PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
- PublishFreeze.Id = %d
- """ % (thisTrait.name, thisTrait.db.id))
- result = self.cursor.fetchone()
-
- if result:
- if result[0] and result[1]:
- mean = result[1]/result[0]
- else:
- mean = 0
- else:
- mean = 0
-
- repr = "%2.3f" % mean
- tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))
- else:
- tr.append(TDCell(HT.TD("--", Class=className, align='left', nowrap='ON'),"--", 0))
-
- #Number of cases
- n_cases_value = 0
- n_cases_repr = "--"
- if (thisTrait.db.type == "Publish"):
- self.cursor.execute("""
- select count(PublishData.value) from PublishData, PublishXRef, PublishFreeze
- where PublishData.Id = PublishXRef.DataId and
- PublishXRef.Id = %s and
- PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
- PublishFreeze.Id = %d
- """ % (thisTrait.name, thisTrait.db.id))
- result = self.cursor.fetchone()
-
- if result:
- if result[0]:
- n_cases_value = result[0]
- n_cases_repr = result[0]
-
- if (n_cases_value == "--"):
- tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
- else:
- tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
-
- elif (thisTrait.db.type == "ProbeSet"):
- self.cursor.execute("""
- select count(ProbeSetData.value) from ProbeSet, ProbeSetXRef, ProbeSetData, ProbeSetFreeze
- where ProbeSet.Name='%s' and
- ProbeSetXRef.ProbeSetId = ProbeSet.Id and
- ProbeSetXRef.DataId = ProbeSetData.Id and
- ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
- ProbeSetFreeze.Name = '%s'
- """ % (thisTrait.name, thisTrait.db.name))
- result = self.cursor.fetchone()
-
- if result:
- if result[0]:
- n_cases_value = result[0]
- n_cases_repr = result[0]
- if (n_cases_value == "--"):
- tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
- else:
- tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
-
- elif (thisTrait.db.type == "Geno"):
- self.cursor.execute("""
- select count(GenoData.value) from GenoData, GenoXRef, GenoFreeze, Geno, Strain
- where Geno.SpeciesId = %s and Geno.Name='%s' and
- GenoXRef.GenoId = Geno.Id and
- GenoXRef.DataId = GenoData.Id and
- GenoXRef.GenoFreezeId = GenoFreeze.Id and
- GenoData.StrainId = Strain.Id and
- GenoFreeze.Name = '%s'
- """ % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, thisTrait.db.riset), thisTrait.name, thisTrait.db.name))
- result = self.cursor.fetchone()
-
- if result:
- if result[0]:
- n_cases_value = result[0]
- n_cases_repr = result[0]
- if (n_cases_value == "--"):
- tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
- else:
- tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
-
- else:
- tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
-
- #XZ: Max LRS column and Max LRS Location column
- if (thisTrait.db.type != "Geno"):
- #LRS and its location
- LRS_score_repr = '--'
- LRS_score_value = 0
- LRS_location_repr = '--'
- LRS_location_value = 1000000
- LRS_flag = 1
-
- #Max LRS and its Locus location
- if hasattr(thisTrait, 'lrs') and hasattr(thisTrait, 'locus') and thisTrait.lrs and thisTrait.locus:
- self.cursor.execute("""
- select Geno.Chr, Geno.Mb from Geno, Species
- where Species.Name = '%s' and
- Geno.Name = '%s' and
- Geno.SpeciesId = Species.Id
- """ % (species, thisTrait.locus))
- result = self.cursor.fetchone()
-
- if result:
- if result[0] and result[1]:
- 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)
-
-
- LRS_score_repr = '%3.1f' % thisTrait.lrs
- LRS_score_value = thisTrait.lrs
- LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) )
- LRS_flag = 0
-
- tr.append(TDCell(HT.TD(LRS_score_repr, Class=className, align='right', nowrap="on"), LRS_score_repr, LRS_score_value))
- tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
-
- if LRS_flag:
- tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value))
- tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
- else:
- tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 0))
- tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 1000000))
-
- tblobj_body.append(tr)
-
- return tblobj_body
-
- def getSortByValue(self):
-
- sortby = ("pv", "up")
-
- return sortby
-
- def nullRecord(self,x):
- if x or x == 0:
- return x
- else:
- return ""
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-22 18:53:15 +0000