# 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 apache, util, Cookie import os import time import pyXLWriter as xl from htmlgen import HTMLgen2 as HT import GeneUtil from base.templatePage import templatePage from utility import webqtlUtil from base import webqtlConfig class IntervalAnalystPage(templatePage): filename = webqtlUtil.genRandStr("Itan_") _scriptfile = "main.py?FormID=intervalAnalyst" #A dictionary that lets us map the html form names "txStart_mm6" -> "Mb Start (mm8)" #the first item is the short name (column headers) and the second item is the long name (dropdown list) # [short name, long name, category] columnNames = {"GeneSymbol" : ["Gene", "Gene Name", 'gene'], "GeneDescription" : ["Description", "Gene Description", 'species'], 'GeneNeighborsCount' : ["Neighbors", "Gene Neighbors", 'gene'], 'GeneNeighborsRange' : ["Neighborhood", "Gene Neighborhood (Mb)", 'gene'], 'GeneNeighborsDensity' : ["Gene Density", "Gene Density (Neighbors/Mb)", 'gene'], "ProteinID" : ["Prot ID", "Protein ID", 'protein'], "Chromosome" : ["Chr", "Chromosome", 'species'], "TxStart" : ["Start", "Mb Start", 'species'], "TxEnd" : ["End", "Mb End", 'species'], "GeneLength" : ["Length", "Kb Length", 'species'], "cdsStart" : ["CDS Start", "Mb CDS Start", 'species'], "cdsEnd" : ["CDS End", "Mb CDS End", 'species'], "exonCount" : ["Num Exons", "Exon Count", 'species'], "exonStarts" : ["Exon Starts", "Exon Starts", 'species'], "exonEnds" : ["Exon Ends", "Exon Ends", 'species'], "Strand" : ["Strand", "Strand", 'species'], "GeneID" : ["Gene ID", "Gene ID", 'species'], "GenBankID" : ["GenBank", "GenBank ID", 'species'], "UnigenID" : ["Unigen", "Unigen ID", 'species'], "NM_ID" : ["NM ID", "NM ID", 'species'], "kgID" : ["kg ID", "kg ID", 'species'], "snpCount" : ["SNPs", "SNP Count", 'species'], "snpDensity" : ["SNP Density", "SNP Density", 'species'], "lrs" : ["LRS", "Likelihood Ratio Statistic", 'misc'], "lod" : ["LOD", "Likelihood Odds Ratio", 'misc'], "pearson" : ["Pearson", "Pearson Product Moment", 'misc'], "literature" : ["Lit Corr", "Literature Correlation", 'misc'], } ###Species Freeze speciesFreeze = {'mouse':'mm9', 'rat':'rn3', 'human':'hg19'} for key in speciesFreeze.keys(): speciesFreeze[speciesFreeze[key]] = key def __init__(self, fd): templatePage.__init__(self, fd) fd.formdata['remote_ip'] = fd.remote_ip if not self.openMysql(): return self.species = fd.formdata.getvalue("species", "mouse") try: self.startMb = float(fd.formdata.getvalue("startMb")) except: self.startMb = 10 try: self.endMb = float(fd.formdata.getvalue("endMb")) except: self.endMb = self.startMb + 10 self.Chr = fd.formdata.getvalue("chromosome", "1") self.xls = fd.formdata.getvalue("xls", "1") try: s1 = int(fd.formdata.getvalue("s1")) s2 = int(fd.formdata.getvalue("s2")) self.diffColDefault = self.diffCol = [s1, s2] except: self.diffColDefault = self.diffCol = [] if self.species != 'mouse': self.diffColDefault = [2, 3]#default is B6 and D2 for other species controlFrm, dispFields = self.genControlForm(fd) geneTable, filename = self.genGeneTable(fd, dispFields) infoTD = HT.TD(width=400, valign= "top") infoTD.append(HT.Paragraph("Interval Analyst : Chr %s" % self.Chr, Class="title"), HT.Strong("Species : "), self.species.title(), HT.BR(), HT.Strong("Database : "), "UCSC %s" % self.speciesFreeze[self.species], HT.BR(), HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(), ) if filename: infoTD.append(HT.BR(), HT.BR(), HT.Href(text="Download", url = "/tmp/" + filename, Class="normalsize") , " output in MS excel format.") mainTable = HT.TableLite(HT.TR(infoTD, HT.TD(controlFrm, Class="doubleBorder", width=400), HT.TD(" ", width="")), cellpadding=10) mainTable.append(HT.TR(HT.TD(geneTable, colspan=3))) self.dict['body'] = HT.TD(mainTable) self.dict['title'] = "Interval Analyst" def genGeneTable(self, fd, dispFields): filename = "" if self.xls: #import pyXLWriter as xl filename = "IntAn_Chr%s_%2.6f-%2.6f" % (self.Chr, self.startMb, self.endMb) filename += ".xls" # Create a new Excel workbook workbook = xl.Writer(os.path.join(webqtlConfig.TMPDIR, filename)) worksheet = workbook.add_worksheet() titleStyle = workbook.add_format(align = 'left', bold = 0, size=18, border = 1, border_color="gray") headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, fg_color = 0x1E, color="white", border = 1, border_color="gray") ##Write title Info worksheet.write([0, 0], "GeneNetwork Interval Analyst Table", titleStyle) worksheet.write([1, 0], "%s%s" % (webqtlConfig.PORTADDR, os.path.join(webqtlConfig.CGIDIR, self._scriptfile))) # worksheet.write([2, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime())) worksheet.write([3, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime())) worksheet.write([4, 0], "Search by : %s" % fd.formdata['remote_ip']) worksheet.write([5, 0], "view region : Chr %s %2.6f - %2.6f Mb" % (self.Chr, self.startMb, self.endMb)) nTitleRow = 7 geneTable = HT.TableLite(Class="collap", cellpadding=5) headerRow = HT.TR(HT.TD(" ", Class="fs13 fwb ffl b1 cw cbrb", width="1")) if self.xls: worksheet.write([nTitleRow, 0], "Index", headingStyle) for ncol, column in enumerate(dispFields): if len(column) == 1: headerRow.append(HT.TD(self.columnNames[column[0]][0], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) if self.xls: colTitle = self.columnNames[column[0]][0] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) else: headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), " (%s)" % self.speciesFreeze[column[1]], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1, align="Center")) if self.xls: colTitle = self.columnNames[column[0]][0] + " (%s)" % self.speciesFreeze[column[1]] worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) #headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), # "(%s %s)" % (column[1].title(), self.speciesFreeze[column[1]]), # Class="colorBlue", NOWRAP=1, align="Center")) geneTable.append(headerRow) geneCol = GeneUtil.loadGenes(self.cursor, self.Chr, self.diffColDefault, self.startMb, self.endMb, species=self.species) for gIndex, theGO in enumerate(geneCol): geneRow = HT.TR(HT.TD(gIndex+1, Class="fs12 fwn b1", align="right")) if self.xls: nTitleRow += 1 worksheet.write([nTitleRow, 0], gIndex + 1) for ncol, column in enumerate(dispFields): if len(column) == 1 or column[1]== self.species: keyValue = "" fieldName = column[0] curSpecies = self.species curGO = theGO if theGO.has_key(fieldName): keyValue = theGO[fieldName] else: fieldName , othSpec = column curSpecies = othSpec subGO = '%sGene' % othSpec keyValue = "" curGO = theGO[subGO] if theGO[subGO].has_key(fieldName): keyValue = theGO[subGO][fieldName] if self.xls: worksheet.write([nTitleRow, ncol+1], keyValue) geneRow.append(self.formatTD(keyValue, fieldName, curSpecies, curGO)) geneTable.append(geneRow) if self.xls: workbook.close() return geneTable, filename def formatTD(self, keyValue, fieldName, Species, theGO): if keyValue is None: keyValue = "" if keyValue != "": if fieldName in ("exonStarts", "exonEnds"): keyValue = string.replace(keyValue, ',', ' ') return HT.TD(HT.Span(keyValue, Class="code", Id="green"), width=350, Class="fs12 fwn b1") elif fieldName in ("GeneDescription"): if keyValue == "---": keyValue = "" return HT.TD(keyValue, Class="fs12 fwn b1", width=300) elif fieldName in ("GeneSymbol"): webqtlLink = HT.Href("./%s?cmd=sch&gene=%s&alias=1&species=%s" % (webqtlConfig.SCRIPTFILE, keyValue, Species), HT.Image("/images/webqtl_search.gif", border=0, valign="top"), target="_blank") if theGO['GeneID']: geneSymbolLink = HT.Href(webqtlConfig.NCBI_LOCUSID % theGO['GeneID'], keyValue, Class="normalsize", target="_blank") else: geneSymbolLink = keyValue return HT.TD(webqtlLink, geneSymbolLink, Class="fs12 fwn b1",NOWRAP=1) elif fieldName == 'UnigenID': try: gurl = HT.Href(webqtlConfig.UNIGEN_ID % tuple(string.split(keyValue,'.')[:2]), keyValue, Class="normalsize", target="_blank") except: gurl = keyValue return HT.TD(gurl, Class="fs12 fwn b1",NOWRAP=1) elif fieldName in ("exonCount", "Chromosome"): return HT.TD(keyValue, Class="fs12 fwn b1",align="right") elif fieldName in ("snpCount"): if keyValue: snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'), theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffColDefault[0], self.diffColDefault[1]), text=theGO["snpCount"], target="_blank", Class="normalsize") else: snpString = keyValue return HT.TD(snpString, Class="fs12 fwn b1",align="right") elif fieldName in ("snpDensity", "GeneLength"): if keyValue: keyValue = "%2.3f" % keyValue else: keyValue = "" return HT.TD(keyValue, Class="fs12 fwn b1",align="right") elif fieldName in ("TxStart", "TxEnd"): return HT.TD("%2.6f" % keyValue, Class="fs12 fwn b1",align="right") else: return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1) else: return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1,align="right") def genControlForm(self, fd): ##desc GeneList self.cursor.execute("Desc GeneList") GeneListFields = self.cursor.fetchall() GeneListFields = map(lambda X: X[0], GeneListFields) #group columns by category--used for creating the dropdown list of possible columns categories = {} for item in self.columnNames.keys(): category = self.columnNames[item] if category[-1] not in categories.keys(): categories[category[-1]] = [item ] else: categories[category[-1]] = categories[category[-1]]+[item] ##List All Species in the Gene Table speciesDict = {} self.cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \ GeneList.SpeciesId = Species.Id group by GeneList.SpeciesId order by Species.Id") results = self.cursor.fetchall() speciesField = categories.pop('species', []) categoriesOrder = ['gene', 'protein'] for item in results: specName, specId = item categoriesOrder.append(specName) speciesDict[specName] = specId AppliedField = [] for item2 in speciesField: if item2 in GeneListFields: self.cursor.execute("select %s from GeneList where SpeciesId = %d and %s is not NULL limit 1 " % (item2, specId, item2)) columnApply = self.cursor.fetchone() if not columnApply: continue elif specName != 'mouse' and item2 in ('snpCount', 'snpDensity'): continue else: pass AppliedField.append(item2) categories[specName] = AppliedField categoriesOrder += ['misc'] ############################################################ ## Create the list of possible columns for the dropdown list ############################################################ allColumnsList = HT.Select(name="allColumns", Class="snpBrowserDropBox") for category in categoriesOrder: allFields = categories[category] if allFields: geneOpt = HT.Optgroup(label=category.title()) for item in allFields: if category in self.speciesFreeze.keys(): geneOpt.append(("%s (%s %s)" % (self.columnNames[item][1], category.title(), self.speciesFreeze[category]), "%s__%s" % (item, self.speciesFreeze[category]))) else: geneOpt.append((self.columnNames[item][1], item)) geneOpt.sort() allColumnsList.append(geneOpt) ###################################### ## Create the list of selected columns ###################################### #cols contains the value of all the selected columns submitCols = cols = fd.formdata.getvalue("columns", "default") if cols == "default": if self.species=="mouse": #these are the same columns that are shown on intervalPage.py cols = ['GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'Strand', 'GeneLength', 'GeneID', 'NM_ID', 'snpCount', 'snpDensity'] elif self.species=="rat": cols = ['GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'GeneLength', 'Strand', 'GeneID', 'UnigenID'] else: #should not happen cols = [] else: if type(cols)==type(""): cols = [cols] colsLst = [] dispFields = [] for column in cols: if submitCols == "default" and column not in ('GeneSymbol') and (column in GeneListFields or column in speciesField): colsLst.append(("%s (%s %s)" % (self.columnNames[column][1], self.species.title(), self.speciesFreeze[self.species]), "%s__%s" % (column, self.speciesFreeze[self.species]))) dispFields.append([column, self.species]) else: column2 = column.split("__") if len(column2) == 1: colsLst.append((self.columnNames[column2[0]][1], column)) dispFields.append([column]) else: thisSpecies = self.speciesFreeze[column2[1]] colsLst.append(("%s (%s %s)" % (self.columnNames[column2[0]][1], thisSpecies.title(), column2[1]), column)) dispFields.append((column2[0], thisSpecies)) selectedColumnsList = HT.Select(name="columns", Class="snpBrowserSelectBox", multiple="true", data=colsLst, size=6) ########################## ## Create the columns form ########################## columnsForm = HT.Form(name="columnsForm", submit=HT.Input(type='hidden'), cgi=os.path.join(webqtlConfig.CGIDIR, self._scriptfile), enctype="multipart/form-data") columnsForm.append(HT.Input(type="hidden", name="fromdatabase", value= fd.formdata.getvalue("fromdatabase", "unknown"))) columnsForm.append(HT.Input(type="hidden", name="species", value=self.species)) if self.diffCol: columnsForm.append(HT.Input(type="hidden", name="s1", value=self.diffCol[0])) columnsForm.append(HT.Input(type="hidden", name="s2", value=self.diffCol[1])) startBox = HT.Input(type="text", name="startMb", value=self.startMb, size=10) endBox = HT.Input(type="text", name="endMb", value=self.endMb, size=10) addButton = HT.Input(type="button", name="add", value="Add", Class="button", onClick="addToList(this.form.allColumns.options[this.form.allColumns.selectedIndex].text, this.form.allColumns.options[this.form.allColumns.selectedIndex].value, this.form.columns)") removeButton = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns.selectedIndex, this.form.columns)") upButton = HT.Input(type="button", name="up", value="Up", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex-1, this.form.columns)") downButton = HT.Input(type="button", name="down", value="Down", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex+1, this.form.columns)") clearButton = HT.Input(type="button", name="clear", value="Clear", Class="button", onClick="deleteAllElements(this.form.columns)") submitButton = HT.Input(type="submit", value="Refresh", Class="button", onClick="selectAllElements(this.form.columns)") selectChrBox = HT.Select(name="chromosome") self.cursor.execute(""" Select Chr_Length.Name, Length from Chr_Length, Species where Chr_Length.SpeciesId = Species.Id AND Species.Name = '%s' Order by Chr_Length.OrderId """ % self.species) results = self.cursor.fetchall() for chrInfo in results: selectChrBox.append((chrInfo[0], chrInfo[0])) selectChrBox.selected.append(self.Chr) innerColumnsTable = HT.TableLite(border=0, Class="collap", cellpadding = 2) innerColumnsTable.append(HT.TR(HT.TD(selectedColumnsList)), HT.TR(HT.TD(clearButton, removeButton, upButton, downButton))) columnsTable = HT.TableLite(border=0, cellpadding=2, cellspacing=0) columnsTable.append(HT.TR(HT.TD(HT.Font("Chr: ", size=-1)), HT.TD(selectChrBox, submitButton)), HT.TR(HT.TD(HT.Font("View: ", size=-1)), HT.TD(startBox, HT.Font("Mb to ", size=-1), endBox, HT.Font("Mb", size=-1))), HT.TR(HT.TD(HT.Font("Show: ", size=-1)), HT.TD(allColumnsList, addButton)), HT.TR(HT.TD(""), HT.TD(innerColumnsTable))) columnsForm.append(columnsTable) #columnsForm.append(HT.Input(type="hidden", name="sort", value=diffCol), # HT.Input(type="hidden", name="identification", value=identification), # HT.Input(type="hidden", name="traitInfo", value=traitInfo)) return columnsForm, dispFields