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+# 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 22:20:21 +0000