From d0911a04958a04042da02a334ccc528dae79cc17 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 27 Mar 2015 20:28:51 +0000 Subject: Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files' --- web/webqtl/intervalAnalyst/IntervalAnalystPage.py | 405 ---------------------- 1 file changed, 405 deletions(-) delete mode 100755 web/webqtl/intervalAnalyst/IntervalAnalystPage.py (limited to 'web/webqtl/intervalAnalyst/IntervalAnalystPage.py') diff --git a/web/webqtl/intervalAnalyst/IntervalAnalystPage.py b/web/webqtl/intervalAnalyst/IntervalAnalystPage.py deleted file mode 100755 index ec9aa29c..00000000 --- a/web/webqtl/intervalAnalyst/IntervalAnalystPage.py +++ /dev/null @@ -1,405 +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 - -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 -- cgit v1.2.3