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-rwxr-xr-xweb/webqtl/intervalAnalyst/GeneUtil.py124
-rwxr-xr-xweb/webqtl/intervalAnalyst/IntervalAnalystPage.py405
-rwxr-xr-xweb/webqtl/intervalAnalyst/__init__.py0
3 files changed, 0 insertions, 529 deletions
diff --git a/web/webqtl/intervalAnalyst/GeneUtil.py b/web/webqtl/intervalAnalyst/GeneUtil.py
deleted file mode 100755
index 43008ecf..00000000
--- a/web/webqtl/intervalAnalyst/GeneUtil.py
+++ /dev/null
@@ -1,124 +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
-
-#Just return a list of dictionaries
-#each dictionary contains sub-dictionary
-def loadGenes(cursor, chrName, diffCol, startMb, endMb, webqtlDb =None, species='mouse'):
- #cursor.execute("desc GeneList")
- #results = cursor.fetchall()
- #fetchFields = map(lambda X:X[0], results)
- fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
- 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
- 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
-
- ##List All Species in the Gene Table
- speciesDict = {}
- cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \
- GeneList.SpeciesId = Species.Id group by GeneList.SpeciesId")
- results = cursor.fetchall()
- for item in results:
- speciesDict[item[0]] = item[1]
-
- ##List current Species and other Species
- speciesId = speciesDict[species]
- otherSpecies = map(lambda X: [X, speciesDict[X]], speciesDict.keys())
- otherSpecies.remove([species, speciesId])
-
- cursor.execute("""SELECT %s from GeneList
- where
- SpeciesId = %d AND Chromosome = '%s' AND
- ((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f))
- order by txStart
- """
- % (string.join(fetchFields, ", "), speciesId, chrName, startMb, endMb, startMb, endMb))
- results = cursor.fetchall()
- GeneList = []
-
- if results:
- for result in results:
- newdict = {}
- for j, item in enumerate(fetchFields):
- newdict[item] = result[j]
- #count SNPs if possible
- if diffCol and species=='mouse':
- cursor.execute("""
- select
- count(*) from BXDSnpPosition
- where
- Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
- StrainId1 = %d AND StrainId2 = %d
- """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1]))
- newdict["snpCount"] = cursor.fetchone()[0]
- newdict["snpDensity"] = newdict["snpCount"]/(newdict["TxEnd"]-newdict["TxStart"])/1000.0
- else:
- newdict["snpDensity"] = newdict["snpCount"] = 0
-
- try:
- newdict['GeneLength'] = 1000.0*(newdict['TxEnd'] - newdict['TxStart'])
- except:
- pass
-
- #load gene from other Species by the same name
- for item in otherSpecies:
- othSpec, othSpecId = item
- newdict2 = {}
-
- cursor.execute("SELECT %s from GeneList where SpeciesId = %d and geneSymbol= '%s' limit 1" %
- (string.join(fetchFields, ", "), othSpecId, newdict["GeneSymbol"]))
- resultsOther = cursor.fetchone()
- if resultsOther:
- for j, item in enumerate(fetchFields):
- newdict2[item] = resultsOther[j]
-
- #count SNPs if possible, could be a separate function
- if diffCol and othSpec == 'mouse':
- cursor.execute("""
- select
- count(*) from BXDSnpPosition
- where
- Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
- StrainId1 = %d AND StrainId2 = %d
- """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1]))
-
- newdict2["snpCount"] = cursor.fetchone()[0]
- newdict2["snpDensity"] = newdict2["snpCount"]/(newdict2["TxEnd"]-newdict2["TxStart"])/1000.0
- else:
- newdict2["snpDensity"] = newdict2["snpCount"] = 0
-
- try:
- newdict2['GeneLength'] = 1000.0*(newdict2['TxEnd'] - newdict2['TxStart'])
- except:
- pass
-
- newdict['%sGene' % othSpec] = newdict2
-
- GeneList.append(newdict)
-
- return GeneList
-
-
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("&nbsp;", 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
diff --git a/web/webqtl/intervalAnalyst/__init__.py b/web/webqtl/intervalAnalyst/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/intervalAnalyst/__init__.py
+++ /dev/null
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 18:42:02 +0000