diff options
Diffstat (limited to 'web/webqtl/qtlminer')
| -rwxr-xr-x | web/webqtl/qtlminer/GeneUtil.py | 658 | ||||
| -rwxr-xr-x | web/webqtl/qtlminer/QTLminer.py | 1237 | ||||
| -rwxr-xr-x | web/webqtl/qtlminer/__init__.py | 0 |
3 files changed, 1895 insertions, 0 deletions
diff --git a/web/webqtl/qtlminer/GeneUtil.py b/web/webqtl/qtlminer/GeneUtil.py new file mode 100755 index 00000000..3ae7f3c0 --- /dev/null +++ b/web/webqtl/qtlminer/GeneUtil.py @@ -0,0 +1,658 @@ +import string +import os + + +from base import webqtlConfig + + +#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 + + + + + + +def loadGenesForQTLminer(cursor, chrName, diffCol, startMb, endMb, webqtlDb =None, species='mouse', databaseA='HC_M2_0606_P', databaseB='HC_M2CB_1205_R', databaseC='Illum_LXS_Hipp_loess0807', str1='C57BL/6J', str2='DBA/2J'): + #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] + + +# fpText = open(os.path.join(webqtlConfig.TMPDIR, "strains") + str(j) + '.txt','wb') +# fpText.write("strain: '%d' \n" % thisone ) +# fpText.close() +# strainids.append(thisone) + + + + + ##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] + +## get pathways + + cursor.execute(""" + select + pathway + FROM + kegg.mmuflat + where + gene = '%s' + """ % (newdict["GeneID"]) ) + + resAAA = cursor.fetchall() + if resAAA: + myFields = ['pathways'] + for j, item in enumerate(myFields): + temp = [] + for k in resAAA: + temp.append(k[j]) + newdict["pathways"] = temp + + cursor.execute(""" + select + name + FROM + kegg.mmuflat + where + gene = '%s' + """ % (newdict["GeneID"]) ) + + resAAA = cursor.fetchall() + if resAAA: + myFields = ['pathwaynames'] + for j, item in enumerate(myFields): + temp = [] + for k in resAAA: + temp.append(k[j]) + newdict["pathwaynames"] = temp + +## get GO terms + + cursor.execute(""" + SELECT + distinct go.term.name + FROM go.gene_product + INNER JOIN go.dbxref ON (go.gene_product.dbxref_id=go.dbxref.id) + INNER JOIN go.association ON (go.gene_product.id=go.association.gene_product_id) + INNER JOIN go.term ON (go.association.term_id=go.term.id) + WHERE + go.dbxref.xref_key = (select mgi from go.genemgi where gene='%s' limit 1) + AND + go.dbxref.xref_dbname = 'MGI' + AND + go.term.term_type='biological_process' + """ % (newdict["GeneID"]) ) + + resAAA = cursor.fetchall() + if resAAA: + myFields = ['goterms'] + for j, item in enumerate(myFields): + temp = [] + for k in resAAA: + temp.append(k[j]) + newdict["goterms"] = temp + + + + + + + newdict["snpDensity"] = newdict["snpCount"] = newdict["snpCountall"] = newdict["snpCountmis"] = newdict["snpCountBXD"] = newdict["snpCountmissel"] = 0 + + #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 + + + +#self.cursor.execute("SELECT geneSymbol, chromosome, txStart, txEnd from GeneList where SpeciesId= 1 and geneSymbol = %s", opt.geneName) + + + + + ## search with gene name... doesnt matter. it changed to start and end position anyway + ##self.cursor.execute("SELECT geneSymbol, chromosome, txStart, txEnd from GeneList where SpeciesId= 1 and geneSymbol = %s", newdict["GeneSymbol"]) + + + #count SNPs for all strains + cursor.execute(""" + SELECT + distinct SnpAll.Id + from + SnpAll + where + SpeciesId = '1' and SnpAll.Chromosome = '%s' AND + SnpAll.Position >= %2.6f and SnpAll.Position < %2.6f AND + SnpAll.Exon='Y' + """ % (newdict["Chromosome"], newdict["TxStart"], newdict["TxEnd"])) + snpfetch = cursor.fetchall() + newdict["snpCountmis"] = len(snpfetch) + +## # count SNPs for selected strains + + sql = """SELECT + distinct SnpAll.Id, `%s`, `%s` + from + SnpAll, SnpPattern + where + SpeciesId = '1' and SnpAll.Chromosome = '%s' AND + SnpAll.Position >= %2.6f and SnpAll.Position < %2.6f and SnpAll.Id = SnpPattern.SnpId AND + SnpPattern.`%s` != SnpPattern.`%s` AND + SnpAll.Exon='Y' + """ % (str1, str2, newdict["Chromosome"], newdict["TxStart"], newdict["TxEnd"], str1, str2) + cursor.execute(sql) + ressnp = cursor.fetchall() + newdict["snpCountmissel"] = len(ressnp) + newdict["hassnp"] = 'n' + if len(ressnp)>0 : + newdict["hassnp"]= 'y' +## ####################################### NEW NEW NEW + + + + + + + + # count Indels for BXD mice + cursor.execute(""" + SELECT + distinct IndelAll.Name, IndelAll.Chromosome, IndelAll.SourceId, IndelAll.Mb_start, + IndelAll.Mb_end, IndelAll.Strand, IndelAll.Type, IndelAll.Size, IndelAll.InDelSequence, + SnpSource.Name + from + SnpSource, IndelAll + where + IndelAll.SpeciesId = '1' and IndelAll.Chromosome = '%s' AND + IndelAll.Mb_start >= %2.6f and IndelAll.Mb_start < (%2.6f+.0010) AND + SnpSource.Id = IndelAll.SourceId + order by IndelAll.Mb_start + """ % (newdict["Chromosome"], newdict["TxStart"], newdict["TxEnd"])) + + ressnp = cursor.fetchall() + newdict["indelCountBXD"] = len(ressnp) + newdict["hasindel"] = 'n' + newdict["hasexpr"] = 'n' + newdict["hascis"] = 'n' + newdict["score"] = 0 + if len(ressnp)>0 : + newdict["hasindel"]= 'y' + +## # cursor.execute(""" +## # select +## # Name from ProbeSet +## # where +## # GeneId = '%s' AND ChipId=4 limit 1 +## # """ % (newdict["GeneID"])) +## # if species=='mouse': +## # cursor.execute(""" +## # select +## # Name from ProbeSet +## # where +## # GeneId = '%s' AND ChipId=4 +## # """ % (newdict["GeneID"])) +## # results = cursor.fetchall() +## # psets = [] +## # for item in results: +## # psets.append(item) +## # newdict["probeset"] = psets +## # +## # else: +## # newdict["probeset"] = "empty" + + + + + if species=='mouse': + cursor.execute(""" + select + distinct 0, + ProbeSet.Name as TNAME, + round(ProbeSetXRef.Mean,1) as TMEAN, + round(ProbeSetXRef.LRS,1) as TLRS, + ProbeSet.Chr_num as TCHR_NUM, + ProbeSet.Mb as TMB, + ProbeSet.Symbol as TSYMBOL, + ProbeSet.name_num as TNAME_NUM + FROM ProbeSetXRef, ProbeSetFreeze, ProbeSet + where + ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol, + alias,GenbankId,UniGeneId, Probe_Target_Description) + AGAINST ('%s' IN BOOLEAN MODE) ) + and ProbeSet.symbol = '%s' + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id + and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1) + """ % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseA)) + resA = cursor.fetchall() + + if resA: + myFields = ['dummyA','probesetA','meanA','newlrsA','probesetchrA','probesetmbA','probesetsymbolA','probesetnamenumA'] + +# fpText = open(os.path.join(webqtlConfig.TMPDIR, "res") + '.txt','wb') + #fpText.write("newdictgeneid '%s' \n" % newdict["GeneId"]) + for j, item in enumerate(myFields): + temp = [] + for k in resA: + # fpText.write("j: result: '%s' \n" % k[j]) + temp.append(k[j]) + newdict[item] = temp + # fpText.close() + + + # put probesetcisA here + + cursor.execute(""" + select + distinct 0, + if( (ProbeSet.Chr = Geno.Chr AND ProbeSetXRef.LRS > 10.0000000 and ABS(ProbeSet.Mb-Geno.Mb) < 10.0000000 ) , concat('yes(',round(ProbeSetXRef.LRS,1),')') , 'no') as cis + FROM Geno, ProbeSetXRef, ProbeSetFreeze, ProbeSet + where + ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol, + alias,GenbankId,UniGeneId, Probe_Target_Description) + AGAINST ('%s' IN BOOLEAN MODE) ) + and ProbeSet.symbol = '%s' + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and Geno.SpeciesId=1 #XZ: I add this line to speed up query + and ProbeSetXRef.Locus = Geno.name + and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id + and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1) + """ % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseA)) + + resA2 = cursor.fetchall() + if resA2: + myFields = ['dummyA2','probesetcisA'] + for j, item in enumerate(myFields): + temp = [] + for k in resA2: + # fpText.write("j: result: '%s' \n" % k[j]) + temp.append(k[j]) + newdict[item] = temp + else: + newdict['probesetcisA'] = '' + + + + # specially for this dataset only + newdict["hasexpr"] = 'n' + if len(newdict["meanA"])>0: + for mym in newdict["meanA"]: + if mym>8: + newdict["hasexpr"] = 'y' + + # specially for this dataset only + newdict["hascis"] = 'n' + if len(newdict["probesetcisA"])>0: + for mym in newdict["probesetcisA"]: + if mym != 'no': + newdict["hascis"] = 'y' + + else: + myFields = ['dummyA','probesetA,''meanA','newlrsA','probesetchrA','probesetmbA','probesetsymbolA','probesetnamenumA', 'probesetcisA'] + for j, item in enumerate(myFields): + newdict[item] = "--" + + # specially for this dataset only + newdict["hasexpr"] = 'n' + newdict["hascis"] = 'n' + newdict["score"] = 0 + +########################## FOR B + + newdict["score"] = 0 + if newdict["hassnp"] == 'y': + newdict["score"] = newdict["score"] + 1 + if newdict["hasexpr"] == 'y': + newdict["score"] = newdict["score"] + 1 + if newdict["hasindel"] == 'y': + newdict["score"] = newdict["score"] + 1 + if newdict["hascis"] == 'y': + newdict["score"] = newdict["score"] + 1 + + + + if species=='mouse': + cursor.execute(""" + select + distinct 0, + ProbeSet.Name as TNAME, + round(ProbeSetXRef.Mean,1) as TMEAN, + round(ProbeSetXRef.LRS,1) as TLRS, + ProbeSet.Chr_num as TCHR_NUM, + ProbeSet.Mb as TMB, + ProbeSet.Symbol as TSYMBOL, + ProbeSet.name_num as TNAME_NUM + FROM ProbeSetXRef, ProbeSetFreeze, ProbeSet + where + ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol, + alias,GenbankId,UniGeneId, Probe_Target_Description) + AGAINST ('%s' IN BOOLEAN MODE) ) + and ProbeSet.symbol = '%s' + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id + and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1) + """ % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseB)) + + resB = cursor.fetchall() + if resB: + myFields = ['dummyB','probesetB','meanB','newlrsB','probesetchrB','probesetmbB','probesetsymbolB','probesetnamenumB'] + +# fpText = open(os.path.join(webqtlConfig.TMPDIR, "res") + '.txt','wb') + #fpText.write("newdictgeneid '%s' \n" % newdict["GeneId"]) + for j, item in enumerate(myFields): + temp = [] + for k in resB: + # fpText.write("j: result: '%s' \n" % k[j]) + temp.append(k[j]) + newdict[item] = temp + # fpText.close() + + + # put probesetcisB here + cursor.execute(""" + select + distinct 0, + if( (ProbeSet.Chr = Geno.Chr AND ProbeSetXRef.LRS > 10.0000000 and ABS(ProbeSet.Mb-Geno.Mb) < 10.0000000 ) , concat('yes(',round(ProbeSetXRef.LRS,1),')') , 'no') as cis + FROM Geno, ProbeSetXRef, ProbeSetFreeze, ProbeSet + where + ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol, + alias,GenbankId,UniGeneId, Probe_Target_Description) + AGAINST ('%s' IN BOOLEAN MODE) ) + and ProbeSet.symbol = '%s' + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and Geno.SpeciesId=1 #XZ: I add this line to speed up query + and ProbeSetXRef.Locus = Geno.name + and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id + and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1) + """ % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseB)) + + resB2 = cursor.fetchall() + if resB2: + myFields = ['dummyB2','probesetcisB'] + for j, item in enumerate(myFields): + temp = [] + for k in resB2: + # fpText.write("j: result: '%s' \n" % k[j]) + temp.append(k[j]) + newdict[item] = temp + else: + newdict['probesetcisB'] = '' + + + else: + myFields = ['dummyB','probesetB,''meanB','newlrsB','probesetchrB','probesetmbB','probesetsymbolB','probesetnamenumB', 'probesetcisB'] + for j, item in enumerate(myFields): + newdict[item] = "--" + + + +########################## + + +########################## FOR C + + + if species=='mouse': + cursor.execute(""" + select + distinct 0, + ProbeSet.Name as TNAME, + round(ProbeSetXRef.Mean,1) as TMEAN, + round(ProbeSetXRef.LRS,1) as TLRS, + ProbeSet.Chr_num as TCHR_NUM, + ProbeSet.Mb as TMB, + ProbeSet.Symbol as TSYMBOL, + ProbeSet.name_num as TNAME_NUM + FROM ProbeSetXRef, ProbeSetFreeze, ProbeSet + where + ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol, + alias,GenbankId,UniGeneId, Probe_Target_Description) + AGAINST ('%s' IN BOOLEAN MODE) ) + and ProbeSet.symbol = '%s' + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id + and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1) + """ % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseC)) + + resC = cursor.fetchall() + if resC: + myFields = ['dummyC','probesetC','meanC','newlrsC','probesetchrC','probesetmbC','probesetsymbolC','probesetnamenumC'] + +# fpText = open(os.path.join(webqtlConfig.TMPDIR, "res") + '.txt','wb') + #fpText.write("newdictgeneid '%s' \n" % newdict["GeneId"]) + for j, item in enumerate(myFields): + temp = [] + for k in resC: + # fpText.write("j: result: '%s' \n" % k[j]) + temp.append(k[j]) + newdict[item] = temp + # fpText.close() + + + # put probesetcisC here + cursor.execute(""" + select + distinct 0, + if( (ProbeSet.Chr = Geno.Chr AND ProbeSetXRef.LRS > 10.0000000 and ABS(ProbeSet.Mb-Geno.Mb) < 10.0000000 ) , concat('yes(',round(ProbeSetXRef.LRS,1),')') , 'no') as cis + FROM Geno, ProbeSetXRef, ProbeSetFreeze, ProbeSet + where + ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol, + alias,GenbankId,UniGeneId, Probe_Target_Description) + AGAINST ('%s' IN BOOLEAN MODE) ) + and ProbeSet.symbol = '%s' + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and Geno.SpeciesId=1 #XZ: I add this line to speed up query + and ProbeSetXRef.Locus = Geno.name + and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id + and ProbeSetFreeze.Id = (select Id from ProbeSetFreeze where Name='%s' limit 1) + """ % (newdict["GeneSymbol"],newdict["GeneSymbol"],databaseC)) + + resC2 = cursor.fetchall() + if resC2: + myFields = ['dummyC2','probesetcisC'] + for j, item in enumerate(myFields): + temp = [] + for k in resC2: + # fpText.write("j: result: '%s' \n" % k[j]) + temp.append(k[j]) + newdict[item] = temp + else: + newdict['probesetcisC'] = '' + + else: + myFields = ['dummyC','probesetC,''meanC','newlrsC','probesetchrC','probesetmbC','probesetsymbolC','probesetnamenumC', 'probesetcisC'] + for j, item in enumerate(myFields): + newdict[item] = "--" + + + + + + + + + #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 + + #newdict['RUDI']='hallo allemaal' + + GeneList.append(newdict) + + + return GeneList + + diff --git a/web/webqtl/qtlminer/QTLminer.py b/web/webqtl/qtlminer/QTLminer.py new file mode 100755 index 00000000..e565cdd7 --- /dev/null +++ b/web/webqtl/qtlminer/QTLminer.py @@ -0,0 +1,1237 @@ +#Note that although this module gets imported a bit, the dict columnNames is never used outside this code. +#Also note that snpBrowser also defines a columnNames dict; it's different. -KA + +from htmlgen import HTMLgen2 as HT +import os +import time +import pyXLWriter as xl + +import GeneUtil +from base.templatePage import templatePage +from utility import webqtlUtil +from base import webqtlConfig + + +_scriptfile = "main.py?FormID=qtlminerresult" + +#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'], +# "probeset" : ["ProbeSet", "ProbeSet", 'gene'], +# "probesetsymbolA" : ["ProbeSet Symbol A", "ProbeSetsymbolA", 'gene'], +# "probesetchrA" : ["probesetchrA", "probesetchrA", 'gene'], + "hassnp" : ["Has nsSNP", "Has nsSNP", 'gene'], + "hasindel" : ["Has indel", "Has indel", 'gene'], + "hasexpr" : ["Has expr", "Has expression", 'gene'], + "hascis" : ["Has cis", "Has cis regulation", 'gene'], + "score" : ["Score", "Score", 'gene'], + "meanA" : ["Expression A", "Expression in dataset 1", 'gene'], + "meanB" : ["Expression B", "Expression in dataset 2", 'gene'], + "meanC" : ["Expression C", "Expression in dataset 3", 'gene'], + "probesetcisA" : ["Cis A", "Cis regulation in dataset 1", 'gene'], + "probesetcisB" : ["Cis B", "Cis regulation in dataset 2", 'gene'], + "probesetcisC" : ["Cis C", "Cis regulation in dataset 3", 'gene'], + "probesetA" : ["ProbeSet A", "ProbeSet in dataset 1", 'gene'], + "probesetB" : ["ProbeSet B", "ProbeSet in dataset 2", 'gene'], + "probesetC" : ["ProbeSet C", "ProbeSet in dataset 3", 'gene'], + "goterms" : ["GO biological process", "GO biological process", 'gene'], + "pathways" : ["KEGG PathwayIDs", "KEGG PathwayIDs", 'gene'], + "pathwaynames" : ["KEGG Pathways", "KEGG Pathways", 'gene'], +# "newlrsA" : ["Lrs A", "lrs A", 'gene'], +# "probesetchrB" : ["probesetchrB", "probesetchrB", 'gene'], +# "newlrsB" : ["lrs B", "lrs B", 'gene'], +# "probesetchrC" : ["probesetchrC", "probesetchrC", 'gene'], +# "newlrsC" : ["lrs C", "lrs C", 'gene'], + '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'], + "snpCountall" : ["SNPs", "SNP Count", 'species'], + "snpCountmis": ["nsSNPs all", "nsSNP Count all strains", 'species'], + "snpCountmissel": ["nsSNPs selected", "nsSNP Count selected strains", 'species'], + "snpDensity" : ["SNP Density", "SNP Density", 'species'], + "indelCountBXD" : ["Indels in BXD mice", "Indel Count in BXD mice", '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 + +class QTLminer (templatePage): ### + filename = webqtlUtil.genRandStr("Itan_") + + javascript_content = """ +<SCRIPT language="JAVASCRIPT"> + +function update4(self,form) { + self.database='leeg'; + +} + + + + +</SCRIPT> +""" + def __init__(self, fd): + templatePage.__init__(self, fd) + if not self.openMysql(): + return + + self.species = fd.formdata.getvalue("species", "mouse") + try: + self.startMb = float(fd.formdata.getvalue("startMb")) + except: + self.startMb = 173 + try: + self.endMb = float(fd.formdata.getvalue("endMb")) + except: + self.endMb = self.startMb + 1 + + self.Chr = fd.formdata.getvalue("chromosome", "1") + + + +######################################################### FOR A + ###### species + + self.cursor.execute(""" + Select + Name, Id from Species + Order by + Id + """ ) + res = self.cursor.fetchall() + self.spA = res + self.spAsel = fd.formdata.getvalue("myspeciesA", "mouse") + + if not hasattr(self,"spA"): + self.spA = res2 + self.spAsel = 'mouse' + + ###### group + + self.cursor.execute(""" + select + distinct InbredSet.Name, InbredSet.FullName + from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze + where + InbredSet.SpeciesId= Species.Id and + Species.Name='%s' and InbredSet.Name != 'BXD300' and + (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) + order by + InbredSet.Name + """ % self.spAsel) + + res = self.cursor.fetchall() + + if not hasattr(self,"grA"): + self.grA = res + self.grAsel = 'BXD' + + if fd.formdata.getvalue('submitter') == 'a1': + self.grA = res + self.grAsel = self.grA[0][0] + else: + self.grAsel = fd.formdata.getvalue("groupA","BXD") + + ###### type + + self.cursor.execute(""" + select + distinct Tissue.Name, concat(Tissue.Name, ' mRNA') + from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue + where + ProbeFreeze.TissueId = Tissue.Id and + ProbeFreeze.InbredSetId = InbredSet.Id and + InbredSet.Name in ('%s') and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeSetFreeze.public > %d + order by Tissue.Name + """ % (self.grAsel,webqtlConfig.PUBLICTHRESH)) + + res = self.cursor.fetchall() + + if not hasattr(self,"tyA"): + self.tyA = res + self.tyAsel = 'Hippocampus' + + if fd.formdata.getvalue('submitter') in ['a1','a2'] : + self.tyA = res + self.tyAsel = self.tyA[0][0] + else: + self.tyAsel = fd.formdata.getvalue("typeA","Hippocampus") + + ###### database + + self.cursor.execute(""" + select + ProbeSetFreeze.Name, ProbeSetFreeze.FullName + from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue + where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeFreeze.TissueId = Tissue.Id and + ProbeFreeze.InbredSetId = InbredSet.Id and + InbredSet.Name in ('%s') and Tissue.name = '%s' and + ProbeSetFreeze.public > %d + order by ProbeSetFreeze.CreateTime desc + """ % (self.grAsel,self.tyAsel,webqtlConfig.PUBLICTHRESH)) + + res = self.cursor.fetchall() + + if not hasattr(self,"daA"): + self.daA = res + self.daAsel = 'HC_M2_0606_P' + + if fd.formdata.getvalue('submitter') in ['a1','a2','a3'] : + self.daA = res + self.daAsel = self.daA[0][0] + else: + self.daAsel = fd.formdata.getvalue("databaseA","HC_M2_0606_P") + + +######################################################### FOR B + ###### species + + self.cursor.execute(""" + Select + Name, Id from Species + Order by + Id + """ ) + res = self.cursor.fetchall() + self.spB = res + self.spBsel = fd.formdata.getvalue("myspeciesB", "mouse") + + if not hasattr(self,"spB"): + self.spB = res + self.spBsel = 'mouse' + + ###### group + + self.cursor.execute(""" + select + distinct InbredSet.Name, InbredSet.FullName + from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze + where + InbredSet.SpeciesId= Species.Id and + Species.Name='%s' and InbredSet.Name != 'BXD300' and + (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) + order by + InbredSet.Name + """ % self.spBsel) + + res = self.cursor.fetchall() + + if not hasattr(self,"grB"): + self.grB = res + self.grBsel = 'CXB' + + if fd.formdata.getvalue('submitter') == 'b1': + self.grB = res + self.grBsel = self.grB[0][0] + else: + self.grBsel = fd.formdata.getvalue("groupB","CXB") + + ###### type + + self.cursor.execute(""" + select + distinct Tissue.Name, concat(Tissue.Name, ' mRNA') + from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue + where + ProbeFreeze.TissueId = Tissue.Id and + ProbeFreeze.InbredSetId = InbredSet.Id and + InbredSet.Name in ('%s') and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeSetFreeze.public > %d + order by Tissue.Name + """ % (self.grBsel,webqtlConfig.PUBLICTHRESH)) + + res = self.cursor.fetchall() + + if not hasattr(self,"tyB"): + self.tyB = res + self.tyBsel = 'Hippocampus' + + if fd.formdata.getvalue('submitter') in ['b1','b2'] : + self.tyB = res + self.tyBsel = self.tyB[0][0] + else: + self.tyBsel = fd.formdata.getvalue("typeB","Hippocampus") + + ###### database + + self.cursor.execute(""" + select + ProbeSetFreeze.Name, ProbeSetFreeze.FullName + from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue + where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeFreeze.TissueId = Tissue.Id and + ProbeFreeze.InbredSetId = InbredSet.Id and + InbredSet.Name in ('%s') and Tissue.name = '%s' and + ProbeSetFreeze.public > %d + order by ProbeSetFreeze.CreateTime desc + """ % (self.grBsel,self.tyBsel,webqtlConfig.PUBLICTHRESH)) + + res = self.cursor.fetchall() + + if not hasattr(self,"daB"): + self.daB = res + self.daBsel = 'HC_M2CB_1205_R' + + if fd.formdata.getvalue('submitter') in ['b1','b2','b3'] : + self.daB = res + self.daBsel = self.daB[0][0] + else: + self.daBsel = fd.formdata.getvalue("databaseB","HC_M2CB_1205_R") + + + +######################################################### FOR C + ###### species + + self.cursor.execute(""" + Select + Name, Id from Species + Order by + Id + """ ) + res = self.cursor.fetchall() + self.spC = res + self.spCsel = fd.formdata.getvalue("myspeciesC", "mouse") + + if not hasattr(self,"spC"): + self.spC = res + self.spCsel = 'mouse' + + ###### group + + self.cursor.execute(""" + select + distinct InbredSet.Name, InbredSet.FullName + from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze + where + InbredSet.SpeciesId= Species.Id and + Species.Name='%s' and InbredSet.Name != 'BXD300' and + (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) + order by + InbredSet.Name + """ % self.spCsel) + + res = self.cursor.fetchall() + + if not hasattr(self,"grC"): + self.grC = res + self.grCsel = 'LXS' + + if fd.formdata.getvalue('submitter') == 'c1': + self.grC = res + self.grCsel = self.grC[0][0] + else: + self.grCsel = fd.formdata.getvalue("groupC","LXS") + + ###### type + + self.cursor.execute(""" + select + distinct Tissue.Name, concat(Tissue.Name, ' mRNA') + from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue + where + ProbeFreeze.TissueId = Tissue.Id and + ProbeFreeze.InbredSetId = InbredSet.Id and + InbredSet.Name in ('%s') and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeSetFreeze.public > %d + order by Tissue.Name + """ % (self.grCsel,webqtlConfig.PUBLICTHRESH)) + + res = self.cursor.fetchall() + + if not hasattr(self,"tyC"): + self.tyC = res + self.tyCsel = 'Hippocampus' + + if fd.formdata.getvalue('submitter') in ['c1','c2'] : + self.tyC = res + self.tyCsel = self.tyC[0][0] + else: + self.tyCsel = fd.formdata.getvalue("typeC","Hippocampus") + + ###### database + + + self.cursor.execute(""" + select + ProbeSetFreeze.Name, ProbeSetFreeze.FullName + from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue + where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeFreeze.TissueId = Tissue.Id and + ProbeFreeze.InbredSetId = InbredSet.Id and + InbredSet.Name in ('%s') and Tissue.name = '%s' and + ProbeSetFreeze.public > %d + order by ProbeSetFreeze.CreateTime desc + """ % (self.grCsel,self.tyCsel,webqtlConfig.PUBLICTHRESH)) + + res = self.cursor.fetchall() + + if not hasattr(self,"daC"): + self.daC = res + self.daCsel = 'Illum_LXS_Hipp_loess0807' + + if fd.formdata.getvalue('submitter') in ['c1','c2','c3'] : + self.daC = res + self.daCsel = self.daC[0][0] + else: + self.daCsel = fd.formdata.getvalue("databaseC","Illum_LXS_Hipp_loess0807") + + + + + + + + + + + + + + + +# self.myspeciesA = fd.formdata.getvalue("myspeciesA", "mouse") +# self.groupA = fd.formdata.getvalue("groupA", "BXD") +# self.typeA = fd.formdata.getvalue("typeA", "Spleen") +# self.databaseA = fd.formdata.getvalue("databaseA", "IoP_SPL_RMA_0509")# + +# self.myspeciesB = fd.formdata.getvalue("myspeciesB", "mouse") +# self.groupB = fd.formdata.getvalue("groupB", "BXD") +# self.typeB = fd.formdata.getvalue("typeB", "Spleen") +# self.databaseB = fd.formdata.getvalue("databaseB", "IoP_SPL_RMA_0509") + + 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 + + + + self.str1 = fd.formdata.getvalue("str1", "C57BL/6J") + self.str2 = fd.formdata.getvalue("str2", "DBA/2J") + self.sorton = fd.formdata.getvalue("sorton", "Position") + + controlFrm, dispFields, dispFields2 = self.genControlForm(fd) + ## if not fd.formdata.getvalue('submitter') in ['a1','a2','a3''a4'] : + + self.cursor.execute("""select Id from Strain where Name='%s' + """ % self.str1 ) + strain1 = self.cursor.fetchone()[0] + self.cursor.execute("""select Id from Strain where Name='%s' + """ % self.str2 ) + strain2 = self.cursor.fetchone()[0] + + filename='' + if fd.formdata.getvalue('submitter') in ['refresh'] or not hasattr(self,"daA"): + geneTable, filename = self.genGeneTable(fd, dispFields, strain1, strain2) + + infoTD = HT.TD(width=400, valign= "top") + infoTD.append(HT.Paragraph("QTLminer : Chr %s" % self.Chr, Class="title"), +# HT.Strong("Species : "), self.species.title(), HT.BR(), + +# HT.Strong("myspeciesA : "), self.myspeciesA, HT.BR(), +# HT.Strong("groupA : "), self.groupA, HT.BR(), +# HT.Strong("typeA : "), self.typeA, HT.BR(), +# HT.Strong("databaseA : "), self.databaseA, HT.BR(), + +# HT.Strong("myspeciesB : "), self.myspeciesB, HT.BR(), +# HT.Strong("groupB : "), self.groupB, HT.BR(), +# HT.Strong("typeB : "), self.typeB, HT.BR(), +# HT.Strong("databaseB : "), self.databaseB, HT.BR(), + +# HT.Strong("spAsel : "), self.spAsel, HT.BR(), +# HT.Strong("grAsel : "), self.grAsel, HT.BR(), +# HT.Strong("tyAsel : "), self.tyAsel, HT.BR(), +# HT.Strong("daAsel : "), self.daAsel, HT.BR(), + +# HT.Strong("spBsel : "), self.spBsel, HT.BR(), +# HT.Strong("grBsel : "), self.grBsel, HT.BR(), +# HT.Strong("tyBsel : "), self.tyBsel, HT.BR(), +# HT.Strong("daBsel : "), self.daBsel, HT.BR(), + +# HT.Strong("chr : "), self.Chr, HT.BR(), +# HT.Strong("formdata.submitter :"), fd.formdata.getvalue("submitter"), HT.BR(), +# HT.Strong("formdata.myspeciesA : "), fd.formdata.getvalue("myspeciesA"), HT.BR(), +# HT.Strong("formdata.groupA: "), fd.formdata.getvalue("groupA") , HT.BR(), +# HT.Strong("formdata.myspeciesB : "), fd.formdata.getvalue("myspeciesB"), HT.BR(), +# HT.Strong("formdata.groupB: "), fd.formdata.getvalue("groupB") , HT.BR(), +# HT.Strong("formdata.type: "), fd.formdata.getvalue("type") , HT.BR(), +# HT.Strong("formdata.database: "), fd.formdata.getvalue("database") , HT.BR(), +# HT.Strong("Database : "), "UCSC %s" % 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) + + if fd.formdata.getvalue('submitter') in ['refresh'] or not hasattr(self,"daA"): + mainTable.append(HT.TR(HT.TD(geneTable, colspan=3))) + + self.dict['body'] = HT.TD(mainTable) + self.dict['title'] = "QTLminer" + + self.cursor.close(); + + def genGeneTable(self, fd, dispFields, strain1, strain2): + + 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, _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.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 column[0]=='meanA': + headerRow.append(HT.TD("Expression in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='meanB': + headerRow.append(HT.TD("Expression in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='meanC': + headerRow.append(HT.TD("Expression in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='probesetcisA': + headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='probesetcisB': + headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='probesetcisC': + headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='probesetA': + headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='probesetB': + headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grBsel, HT.BR(), self.tyBsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='probesetC': + headerRow.append(HT.TD("Probeset in" , HT.BR(), self.grCsel, HT.BR(), self.tyCsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='hasexpr': + headerRow.append(HT.TD("Has expression in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='hascis': + headerRow.append(HT.TD("Cis regulated in" , HT.BR(), self.grAsel, HT.BR(), self.tyAsel, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='snpCountmis': + headerRow.append(HT.TD("nsSNPs" , HT.BR(), "all strains", HT.BR(), " ", Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + elif column[0]=='snpCountmissel': + headerRow.append(HT.TD("nsSNPs" , HT.BR(), self.str1, " vs", HT.BR(), self.str2, Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + + + + + elif len(column) == 1: + # header + headerRow.append(HT.TD(columnNames[column[0]][0], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + else: + # header + headerRow.append(HT.TD(columnNames[column[0]][0], HT.BR(), " (%s)" % speciesFreeze[column[1]], + Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1, align="Center")) + if self.xls: + colTitle = columnNames[column[0]][0] + " (%s)" % speciesFreeze[column[1]] + worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle) + worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle)) + #headerRow.append(HT.TD(columnNames[column[0]][0], HT.BR(), + # "(%s %s)" % (column[1].title(), speciesFreeze[column[1]]), + # Class="colorBlue", NOWRAP=1, align="Center")) + geneTable.append(headerRow) + + geneColnul = GeneUtil.loadGenesForQTLminer(self.cursor, self.Chr, self.diffColDefault, self.startMb, self.endMb, species=self.species, databaseA=self.daAsel, databaseB=self.daBsel, databaseC=self.daCsel, str1=self.str1, str2=self.str2) + + # scores = [] + # for gIndex, theGO in enumerate(geneCol): + # keyValue = "" + # fieldName = 'score' + # if theGO.has_key(fieldName): + # keyValue = theGO[fieldName] + # scores.append(keyValue) + + sort_on = "TxStart" + myrev = False + if self.sorton == "Score": + sort_on = "score" + myrev = True + geneColeen = [(dict_[sort_on], dict_) for dict_ in geneColnul] + geneColeen.sort(reverse=myrev) + geneCol = [dict_ for (key, dict_) in geneColeen] + + + + 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, strain1, strain2)) + + geneTable.append(geneRow) + + if self.xls: + workbook.close() + return geneTable, filename + + def formatTD(self, keyValue, fieldName, Species, theGO, strain1, strain2): + 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/%s?cmd=sch&gene=%s&alias=1&species=%s" % (webqtlConfig.CGIDIR, 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"): + return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1) + elif fieldName in ("snpCountmis"): + snpString = HT.Href(url="%s?FormID=SnpBrowserResultPage&submitStatus=1&chr=%s&start=%s&end=%s&domain=Exon&variant=SNP" % (os.path.join(webqtlConfig.CGIDIR, 'main.py'),theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"] ), text=theGO["snpCountmis"], target="_blank", Class="normalsize") + return HT.TD(snpString, Class="fs12 fwn b1",NOWRAP=1) + elif fieldName in ("snpCountmissel"): + snpString = HT.Href(url="%s?FormID=SnpBrowserResultPage&submitStatus=1&chr=%s&start=%s&end=%s&domain=Exon&variant=SNP&customStrain=1&diffAlleles=1&chosenStrains=%s,%s" % (os.path.join(webqtlConfig.CGIDIR, 'main.py'),theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], self.str1, self.str2 ), text=theGO["snpCountmissel"], target="_blank", Class="normalsize") + return HT.TD(snpString, Class="fs12 fwn b1",NOWRAP=1) + + +# if keyValue: +# snpString = HT.Href(url="%s?chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'snpBrowser.py'), 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") + elif fieldName in ("score"): + return HT.TD("%1d" % keyValue, Class="fs12 fwn b1",align="right") + elif fieldName in ("pathways", "pathwaynames", "goterms"): + html = HT.Paragraph(Class="fs12 fwn b1") + for kk in keyValue: + html.append(kk,HT.BR()) + return HT.TD(html, Class="fs12 fwn b1",align="right",NOWRAP=1) + elif fieldName in ("probesetA", "probesetB", "probesetC"): + html = HT.Paragraph(Class="fs12 fwn b1") + for kk in keyValue: + html.append(kk,HT.BR()) + return HT.TD(html, Class="fs12 fwn b1",align="right") + elif fieldName in ("probesetsymbolA"): + html = HT.Paragraph(Class="fs12 fwn b1") + for kk in keyValue: + html.append(kk,HT.BR()) + return HT.TD(html, Class="fs12 fwn b1",align="right") + elif fieldName in ("meanA", "meanB", "meanC"): + html = HT.Paragraph(Class="fs12 fwn b1") + for kk in keyValue: + html.append(str(round(kk,1)),HT.BR()) + return HT.TD(html, Class="fs12 fwn b1",align="right") + elif fieldName in ("hassnp", "hasindel", "hasexpr","hascis"): + html = HT.Paragraph(Class="fs12 fwn b1") + for kk in keyValue: + html.append(kk,HT.BR()) + return HT.TD(html, Class="fs12 fwn b1",align="right") + elif fieldName in ("newlrsA", "newlrsB", "newlrsC"): + html = HT.Paragraph(Class="fs12 fwn b1") + for kk in keyValue: + html.append(str(round(kk,1)),HT.BR()) + return HT.TD(html, Class="fs12 fwn b1",align="right") + elif fieldName in ("probesetcisA", "probesetcisB", "probesetcisC"): + html = HT.Paragraph(Class="fs12 fwn b1") + for kk in keyValue: + html.append(kk,HT.BR()) +# if kk==0: +# html.append('no',HT.BR()) +# if kk==1: +# html.append('yes',HT.BR()) + return HT.TD(html, 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 getStrainNameList(self, strain_data): +# return strain_data[1:] + def getStrainNamePair(self): + strainNamePair=[] + query ='SELECT * FROM SnpPattern limit 1' + self.cursor.execute(query) + num_fields = len(self.cursor.description) + field_names = [i[0] for i in self.cursor.description] + strainsNameList=field_names[1:] + for index, name in enumerate(strainsNameList): + strainNamePair.append((name,name)) + return strainNamePair + + 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 columnNames.keys(): + category = 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'] + + s1_data = self.getStrainNamePair() + self.allStrainNames = s1_data[1:] + + + + ############################################################ + ## Create the list of possible columns for the dropdown list + ############################################################ + allColumnsList = HT.Select(name="allColumns", Class="snpBrowserDropBox")#onChange="addToList(this.form.allColumns.options[this.form.allColumns.selectedIndex].text, this.form.allColumns.options[this.form.allColumns.selectedIndex].value, this.form.columns)") + + for category in categoriesOrder: + allFields = categories[category] + if allFields: + geneOpt = HT.Optgroup(label=category.title()) + for item in allFields: + if category in speciesFreeze.keys(): + geneOpt.append(("%s (%s %s)" % (columnNames[item][1], category.title(), speciesFreeze[category]), + "%s__%s" % (item, speciesFreeze[category]))) + else: + geneOpt.append((columnNames[item][1], item)) + geneOpt.sort() + allColumnsList.append(geneOpt) + + allColumnsList2 = HT.Select(name="allColumns2", Class="snpBrowserDropBox") + for item in self.allStrainNames: + allColumnsList2.append(item) + + ###################################### + ## 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', 'goterms', 'pathwaynames', 'Chromosome', 'TxStart', 'snpCountmis', 'snpCountmissel', 'meanA', 'meanB', 'meanC', 'probesetcisA','probesetcisB','probesetcisC', 'probesetA','probesetB','probesetC', 'indelCountBXD','hassnp','hasindel','hasexpr','hascis','score'] + 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)" % (columnNames[column][1], self.species.title(), speciesFreeze[self.species]), + "%s__%s" % (column, speciesFreeze[self.species]))) + dispFields.append([column, self.species]) + else: + column2 = column.split("__") + if len(column2) == 1: + colsLst.append((columnNames[column2[0]][1], column)) + dispFields.append([column]) + else: + thisSpecies = speciesFreeze[column2[1]] + colsLst.append(("%s (%s %s)" % (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) + + + + ######### now for the strains!!!!!! + + #cols contains the value of all the selected columns + submitCols2 = cols2 = fd.formdata.getvalue("columns2", "default") + + if cols2 == "default": + if self.species=="mouse": #these are the same columns that are shown on intervalPage.py + cols2 = ['C57BL/6J', 'DBA/2J',] + else: + #should not happen + cols2 = [] + else: + if type(cols2)==type(""): + cols2 = [cols2] + + colsLst2 = [] + dispFields2 = [] + for column2 in cols2: +# if submitCols2 == "default" and (column in GeneListFields or column in speciesField): +# colsLst2.append(("%s (%s %s)" % (columnNames[column][1], self.species.title(), speciesFreeze[self.species]), +# "%s__%s" % (column, speciesFreeze[self.species]))) +# dispFields.append([column, self.species]) +# else: +# column2 = column.split("__") +# if len(column2) == 1: + colsLst2.append((column2, column2)) + dispFields2.append([column2]) + selectedColumnsList2 = HT.Select(name="columns2", Class="snpBrowserSelectBox", multiple="true", data=colsLst2, size=6) + + ######### now for the sorton + + #cols contains the value of all the selected columns + submitCols3 = cols3 = fd.formdata.getvalue("columns3", "default") + + if cols3 == "default": + if self.species=="mouse": #these are the same columns that are shown on intervalPage.py + cols3 = ['Position', 'Score',] + else: + #should not happen + cols3 = [] + else: + if type(cols3)==type(""): + cols3 = [cols3] + + colsLst3 = [] + dispFields3 = [] + for column3 in cols3: + colsLst3.append((column3, column3)) + dispFields3.append([column3]) + selectedColumnsList3 = HT.Select(name="columns3", Class="snpBrowserSelectBox", multiple="true", data=colsLst3, size=6) + + + + + + ########################## + ## Create the columns form + ########################## + columnsForm = HT.Form(name="columnsForm", submit=HT.Input(type='hidden'), cgi=os.path.join(webqtlConfig.CGIDIR, _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)) + columnsForm.append(HT.Input(type="hidden", name="submitter", value="empty")) + 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)") +# addButton2 = HT.Input(type="button", name="add", value="Add", Class="button", onClick="addToList(this.form.allColumns2.options[this.form.allColumns2.selectedIndex].text, this.form.allColumns2.options[this.form.allColumns2.selectedIndex].value, this.form.columns2)") + removeButton = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns.selectedIndex, this.form.columns)") +# removeButton2 = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns2.selectedIndex, this.form.columns2)") + 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="Analyze QTL interval", Class="button", onClick="Javascript:this.form.submitter.value='refresh';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) + +############################################ 2 strain boxes + + selectstr1 = HT.Select(name="str1") + for item in self.allStrainNames: + selectstr1.append(item[0]) + selectstr1.selected.append(self.str1) + + selectstr2 = HT.Select(name="str2") + for item in self.allStrainNames: + selectstr2.append(item[0]) + selectstr2.selected.append(self.str2) + +############################################ select sort on + + selectsorton = HT.Select(name="sorton") + selectsorton.append('Position') + selectsorton.append('Score') + selectsorton.selected.append('Position') + + +############################################ + selectSpeciesBoxA = HT.Select(name="myspeciesA",onChange="Javascript:this.form.submitter.value='s2';submit();") + for speciesInfo in self.spA: + name = '' + if speciesInfo[0]=='mouse': + name='Mouse' + elif speciesInfo[0]=='rat': + name='Rat' + elif speciesInfo[0]=='arabidopsis': + name='Arabidopsis thaliana' + elif speciesInfo[0]=='human': + name='Human' + elif speciesInfo[0]=='barley': + name='Barley' + elif speciesInfo[0]=='drosophila': + name='Drosophila' + elif speciesInfo[0]=='macaque monkey': + name='Macaque Monkey' + + selectSpeciesBoxA.append((name, speciesInfo[0])) + selectSpeciesBoxA.selected.append(self.spAsel) + + selectGroupBoxA = HT.Select(name="groupA",onChange="Javascript:this.form.submitter.value='a2';submit();") + for groupInfo in self.grA: + selectGroupBoxA.append((groupInfo[1], groupInfo[0])) + selectGroupBoxA.selected.append(self.grAsel) + + selectTypeBoxA = HT.Select(name="typeA",onChange="Javascript:this.form.submitter.value='a3';submit();") + for typeInfo in self.tyA: + selectTypeBoxA.append((typeInfo[0] + ' mRNA', typeInfo[0])) + selectTypeBoxA.selected.append(self.tyAsel) + + selectDatabaseBoxA = HT.Select(name="databaseA",onChange="Javascript:this.form.submitter.value='a4';submit();") + for databaseInfo in self.daA: + selectDatabaseBoxA.append((databaseInfo[1], databaseInfo[0])) + selectDatabaseBoxA.selected.append(self.daAsel) + +############################# +############################################ + selectSpeciesBoxB = HT.Select(name="myspeciesB",onChange="Javascript:this.form.submitter.value='b1';submit();") + for speciesInfo in self.spB: + name = '' + if speciesInfo[0]=='mouse': + name='Mouse' + elif speciesInfo[0]=='rat': + name='Rat' + elif speciesInfo[0]=='arabidopsis': + name='Arabidopsis thaliana' + elif speciesInfo[0]=='human': + name='Human' + elif speciesInfo[0]=='barley': + name='Barley' + elif speciesInfo[0]=='drosophila': + name='Drosophila' + elif speciesInfo[0]=='macaque monkey': + name='Macaque Monkey' + + selectSpeciesBoxB.append((name, speciesInfo[0])) + selectSpeciesBoxB.selected.append(self.spBsel) + + selectGroupBoxB = HT.Select(name="groupB",onChange="Javascript:this.form.submitter.value='b2';submit();") + for groupInfo in self.grB: + selectGroupBoxB.append((groupInfo[1], groupInfo[0])) + selectGroupBoxB.selected.append(self.grBsel) + + selectTypeBoxB = HT.Select(name="typeB",onChange="Javascript:this.form.submitter.value='b3';submit();") + for typeInfo in self.tyB: + selectTypeBoxB.append((typeInfo[0] + ' mRNA', typeInfo[0])) + selectTypeBoxB.selected.append(self.tyBsel) + + selectDatabaseBoxB = HT.Select(name="databaseB",onChange="Javascript:this.form.submitter.value='b4';submit();") + for databaseInfo in self.daB: + selectDatabaseBoxB.append((databaseInfo[1], databaseInfo[0])) + selectDatabaseBoxB.selected.append(self.daBsel) + +############################################ +############################# +############################################ + selectSpeciesBoxC = HT.Select(name="myspeciesC",onChange="Javascript:this.form.submitter.value='c1';submit();") + for speciesInfo in self.spC: + name = '' + if speciesInfo[0]=='mouse': + name='Mouse' + elif speciesInfo[0]=='rat': + name='Rat' + elif speciesInfo[0]=='arabidopsis': + name='Arabidopsis thaliana' + elif speciesInfo[0]=='human': + name='Human' + elif speciesInfo[0]=='barley': + name='Barley' + elif speciesInfo[0]=='drosophila': + name='Drosophila' + elif speciesInfo[0]=='macaque monkey': + name='Macaque Monkey' + + selectSpeciesBoxC.append((name, speciesInfo[0])) + selectSpeciesBoxC.selected.append(self.spCsel) + + selectGroupBoxC = HT.Select(name="groupC",onChange="Javascript:this.form.submitter.value='c2';submit();") + for groupInfo in self.grC: + selectGroupBoxC.append((groupInfo[1], groupInfo[0])) + selectGroupBoxC.selected.append(self.grCsel) + + selectTypeBoxC = HT.Select(name="typeC",onChange="Javascript:this.form.submitter.value='c3';submit();") + for typeInfo in self.tyC: + selectTypeBoxC.append((typeInfo[0] + ' mRNA', typeInfo[0])) + selectTypeBoxC.selected.append(self.tyCsel) + + selectDatabaseBoxC = HT.Select(name="databaseC",onChange="Javascript:this.form.submitter.value='c4';submit();") + for databaseInfo in self.daC: + selectDatabaseBoxC.append((databaseInfo[1], databaseInfo[0])) + selectDatabaseBoxC.selected.append(self.daCsel) + +############################################ + + + + +############################# + + + + + innerColumnsTable = HT.TableLite(border=0, Class="collap", cellpadding = 2) + innerColumnsTable.append(HT.TR(HT.TD(selectedColumnsList)), + HT.TR(HT.TD(clearButton, removeButton, upButton, downButton))) +# innerColumnsTable2 = HT.TableLite(border=0, Class="collap", cellpadding = 2) +# innerColumnsTable2.append(HT.TR(HT.TD(selectedColumnsList2)), +# HT.TR(HT.TD(removeButton2))) + columnsTable = HT.TableLite(border=0, cellpadding=2, cellspacing=0) + columnsTable.append( + HT.TR(HT.TD(HT.Font(" ")), + HT.TD(HT.Strong("Select the QTL interval"))), + HT.TR(HT.TD(HT.Font("Chr: ", size=-1)), + HT.TD(selectChrBox)), + 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(" ", size=-1)), + HT.TD(" ")), + HT.TR(HT.TD(HT.Font(" ")), + HT.TD(HT.Strong("Select two mouse strains for inclusion of nsSNP count"))), + HT.TR(HT.TD(HT.Font("Strains: ", size=-1)), + HT.TD(selectstr1,selectstr2)), + HT.TR(HT.TD(HT.Font(" ", size=-1)), + HT.TD(" ")), + HT.TR(HT.TD(HT.Font(" ")), + HT.TD(HT.Strong("Select 3 datasets for inclusion of expression and cis-activity data"))), + HT.TR(HT.TD(HT.Font(" ", size=-1)), + HT.TD(" ")), + HT.TR(HT.TD(" "), + HT.TD(HT.Font("Dataset 1", size=-1))), + HT.TR(HT.TD(HT.Font("Species: ", size=-1)), + HT.TD(selectSpeciesBoxA)), + HT.TR(HT.TD(HT.Font("Group: ", size=-1)), + HT.TD(selectGroupBoxA)), + HT.TR(HT.TD(HT.Font("Type: ", size=-1)), + HT.TD(selectTypeBoxA)), + HT.TR(HT.TD(HT.Font("Database: ", size=-1)), + HT.TD(selectDatabaseBoxA)), + HT.TR(HT.TD(HT.Font(" ", size=-1)), + HT.TD(" ")), + HT.TR(HT.TD(" "), + HT.TD(HT.Font("Dataset 2", size=-1))), + HT.TR(HT.TD(HT.Font("Species: ", size=-1)), + HT.TD(selectSpeciesBoxB)), + HT.TR(HT.TD(HT.Font("Group: ", size=-1)), + HT.TD(selectGroupBoxB)), + HT.TR(HT.TD(HT.Font("Type: ", size=-1)), + HT.TD(selectTypeBoxB)), + HT.TR(HT.TD(HT.Font("Database: ", size=-1)), + HT.TD(selectDatabaseBoxB)), + HT.TR(HT.TD(HT.Font(" ", size=-1)), + HT.TD(" ")), + HT.TR(HT.TD(" "), + HT.TD(HT.Font("Dataset 3", size=-1))), + HT.TR(HT.TD(HT.Font("Species: ", size=-1)), + HT.TD(selectSpeciesBoxC)), + HT.TR(HT.TD(HT.Font("Group: ", size=-1)), + HT.TD(selectGroupBoxC)), + HT.TR(HT.TD(HT.Font("Type: ", size=-1)), + HT.TD(selectTypeBoxC)), + HT.TR(HT.TD(HT.Font("Database: ", size=-1)), + HT.TD(selectDatabaseBoxC)), +# HT.TR(HT.TD(""), +# HT.TD(innerColumnsTable2)), + HT.TR(HT.TD(HT.Font(" ", size=-1)), + HT.TD(" ")), + HT.TR(HT.TD(HT.Font(" ")), + HT.TD(HT.Strong("Optionally, choose additional data to display"))), + HT.TR(HT.TD(HT.Font("Show: ", size=-1)), + HT.TD(allColumnsList, addButton)), + HT.TR(HT.TD(HT.Font("Selected:",size=-1)), + HT.TD(innerColumnsTable)), + HT.TR(HT.TD(HT.Font(" ", size=-1)), + HT.TD(" ")), + HT.TR(HT.TD(HT.Font("Sort by: ", size=-1)), + HT.TD(selectsorton)), + HT.TR(HT.TD(HT.Font(" ", size=-1)), + HT.TD(" ")), + HT.TR(HT.TD(HT.Font(" ", size=-1)), + HT.TD(submitButton)), + + ) + 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, dispFields2 diff --git a/web/webqtl/qtlminer/__init__.py b/web/webqtl/qtlminer/__init__.py new file mode 100755 index 00000000..e69de29b --- /dev/null +++ b/web/webqtl/qtlminer/__init__.py |