From 8debdcba26b5e03d6dab729116523f1f91c03752 Mon Sep 17 00:00:00 2001 From: Itoshi NIKAIDO Date: Wed, 12 Nov 2008 18:32:52 +0900 Subject: [PATCH] First version --- README | 4 ++ app.yaml | 12 ++++ data/expressions.table.100.txt | 100 +++++++++++++++++++++++++++++++++ gaexpr2.py | 69 +++++++++++++++++++++++ index.yaml | 11 ++++ myloader.py | 29 ++++++++++ 6 files changed, 225 insertions(+) create mode 100644 app.yaml create mode 100644 data/expressions.table.100.txt create mode 100644 gaexpr2.py create mode 100644 index.yaml create mode 100644 myloader.py diff --git a/README b/README index e69de29..f21ef84 100644 --- a/README +++ b/README @@ -0,0 +1,4 @@ +Simple Gene Expression Database on Google App Engine. +The software can be distributed and modified under the terms of GPL. + +Itoshi NIKAIDO \ No newline at end of file diff --git a/app.yaml b/app.yaml new file mode 100644 index 0000000..0dfd133 --- /dev/null +++ b/app.yaml @@ -0,0 +1,12 @@ +application: gaexpr2 +version: 1 +runtime: python +api_version: 1 + +handlers: +- url: /load + script: myloader.py + login: admin + +- url: /.* + script: gaexpr2.py diff --git a/data/expressions.table.100.txt b/data/expressions.table.100.txt new file mode 100644 index 0000000..b40dc20 --- /dev/null +++ b/data/expressions.table.100.txt @@ -0,0 +1,100 @@ +"100001_at","Cd3g","12502","CD3 antigen, gamma polypeptide","3.91402067987102","3.86048940075989","3.9226567995032","3.82994004758123","3.78806242346122","3.77267688173767","3.84807716166765","3.85425840358991" +"100002_at","Itih3","16426","inter-alpha trypsin inhibitor, heavy chain 3","4.51838858869332","4.59160927124211","4.56999793958802","4.49777715514184","4.48301571218716","4.69794489190027","4.49316555882565","4.56600832502491" +"100003_at","Ryr1","20190","ryanodine receptor 1, skeletal muscle","3.56895159574902","3.64884091019301","3.44462092444474","3.34705357171938","3.50180242126707","3.60658428129874","3.42365953750467","3.38146262466952" +"100004_at","Ints7","77065","integrator complex subunit 7","5.15442426898486","5.34968382938241","5.27563022734073","5.28207635140323","5.33243874114884","5.33356715051805","5.27292229523532","5.19690206461823" +"100005_at","Traf4","22032","Tnf receptor associated factor 4","7.39399802125076","7.21609076549876","7.64331222762246","7.28007039757366","7.45546937738617","7.449461282249","8.01154198942404","8.02284332953774" +"100006_at","Cdh11","12552","cadherin 11","4.91445827133745","5.11348855253945","4.91042291489008","6.7746405342459","4.40613913307813","4.8390261286607","4.62909207197646","5.24576111072664" +"100007_at","Irf2bp1","272359","interferon regulatory factor 2 binding protein 1","7.98366188779707","8.00223183756374","7.86242997863333","7.95459382757281","7.9628977404331","8.02485391545101","7.88347385988436","7.75476700656901" +"100009_r_at","Sox2","20674","SRY-box containing gene 2","2.71905545759995","2.90700203981044","2.61706170058241","2.60927692855996","2.52016270511301","2.7785284004224","2.66672496674777","2.50522480337477" +"100010_at","Klf3","16599","Kruppel-like factor 3 (basic)","7.33378396795106","6.98986302839952","7.17324242534493","7.50682743941638","7.07367314255488","7.11883155526001","7.0636145384302","7.0813500648079" +"100011_at","Klf3","16599","Kruppel-like factor 3 (basic)","6.1909989615059","5.98150966408347","5.94018297913737","6.20740495029591","5.9511629444821","5.90693491495341","5.84563875951237","5.65649571075598" +"100012_at","Laptm5","16792","lysosomal-associated protein transmembrane 5","7.03073270484676","7.08590049750125","7.02628273428255","6.99288276524414","7.11227130268838","7.35080036836425","6.96809575590258","7.1029111661391" +"100013_at","Ifi35","70110","interferon-induced protein 35","6.65956614979078","7.9576553596476","7.83718997196141","7.26452087398922","6.4029277133236","7.67471908750571","7.86276687671477","7.17766882016684" +"100014_at","Tlk2","24086","tousled-like kinase 2 (Arabidopsis)","6.00772147163486","5.91958527072353","6.00300403627907","6.16586188855092","5.92486683337378","5.80444145220944","6.03426277032315","5.89484560984652" +"100015_at","Yes1","22612","Yamaguchi sarcoma viral (v-yes) oncogene homolog 1","5.55659634531289","5.62794976614898","5.54055845102638","5.62568381784204","5.66286829939971","5.69273948614037","5.55039732380637","5.63655596640604" +"100016_at","Mmp11","17385","matrix metallopeptidase 11","5.53343899168819","5.37505570651313","5.42306587084381","5.73899634087273","5.49860135810993","5.5205504687894","5.34069175191491","5.76034910884656" +"100017_at","Mybph","53311","myosin binding protein H","5.10718291416244","5.09355565088066","5.11596195301764","5.01201488812236","5.04414339340111","5.04532776089118","4.97291004649008","5.05932539983222" +"100018_at","Mtf1","17764","metal response element binding transcription factor 1","6.62219052551553","6.75697686939467","6.68897332699945","6.6909699555145","6.54879083631546","6.69375435147322","6.65305379190625","6.63869588590124" +"100019_at","Vcan","13003","versican","8.77066780074002","10.3060493024197","10.0927518834875","9.86516481266443","8.1995034549915","10.4613502759386","9.95370945184203","8.47960415675144" +"100020_at","Slc4a2","20535","solute carrier family 4 (anion exchanger), member 2","8.26398997198325","7.4369724705527","7.5421466629839","7.88491790976918","8.27731481606914","7.29845448291053","7.47059172728134","7.35233450103139" +"100021_at","Chrna1","11435","cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)","3.24876887522302","3.36533599014078","3.27221628005878","3.2822983497657","3.33252627354033","3.49407799220074","3.23848289500728","3.29211340832914" +"100022_at","Cish","12700","cytokine inducible SH2-containing protein","6.9712357218742","7.1183385186969","7.39061914567046","7.36349703571499","6.84298638920665","7.23672094861154","7.23816192004161","7.14090404403839" +"100023_at","Mybl2","17865","myeloblastosis oncogene-like 2","6.44747510162543","6.50808782118406","6.51362382569757","6.40782447186514","6.65783260800643","6.58874735922804","6.40925344166586","6.64475237955889" +"100024_at","Shroom3","27428","shroom family member 3","3.62355591746767","3.57309250763978","3.66351920848641","3.64165030686049","3.97340738841243","3.48513220289389","3.50017947877475","3.48910147674094" +"100026_at","Bcat1","12035","branched chain aminotransferase 1, cytosolic","8.10037556315974","7.56391087890277","7.35277364879145","7.27244417445985","8.35938014756244","7.48596721459006","7.24640935371159","7.2737055709014" +"100027_s_at","Pex14","56273","peroxisomal biogenesis factor 14","7.78170225561569","7.84442499357491","8.16068327186245","7.71887473601096","7.7821056679674","7.85384583515913","8.41576720622268","8.27656713503348" +"100028_r_at","Pex14","56273","peroxisomal biogenesis factor 14","6.77930868158746","6.72321046452828","6.82134160053452","6.45218834535986","6.72593387261567","6.78670907929116","6.79854306765804","6.7186134957278" +"100029_at","Pex14","56273","peroxisomal biogenesis factor 14","8.60912217851464","8.66746720316924","8.7843106572273","8.52287634693345","8.6720329655938","8.8041380242159","8.86080297421653","8.85064927616535" +"100030_at","Upp1","22271","uridine phosphorylase 1","5.74898813063902","5.68543469195091","5.73214570051155","5.56272258804175","5.81980947779316","5.76256195093109","5.53588826940243","5.57663822029935" +"100032_at","Sp1","20683","trans-acting transcription factor 1","7.2512287881874","6.99686857530699","6.48020908236951","6.51062073908589","7.1541419553205","6.81156866953054","6.63009501630272","6.03987111250201" +"100033_at","Msh2","17685","mutS homolog 2 (E. coli)","6.58711408280799","6.51259245706503","6.53097480044129","6.69886500694309","6.72171506860521","6.36510844968128","6.37759782870563","6.1711525424929" +"100034_at","Serpinb5","20724","serine (or cysteine) peptidase inhibitor, clade B, member 5","3.29379077304444","3.34688599340688","3.28324622994483","3.28435243398798","3.29837441912312","3.39928708124919","3.24736740857333","3.42779419024264" +"100035_at","Npr1","18160","natriuretic peptide receptor 1","3.02489722954230","3.07707495684981","2.88989455131565","2.93871330416049","3.02876918614866","2.94346155474264","2.89285712658127","3.01075002255525" +"100037_at","Ddx18","66942","DEAD (Asp-Glu-Ala-Asp) box polypeptide 18","6.13633705059858","6.33779854054448","6.54169470153708","6.49558686176687","6.40968267993579","6.41453957074392","6.6033084242002","6.34511268296231" +"100039_at","Tmem4","56530","transmembrane protein 4","7.22421095110971","6.9963119136427","6.7358748311019","7.47252473222022","6.95258876399653","6.87119180639236","6.69551531291619","6.91621705668372" +"100040_at","Mrpl17","27397","mitochondrial ribosomal protein L17","6.16207406435424","6.23469166135865","6.27733483120653","6.05333276700194","6.28283066943599","6.39709700297115","6.63640255956513","6.5713036638858" +"100041_at","Slc25a39","68066","solute carrier family 25, member 39","8.53536714049675","8.73354871123547","8.82357072276793","8.73266232783292","8.57471100734962","8.6320129655963","9.27972713774574","9.570346168652" +"100042_at","Hagh","14651","hydroxyacyl glutathione hydrolase","5.9531158225293","5.9849924760062","6.10920866960401","5.88426770550652","6.05224723876638","5.97066336148089","6.64355464310742","6.6611183085398" +"100043_f_at","Psapl1","76943","prosaposin-like 1","6.26976446316037","6.40708227575407","6.22590042276644","6.15822548022723","6.42228842377203","6.46847052191788","6.14090711140107","6.27427662690048" +"100044_at","Cldn11","18417","claudin 11","3.1910523643351","3.22284451327448","3.13192103568967","3.08256439843727","3.06805997035922","3.14325636097545","3.01383554490004","2.98455015215692" +"100046_at","Mthfd2","17768","methylenetetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase","8.50284667306742","8.09835374852393","8.6742575695983","7.63998486500234","9.13399402549205","8.22232248677964","9.0405350573963","8.2675475644565" +"100047_at","Snap25","20614","synaptosomal-associated protein 25","3.63676179833317","4.87160037111604","4.10179970693365","4.84576530640815","3.67621986467473","5.61112908435087","4.79343698736441","5.03878318486319" +"100048_at","Rap1a","109905","RAS-related protein-1a","4.08932785198337","4.20214817475246","4.3093703248563","4.42396021009687","4.09721131421143","4.18607550186876","4.28033301640113","4.15233816100433" +"100049_at","Hmga1","15361","high mobility group AT-hook 1","3.18437421203526","3.12678157797569","3.0727387542405","3.0670448131605","3.02097411598411","3.04065779067332","3.01714245510256","3.07327630029615" +"100050_at","Id1","15901","inhibitor of DNA binding 1","6.55163857223864","8.56060064404885","8.8420817628129","7.5013119110432","8.20995704746554","8.47076528246324","8.90201466261408","6.65017515420572" +"100051_at","Stom","13830","stomatin","8.29329072302228","8.92890431648315","9.53810742025969","8.6211649872483","8.10848413181679","8.9896425506","9.35503525971462","9.02761572454584" +"100052_at","Stom","13830","stomatin","5.80489150075625","5.69970696955525","5.71221136038498","5.44308181463061","5.70832158223209","5.77903534988001","5.55265854865315","5.52443798959228" +"100054_s_at","D2Wsu81e","227695","DNA segment, Chr 2, Wayne State University 81, expressed","7.08642969592103","7.45946290188683","7.29066781895109","7.13875155739322","7.10594320732103","7.32530838488656","7.22467908208909","6.90697629758202" +"100056_at","Fbxw2","30050","F-box and WD-40 domain protein 2","7.67114735736364","7.55810269767745","7.46662140410232","7.44207473617759","7.44883083588457","7.4386337486986","7.4987096872802","7.26405533809282" +"100057_at","Nsmce1","67711","non-SMC element 1 homolog (S. cerevisiae)","6.69086967135867","6.06855635345885","6.2756811682145","6.56529125508941","6.79196782766007","6.08705462606009","6.2994022549816","6.34094907564807" +"100058_at","2810453I06Rik","67238","RIKEN cDNA 2810453I06 gene","6.16237338308924","6.0343862925938","5.93971355660865","6.04811157862126","5.99179380524576","6.06415106352367","5.85861940520186","5.95040068171831" +"100059_at","Cyba","13057","cytochrome b-245, alpha polypeptide","8.9566115298866","8.60049486019247","8.49468722355533","8.37681810525178","8.70687000461009","8.52758503181787","8.27536967293141","7.72773995600602" +"100060_i_at","Klk1","16612","kallikrein 1","2.80755351440566","2.61238060842766","2.7471038188482","2.67417596075844","2.69386231620361","2.76816515602477","2.79611523793408","2.75023940899011" +"100061_f_at","Klk1","16612","kallikrein 1","5.0931599471046","5.22695006436805","4.94835688441007","4.77195955110029","5.08388806651074","5.11467787679755","4.88125031676643","4.8109897799646" +"100062_at","Mcm3","17215","minichromosome maintenance deficient 3 (S. cerevisiae)","6.13210233158","6.0277558192611","5.7713742576953","5.80574604700893","6.97229106224603","5.84888446675243","5.84735283399469","5.59690394185658" +"100064_f_at","Gja1","14609","gap junction membrane channel protein alpha 1","5.97119485310125","4.36590746632155","4.32732573834768","3.84682064112362","6.62050886377718","4.46757091750325","4.82621872356274","3.90371852681498" +"100065_r_at","Gja1","14609","gap junction membrane channel protein alpha 1","2.93334448022115","2.41263006738105","2.43870611461528","2.24618485654030","3.30411525023994","2.47453715914146","2.60294241170635","2.31402972916752" +"100066_at","Gart","14450","phosphoribosylglycinamide formyltransferase","6.65276777498525","7.24403977583033","7.17447211053171","6.70547789317025","7.03851685307438","7.12898707222538","7.32980387966927","6.76643144264716" +"100067_at","Akr1b3","11677","aldo-keto reductase family 1, member B3 (aldose reductase)","4.77433873232843","4.73633177678975","4.73168278549613","4.62525544284318","4.64260586150549","4.82788773017513","4.583449596209","4.75082494540196" +"100068_at","Aldh1a1","11668","aldehyde dehydrogenase family 1, subfamily A1","4.08721620683705","4.05873541291936","6.90517594287592","3.89161779978995","4.04044515006885","4.29670882188333","6.71886807834916","3.59462945957234" +"100069_at","Cyp2f2","13107","cytochrome P450, family 2, subfamily f, polypeptide 2","5.84257059485449","7.4607302094638","8.17342615546338","7.1103820601753","5.43248156434221","7.48583392604325","8.6936110935694","8.66261447822165" +"100071_at","Mup2","17841","major urinary protein 2","6.04325405148726","6.05023643968593","6.00891177458859","5.96006718026136","6.08291088671416","6.1663219041107","5.79585335022223","6.07671408706122" +"100072_at","Ciao1","26371","cytosolic iron-sulfur protein assembly 1 homolog (S. cerevisiae)","7.07094587535625","7.3322717922129","7.45218845514558","7.27823796933532","7.20636329172166","7.31438783239588","7.61296236989127","7.53105084807424" +"100073_at","N6amt2","68043","N-6 adenine-specific DNA methyltransferase 2 (putative)","5.32478936759536","5.46265269748947","5.49691921830324","5.20113064188802","5.65036346947223","5.3895660749071","5.768611396893","5.82145024521064" +"100074_at","Tmed9","67511","transmembrane emp24 protein transport domain containing 9","7.74879152957048","7.91749371161821","6.93190143409114","6.9219570607986","7.84992327460449","7.68176121851391","7.25948180361202","6.72279309724521" +"100078_at","Apoa4","11808","apolipoprotein A-IV","5.51133709638887","5.45925671062718","5.51146772406884","5.36934320965537","5.38632913056910","5.5581695000002","5.40447625336214","5.42417904373738" +"100079_at","Ndufb9","66218","NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9","8.01005932051878","8.16003112902456","8.55452880723772","8.36649760395473","8.06256145102287","8.13300886566078","8.96474010478811","9.41251068552672" +"100080_at","Psp","19194","parotid secretory protein","5.69294811425092","5.72400698056225","5.51655932574348","5.48549181395825","5.53986173412638","5.9017941445109","5.41740301648421","5.62445999312234" +"100081_at","Stip1","20867","stress-induced phosphoprotein 1","6.59356406212048","6.69038736914925","6.58386593562042","6.45491158211409","7.00946336745947","6.69923960028961","6.9540541705656","6.64499072799041" +"100082_at","Tcf1","21405","transcription factor 1","6.08983598672262","6.19048349531161","6.04968291562508","5.92628787217261","6.12703911583049","6.28380339307234","5.9705693031696","5.92386121275429" +"100084_at","Vil2","22350","villin 2","5.90789177463452","5.51052667897848","5.57078421405891","5.33762430374154","5.80563481504734","5.55229215064892","5.45042522519557","5.18084386938754" +"100085_at","Ggt1","14598","gamma-glutamyltransferase 1","4.66521349871745","4.65034594756753","4.66255622097006","4.60978787893265","4.63794098178914","4.58513692630757","4.52412158271627","4.61720953004194" +"100086_at","Lrpap1","16976","low density lipoprotein receptor-related protein associated protein 1","7.45718665909108","8.0692746014712","7.72542889546941","7.67704833391523","7.2860011454088","7.95952270361284","7.57797416734373","7.50736277471993" +"100088_at","Ppp1cb","19046","protein phosphatase 1, catalytic subunit, beta isoform","7.07640614461333","6.58170989735744","6.4476463609243","7.17386947379488","7.07106927941093","6.7852747500727","6.75814366746138","7.02823673291683" +"100089_at","Ppic","19038","peptidylprolyl isomerase C","7.67674976456746","7.24420662039334","7.44988628712088","8.1776532458961","7.38636067172225","7.37181688709482","7.77717360125488","7.62510023063909" +"100091_at","Slc35b1","110172","solute carrier family 35, member B1","8.0423217644664","8.31317634781729","8.18769359571052","8.32368839721256","8.1420323706116","8.22956849964395","8.32169129670282","8.3278169546413" +"100093_at","Pctk1","18555","PCTAIRE-motif protein kinase 1","8.05038616579357","8.01633309781795","7.95084748018111","8.01616786131376","8.07797877890022","7.8532325621143","7.98470221955329","7.82731592571535" +"100094_at","Supt5h","20924","suppressor of Ty 5 homolog (S. cerevisiae)","8.21190960201516","8.38224387297797","8.42622374737691","8.63733182238196","8.10192048284663","8.09290329400234","8.38787476732836","8.13078440276005" +"100095_at","Scarb1","20778","scavenger receptor class B, member 1","8.66316184969754","8.03835590069543","8.7046364930271","7.61904994761129","8.596460646676","7.84053975893903","9.36059474588987","10.1370903915496" +"100099_at","Smpd1","20597","sphingomyelin phosphodiesterase 1, acid lysosomal","8.68299431889784","8.59218109131006","8.7900376011289","8.72318922400422","8.51780920353504","8.4459310543344","8.8718903563861","8.76328393606055" +"100100_at","Serpinb1a","66222","serine (or cysteine) peptidase inhibitor, clade B, member 1a","2.97440196807818","2.89867491349218","2.95377144888743","3.15009642353625","2.87539544890276","2.89045757241528","2.92523332044016","3.16888902026947" +"100101_at","Snrpa","53607","small nuclear ribonucleoprotein polypeptide A","8.66459339507297","8.46374572638083","8.20644626307288","8.16881582488328","8.6948447771254","8.45261811942184","8.2632329669117","8.03667201872484" +"100103_f_at","2210010C04Rik","67373","RIKEN cDNA 2210010C04 gene","7.21416555595838","7.50156232136853","7.32133154919033","7.17491945620849","7.34878291363691","7.67211635185855","7.23030526741741","7.32507770649687" +"100104_r_at","2210010C04Rik","67373","RIKEN cDNA 2210010C04 gene","2.59151468439212","2.69611664304052","2.66925826376479","2.67374854914436","2.72609531976149","2.9880907032828","2.63877154178844","2.76744182489512" +"100106_at","Tff3","21786","trefoil factor 3, intestinal","7.21294355243637","7.3083743963111","7.24387242868989","7.2285598850931","7.3643632736952","7.472866055407","7.20213612923683","7.29058305742924" +"100109_s_at","Krt13","16663","keratin 13","3.85013306605576","3.84557174689684","3.97242297549935","4.17269538769842","3.84679405357091","3.9901624977392","3.96987462995189","4.20657645130137" +"100112_at","Cxcl12","20315","chemokine (C-X-C motif) ligand 12","8.00479351605525","9.2385033922734","8.7887201931872","9.74690732752986","6.73656794897517","8.46182608318391","8.20618077799589","8.59870334484671" +"100113_s_at","Kifap3","16579","kinesin-associated protein 3","7.20385716493431","7.0152789595622","7.14671160729107","8.1942202156208","7.12657591229689","6.9383089165441","7.1009015793706","7.4294903469018" +"100115_at","Qrich1","69232","glutamine-rich 1","6.78657838122618","6.73910800919661","6.70707523844655","6.83651466026461","6.86123517444212","6.64695514340216","6.69559625346045","6.65981194876889" +"100116_at","2810417H13Rik","68026","RIKEN cDNA 2810417H13 gene","5.69751032835142","5.02121336249985","5.2971498365844","5.57189171704607","6.70132690169374","4.8750008475469","5.44973711419018","5.4494386443155" +"100117_at","Diablo","66593","diablo homolog (Drosophila)","3.66866762812948","3.61894887818888","3.5530189773985","3.53611158910744","3.61949417890112","3.68139503237748","3.5018103525741","3.63942760371009" +"100120_at","Nid1","18073","nidogen 1","5.60083254918012","6.27910204837096","6.24626605365976","5.97469491674857","6.1299223516144","6.59065902984129","6.47126331337965","5.66489421862817" +"100122_at","Gnb5","14697","guanine nucleotide binding protein, beta 5","5.053475761329","6.1915928900906","5.81676218625271","5.25138601812595","4.70824607007577","5.82778682889258","6.15434637494878","5.25302596128488" +"100123_f_at","Itgb1","16412","integrin beta 1 (fibronectin receptor beta)","10.2704303262774","10.1053917112769","9.99403356317067","10.5215981679771","10.0886128459229","10.0487128678678","10.0666742421776","9.60805969596077" +"100124_r_at","Itgb1","16412","integrin beta 1 (fibronectin receptor beta)","8.19941460646116","8.00352250536404","7.98188042286518","8.24221539518156","8.05367935310704","8.00722325753334","7.9218797064865","7.71119106624727" +"100125_at","Pa2g4","18813","proliferation-associated 2G4","4.82747547386031","5.51364384043782","5.23947645719342","5.02217662701327","5.40192051050507","5.26787457832696","5.39176476570711","4.8244673977342" +"100126_at","Chrac1","93696","chromatin accessibility complex 1","7.2580888491588","7.23413215431925","6.99225923660368","7.29635102347186","7.14066336725164","7.05160025313983","7.04035255406212","6.88431917090892" +"100127_at","Crabp2","12904","cellular retinoic acid binding protein II","3.20424924215631","3.10658995938016","3.06563230419154","2.91255505030030","3.19251063779006","3.03014122604828","3.04186910308802","2.97699253471169" +"100128_at","Cdc2a","12534","cell division cycle 2 homolog A (S. pombe)","8.17040477156928","7.7070517189062","7.61493900205238","7.76780694798358","8.97483048534271","7.61433085338071","7.78289338629718","7.54002967053012" +"100130_at","Jun","16476","Jun oncogene","6.9895450935826","7.36703331526411","7.15036035758897","6.88371943477097","6.92039071832227","7.16851779179701","6.77484416727456","6.57822422125072" +"100131_at","Scg5","20394","secretogranin V","3.38522232428901","3.35449496422098","3.14061170564755","3.13094412251619","3.34207744389829","3.36231382168421","3.021182025839","3.17306072395394" diff --git a/gaexpr2.py b/gaexpr2.py new file mode 100644 index 0000000..01f2cef --- /dev/null +++ b/gaexpr2.py @@ -0,0 +1,69 @@ +import wsgiref.handlers + +from google.appengine.ext import webapp +from google.appengine.ext import search +from google.appengine.ext.webapp.util import run_wsgi_app + +class MainPage(webapp.RequestHandler): + def get(self): + + url = "http://chart.apis.google.com/chart?cht=lc&chco=1E5692,3E9A3B&chs=200x125&chxt=x,y&chxl=0:|0|2|4|6|8|10|1:|2|4|6|8|10&chds=2,10&chd=t:" + self.response.headers['Content-Type'] = 'text/html' + self.response.out.write('') + + # I use the webapp framework to retrieve the keyword + keyword = self.request.get('keyword') + + if not keyword: + self.response.out.write("No keyword has been set") + else: + # Search the 'Expression' Entity based on our keyword + query = search.SearchableQuery('Expression') + query.Search(keyword) + for result in query.Run(): + # Annotation + self.response.out.write('
')
+         self.response.out.write('Affy ID: %s\n'     % result['affy_id'])
+         self.response.out.write('Gene Symbol: %s\n' % result['gene_symbol'])
+         self.response.out.write('Gene Name: %s\n'   % result['gene_name'])
+         self.response.out.write('Entrez Gene: ' % result['entrezid'] + "%s\n" % result['entrezid'])
+         self.response.out.write('
') + + # Graph (Using Google Chart API) + evector = ",".join([`result['evector_day' + suffix]` for suffix in ["0", "2", "4", "10"]]) + ppargox = ",".join([`result['ppargox_day' + suffix]` for suffix in ["0", "2", "4", "10"]]) + graph = url + evector + "|" + ppargox + self.response.out.write('' % graph) + + self.response.out.write('
Back
') + self.response.out.write('') + +class IdSearchForm(webapp.RequestHandler): + def get(self): + self.response.headers['Content-Type'] = 'text/html' + self.response.out.write(""" + + +

Gene Expression Database

+
+
+ Keyword: + (ex. 100005_at, Traf4) +
+
+
+ Itoshi NIKAIDO, Ph. D., dritoshi at gmail dot com + + """) + + +application = webapp.WSGIApplication( + [('/', MainPage), + ('/search', IdSearchForm)], + debug=True) + +def main(): + run_wsgi_app(application) + +if __name__ == "__main__": + main() diff --git a/index.yaml b/index.yaml new file mode 100644 index 0000000..a3b9e05 --- /dev/null +++ b/index.yaml @@ -0,0 +1,11 @@ +indexes: + +# AUTOGENERATED + +# This index.yaml is automatically updated whenever the dev_appserver +# detects that a new type of query is run. If you want to manage the +# index.yaml file manually, remove the above marker line (the line +# saying "# AUTOGENERATED"). If you want to manage some indexes +# manually, move them above the marker line. The index.yaml file is +# automatically uploaded to the admin console when you next deploy +# your application using appcfg.py. diff --git a/myloader.py b/myloader.py new file mode 100644 index 0000000..e94affb --- /dev/null +++ b/myloader.py @@ -0,0 +1,29 @@ +from google.appengine.api import users +from google.appengine.ext import bulkload +from google.appengine.api import datastore_types +from google.appengine.ext import search + +class ExpressionLoader(bulkload.Loader): + def __init__(self): + # Our 'Expression' entity contains a affyid string and an expression float data + bulkload.Loader.__init__(self, 'Expression', + [('affy_id', str), + ('gene_symbol', str), + ('entrezid', str), + ('gene_name', str), + ('evector_day0', float), + ('evector_day2', float), + ('evector_day4', float), + ('evector_day10', float), + ('ppargox_day0', float), + ('ppargox_day2', float), + ('ppargox_day4', float), + ('ppargox_day10', float), + ]) + + def HandleEntity(self, entity): + ent = search.SearchableEntity(entity) + return ent + +if __name__ == '__main__': + bulkload.main(ExpressionLoader())