| Previous changeset 0:fa06ddcae68e (2019-04-11) Next changeset 2:4c626e984fde (2019-04-12) |
|
Commit message:
Deleted selected files |
|
removed:
nucDyn_stats.xml test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.gff test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png test-data/genes.gff |
| b |
| diff -r fa06ddcae68e -r 21a0f28aea68 nucDyn_stats.xml --- a/nucDyn_stats.xml Thu Apr 11 04:01:48 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,76 +0,0 @@ -<tool id="nucDyn_stats" name="Nucleosome Dynamics Statistics" version="0.1"> - <description>: statistics on Nucleosome Dynamics analysis</description> - <requirements> - <requirement type="binary">docker</requirement> - </requirements> - <command> -<![CDATA[ - ln -f -s $output_gw_png_file $output_gw_png_file\.png; - docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucldyn nucDyn_stats --input $gff_file - #if $assembly.source == "buildin": - --genome ${assembly.ref_genome_gff_buildin} - #else if $assembly.source == "history": - --genome ${assembly.ref_genome_gff_history} - #end if - --out_genes $output_genes_csv_file --out_gw $output_gw_png_file\.png; - rm $output_gw_png_file\.png -]]> - </command> - <inputs> - <param name="gff_file" type="data" format="gff" label="Input Nucleosome Calls"/> - <conditional name="assembly"> - <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their chromosome sizes and their annotated genes."> - <option value="buildin" selected="True">Use a built-in genome</option> - <option value="history">Use a genome from the history</option> - </param> - <when value="buildin"> - <param name="ref_genome_gff_buildin" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="nucldyn_publicdata.loc"> - <column name="name" index="2"/> - <column name="value" index="4"/> - </options> - </param> - </when> - <when value="history"> - <param name="ref_genome_gff_history" type="data" format="gff" label="Select gene annotations for your reference genome" help="Check below the documentation for lerning about the file format."/> - </when> - </conditional> -</inputs> - <outputs> - <data format="csv" name="output_genes_csv_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" /> - <data format="png" name="output_gw_png_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.png" /> - </outputs> -<tests> - <test> - <param name="gff_file" value="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" /> - <param name="ref_genome_gff_buildin" value="genes.gff" /> - <output name="output_genes_csv_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv" /> - <output name="output_gw_png_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png" /> - </test> -</tests> - <help> -.. class:: warningmark - - -Check the documentation for setting the tool parameters at the source code repository: http://mmb.irbbarcelona.org/gitlab/NuclDynamics/docker - ------ - -.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png - :height: 80 - :width: 200 - -**http://mmb.irbbarcelona.org/NucleosomeDynamics** - </help> - <citations> - <citation type="bibtex"> -@misc{github, - author = {Buitrago D}, - year = {2019}, - title = {Nucleosome Dynamics suite: containerized installation}, - publisher = {GitLab}, - journal = {GitLab repository}, - url = {http://mmb.irbbarcelona.org/gitlab/NuclDynamics/docker}, -}</citation> - </citations> -</tool> |
| b |
| diff -r fa06ddcae68e -r 21a0f28aea68 test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.gff --- a/test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.gff Thu Apr 11 04:01:48 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,722 +0,0 @@\n-chrII\tNucleosomeDynamics\tNucleosome change\t 12453\t 12686\t0.0145905861502489\t.\t.\tnreads=3.35583137722519;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 16527\t 16679\t0.0116178639233301\t.\t.\tnreads=3.32010826742652;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 17813\t 17978\t0.00244022288092387\t.\t.\tnreads=3.76846113314784;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 37509\t 37662\t0.0188279663158348\t.\t.\tnreads=3.0026735322627;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 37680\t 37965\t0.000449408121787405\t.\t.\tnreads=4.90937327810431;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 42220\t 42420\t0.00515117881707874\t.\t.\tnreads=3.62446352577001;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 48952\t 49138\t0.0174820397546826\t.\t.\tnreads=3.12224345105165;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 60041\t 60213\t0.00752990883595927\t.\t.\tnreads=3.46115105617404;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 63974\t 64184\t0.0204239568573379\t.\t.\tnreads=3.26787918041301;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 66137\t 66370\t0.00693722416549654\t.\t.\tnreads=3.75995674495063;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 67666\t 67853\t0.0130522050957899\t.\t.\tnreads=3.27843468004489;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 83543\t 83768\t0.00784042922041864\t.\t.\tnreads=3.76569634817574;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t 84503\t 84695\t0.00565162083864906\t.\t.\tnreads=3.51913948422993;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t100895\t101079\t0.00328559494434197\t.\t.\tnreads=3.49612711163579;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t102972\t103183\t0.016066352618141\t.\t.\tnreads=3.13361957497686;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t111868\t112024\t0.00827526598026395\t.\t.\tnreads=3.28236436923612;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t112026\t112197\t0.00711596807380461\t.\t.\tnreads=3.319806541034;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t113316\t113539\t0.0156579178808079\t.\t.\tnreads=3.26569919496744;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t129897\t130126\t0.00723063033856206\t.\t.\tnreads=3.51596796674879;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t130219\t130416\t0.00899578220783154\t.\t.\tnreads=3.2723888779058;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t132392\t132606\t0.00173707815491035\t.\t.\tnreads=4.02662169323612;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t133206\t133353\t0.00168259823192981\t.\t.\tnreads=3.91398928842213;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t137835\t138022\t0.0146307154924034\t.\t.\tnreads=3.08238713768598;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t148949\t149128\t0.00115027267845828\t.\t.\tnreads=4.14991562271917;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t152173\t152392\t0.00951896231119845\t.\t.\tnreads=3.21384712277598;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t158820\t158997\t0.014414513826024\t.\t.\tnreads=3.28597347026273;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t160361\t160595\t0.00199662589187645\t.\t.\tnreads=3.97299983453989;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t161917\t162147\t0.00121692808894827\t.\t.\tnreads=4.16451475700319;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t174416\t174714\t0.00167828549687881\t.\t.\tnreads=4.36168166820924;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t180285\t180470\t0.0147842620468716\t.\t.\tnreads=3.2597904945036;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t182387\t182621\t0.0159426126016425\t.\t.\tnreads=3.23953338918331;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t187542\t187718\t0.0178493243773248\t.\t.\tnreads=3.11092672610303;class=INCLUSION\n-chrII\tNucleosomeDynamics\tNucleosome change\t189409\t189689\t0.018972729193041\t.\t.\tnreads=3.2438261'..b'0221852003573124\t.\t.\tnreads=7.21930905283428;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t693344\t693490\t0.0273059454017113\t.\t.\tnreads=7.77870540390462;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t697845\t697991\t0.0195951790864501\t.\t.\tnreads=4.36691141328305;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t699808\t699954\t0.00338227722955859\t.\t.\tnreads=3.59199785237705;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t700602\t700748\t0.00251775704169176\t.\t.\tnreads=3.41650172354926;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t702904\t703050\t0.0147855340742839\t.\t.\tnreads=4.07260520855324;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t703637\t703783\t0.0102936557102701\t.\t.\tnreads=4.6813244146974;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t704184\t704330\t0.00414879387520062\t.\t.\tnreads=3.70123431053916;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t705380\t705526\t0.00406599532113429\t.\t.\tnreads=3.26413962176605;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t709388\t709534\t0.00224676500714206\t.\t.\tnreads=3.12630433523633;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t713900\t714046\t0.00816181459253048\t.\t.\tnreads=3.16174809475912;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t717871\t718017\t0.057109950167053\t.\t.\tnreads=3.82106608848013;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t722917\t723063\t0.00805214841410655\t.\t.\tnreads=4.7413121521035;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t736374\t736520\t0.00571656796503463\t.\t.\tnreads=3.40969801524672;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t737912\t738058\t0.00509900158254555\t.\t.\tnreads=3.90501641175755;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t745773\t745919\t0.0174972781192012\t.\t.\tnreads=3.19492017334846;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t748271\t748417\t0.000790192189664131\t.\t.\tnreads=3.97458483683383;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t748942\t749088\t0.0142928404376486\t.\t.\tnreads=3.5783893574324;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t750526\t750672\t0.0190051854037714\t.\t.\tnreads=3.96720262588548;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t752034\t752180\t0.00143558251799832\t.\t.\tnreads=5.81263048759728;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t755481\t755627\t0.0115875650175342\t.\t.\tnreads=3.94129140930941;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t755551\t755697\t0.00562619672282293\t.\t.\tnreads=4.68664474846765;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t756115\t756261\t0.0185854741565688\t.\t.\tnreads=3.0859207780792;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t760010\t760156\t0.0939693182709882\t.\t.\tnreads=3.55922328517796;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t763852\t763998\t0.0175966985920274\t.\t.\tnreads=3.50362995387377;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t765569\t765715\t0.0273108299794435\t.\t.\tnreads=3.14312082056471;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t775680\t775826\t0.0641355120366329\t.\t.\tnreads=5.25112328718539;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t778732\t778878\t0.0476835261083793\t.\t.\tnreads=4.21286858736339;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t779793\t779939\t0.0485459478943652\t.\t.\tnreads=3.33519206455949;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t780429\t780575\t3.48157289709105e-07\t.\t.\tnreads=4.54477339667449;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t790246\t790392\t0.0281237174187084\t.\t.\tnreads=6.39292400564415;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t791471\t791617\t0.00919533834621312\t.\t.\tnreads=3.23868139790627;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t793101\t793247\t5.86718265191246e-06\t.\t.\tnreads=5.57107501563057;class=SHIFT -\n-chrII\tNucleosomeDynamics\tNucleosome change\t804122\t804268\t0.0968659516978201\t.\t.\tnreads=3.52867766756143;class=SHIFT -\n' |
| b |
| diff -r fa06ddcae68e -r 21a0f28aea68 test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv --- a/test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv Thu Apr 11 04:01:48 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5681 +0,0 @@\n-Name,Inclusions,Evictions,Shifts+,Shifts-\n-Q0080 (ATP8 AAP1),0,0,0,0\n-Q0085 (ATP6 OLI2 OLI4 PHO1),0,0,0,0\n-Q0130 (OLI1 ATP9 OLI3),0,0,0,0\n-Q0275 (COX3 OXI2),0,0,0,0\n-YAL001C (TFC3 FUN24 TSV115),0,0,0,0\n-YAL002W (VPS8 FUN15 VPL8 VPT8),0,0,0,0\n-YAL003W (EFB1 TEF5),0,0,0,0\n-YAL004W,0,0,0,0\n-YAL005C (SSA1 YG100),0,0,0,0\n-YAL007C (ERP2),0,0,0,0\n-YAL008W (FUN14),0,0,0,0\n-YAL009W (SPO7),0,0,0,0\n-YAL010C (MDM10 FUN37),0,0,0,0\n-YAL011W (SWC3 SWC1),0,0,0,0\n-YAL012W (CYS3 CYI1 FUN35 STR1),0,0,0,0\n-YAL013W (DEP1 FUN54),0,0,0,0\n-YAL014C (SYN8 SLT2 UIP2),0,0,0,0\n-YAL015C (NTG1 FUN33 SCR1 ogg2),0,0,0,0\n-YAL016C-B,0,0,0,0\n-YAL016W (TPD3 FUN32),0,0,0,0\n-YAL017W (PSK1 FUN31),0,0,0,0\n-YAL018C,0,0,0,0\n-YAL019W (FUN30),0,0,0,0\n-YAL020C (ATS1 FUN28 KTI13),0,0,0,0\n-YAL021C (CCR4 FUN27 NUT21),0,0,0,0\n-YAL022C (FUN26),0,0,0,0\n-YAL023C (PMT2 FUN25),0,0,0,0\n-YAL024C (LTE1 MSI2),0,0,0,0\n-YAL025C (MAK16),0,0,0,0\n-YAL026C (DRS2 FUN38 SWA3),0,0,0,0\n-YAL027W (SAW1),0,0,0,0\n-YAL028W (FRT2 HPH2),0,0,0,0\n-YAL029C (MYO4 FUN22 SHE1),0,0,0,0\n-YAL030W (SNC1),0,0,0,0\n-YAL031C (GIP4 FUN21),0,0,0,0\n-YAL032C (PRP45 FUN20),0,0,0,0\n-YAL033W (POP5 FUN53),0,0,0,0\n-YAL034C (FUN19),0,0,0,0\n-YAL034C-B (YAL035C-A),0,0,0,0\n-YAL034W-A (MTW1 DSN3 NSL2),0,0,0,0\n-YAL035W (FUN12 yIF2),0,0,0,0\n-YAL036C (RBG1 FUN11),0,0,0,0\n-YAL037C-A,0,0,0,0\n-YAL037C-B,0,0,0,0\n-YAL037W,0,0,0,0\n-YAL038W (CDC19 PYK1),0,0,0,0\n-YAL039C (CYC3),0,0,0,0\n-YAL040C (CLN3 DAF1 FUN10 WHI1),0,0,0,0\n-YAL041W (CDC24 CLS4),0,0,0,0\n-YAL042W (ERV46 FUN9),0,0,0,0\n-YAL043C (PTA1 FUN39),0,0,0,0\n-YAL044C (GCV3),0,0,0,0\n-YAL044W-A,0,0,0,0\n-YAL045C,0,0,0,0\n-YAL046C (AIM1),0,0,0,0\n-YAL047C (SPC72 LDB4),0,0,0,0\n-YAL047W-A,0,0,0,0\n-YAL048C (GEM1 GON1),0,0,0,0\n-YAL049C (AIM2),0,0,0,0\n-YAL051W (OAF1 YAF1),0,0,0,0\n-YAL053W (FLC2 HUF2),0,0,0,0\n-YAL054C (ACS1 FUN44),0,0,0,0\n-YAL055W (PEX22 YAF5),0,0,0,0\n-YAL056W (GPB2 KRH1),0,0,0,0\n-YAL058W (CNE1 FUN48),0,0,0,0\n-YAL059W (ECM1),0,0,0,0\n-YAL060W (BDH1 BDH),0,0,0,0\n-YAL061W (BDH2),0,0,0,0\n-YAL062W (GDH3 FUN51),0,0,0,0\n-YAL064W-B,0,0,0,0\n-YAL067C (SEO1),0,0,0,0\n-YAR002C-A (ERP1),0,0,0,0\n-YAR002W (NUP60),0,0,0,0\n-YAR003W (SWD1 CPS50 FUN16 SAF49),0,0,0,0\n-YAR007C (RFA1 BUF2 FUN3 RPA1),0,0,0,0\n-YAR008W (SEN34 FUN4),0,0,0,0\n-YAR014C (BUD14),0,0,0,0\n-YAR015W (ADE1),0,0,0,0\n-YAR018C (KIN3 FUN52 NPK1),0,0,0,0\n-YAR019C (CDC15 LYT1),0,0,0,0\n-YAR023C,0,0,0,0\n-YAR027W (UIP3),0,0,0,0\n-YAR028W,0,0,0,0\n-YAR029W,0,0,0,0\n-YAR033W (MST28),0,0,0,0\n-YAR035W (YAT1),0,0,0,0\n-YAR042W (SWH1 OSH1 YAR044W),0,0,0,0\n-YAR066W,0,0,0,0\n-YBL001C (ECM15),1,0,0,0\n-YBL002W (HTB2),0,0,0,0\n-YBL003C (HTA2 H2A2),0,0,0,0\n-YBL004W (UTP20),0,1,2,3\n-YBL005W (PDR3 AMY2 TPE2),1,0,1,3\n-YBL006C (LDB7 RSC14),0,0,0,0\n-YBL007C (SLA1),1,0,3,0\n-YBL008W (HIR1),1,1,0,1\n-YBL009W (ALK2),0,2,0,0\n-YBL010C,0,0,0,0\n-YBL011W (SCT1 GAT2),2,0,0,2\n-YBL014C (RRN6),1,2,4,1\n-YBL015W (ACH1),1,0,2,0\n-YBL016W (FUS3 DAC2),0,0,0,0\n-YBL017C (PEP1 VPS10 VPT1),3,2,2,5\n-YBL018C (POP8),0,0,0,0\n-YBL019W (APN2 ETH1),0,0,0,0\n-YBL020W (RFT1),1,0,0,1\n-YBL021C (HAP3),0,0,0,0\n-YBL022C (PIM1 LON1),1,0,1,1\n-YBL023C (MCM2),0,0,0,1\n-YBL024W (NCL1 TRM4),1,0,1,0\n-YBL025W (RRN10),0,0,0,0\n-YBL026W (LSM2 SMX5 SNP3),0,0,0,0\n-YBL027W (RPL19B),0,1,0,0\n-YBL028C,0,0,0,0\n-YBL029C-A,0,0,0,0\n-YBL029W,0,0,0,0\n-YBL030C (PET9 AAC2 ANC2 OP1),0,0,0,0\n-YBL031W (SHE1),1,0,0,0\n-YBL032W (HEK2 KHD1),1,0,0,0\n-YBL033C (RIB1),1,0,1,0\n-YBL034C (STU1),0,2,1,0\n-YBL035C (POL12),1,0,0,0\n-YBL036C,0,0,0,0\n-YBL037W (APL3),1,0,2,0\n-YBL038W (MRPL16),0,0,0,0\n-YBL039C (URA7),0,0,1,2\n-YBL039W-B (YBL039W-A),0,0,1,0\n-YBL040C (ERD2),0,1,1,0\n-YBL041W (PRE7 PRS3),0,0,0,0\n-YBL042C (FUI1),0,0,0,0\n-YBL043W (ECM13),0,0,0,0\n-YBL045C (COR1 QCR1),0,0,1,0\n-YBL046W (PSY4),2,0,0,2\n-YBL047C (EDE1 BUD15),2,1,2,4\n-YBL049W (MOH1),0,0,0,0\n-YBL050W (SEC17 RNS3),0,0,0,0\n-YBL051C (PIN4 MDT1),0,0,0,0\n-YBL052C (SAS3),0,1,0,0\n-YBL054W (TOD6 PBF1),0,1,1,0\n-YBL055C (Tat-D),0,0,1,0\n-YBL056W (PTC3),0,0,0,1\n-YBL057C (PTH2),1,0,0,0\n-YBL058W (SHP1 UBX1),2,1,0,1\n-YBL059C-A (CMC2),0,0,0,0\n-YBL059W,0,0,0,0\n-YBL060W (YEL1),0'..b',0,0\n-YPR032W (SRO7 SNI1 SOP1),0,0,0,0\n-YPR033C (HTS1 TSM4572),0,0,0,0\n-YPR034W (ARP7 RSC11 SWP61),0,0,0,0\n-YPR035W (GLN1),0,0,0,0\n-YPR036W (VMA13 CLS11),0,0,0,0\n-YPR036W-A,0,0,0,0\n-YPR037C (ERV2),0,0,0,0\n-YPR040W (TIP41),0,0,0,0\n-YPR041W (TIF5 SUI5),0,0,0,0\n-YPR042C (PUF2),0,0,0,0\n-YPR043W (RPL43A),0,0,0,0\n-YPR044C (OPI11),0,0,0,0\n-YPR045C (THP3 MNI2),0,0,0,0\n-YPR046W (MCM16),0,0,0,0\n-YPR047W (MSF1),0,0,0,0\n-YPR048W (TAH18),0,0,0,0\n-YPR049C (ATG11 CVT9),0,0,0,0\n-YPR050C,0,0,0,0\n-YPR051W (MAK3 NAA30),0,0,0,0\n-YPR052C (NHP6A),0,0,0,0\n-YPR053C,0,0,0,0\n-YPR054W (SMK1),0,0,0,0\n-YPR055W (SEC8),0,0,0,0\n-YPR056W (TFB4),0,0,0,0\n-YPR057W (BRR1),0,0,0,0\n-YPR058W (YMC1),0,0,0,0\n-YPR059C,0,0,0,0\n-YPR060C (ARO7 HGS1 OSM2 TYR7),0,0,0,0\n-YPR061C (JID1),0,0,0,0\n-YPR062W (FCY1 yCD),0,0,0,0\n-YPR063C,0,0,0,0\n-YPR065W (ROX1 REO1),0,0,0,0\n-YPR067W (ISA2),0,0,0,0\n-YPR068C (HOS1),0,0,0,0\n-YPR069C (SPE3),0,0,0,0\n-YPR070W (MED1),0,0,0,0\n-YPR071W,0,0,0,0\n-YPR072W (NOT5),0,0,0,0\n-YPR073C (LTP1),0,0,0,0\n-YPR074C (TKL1),0,0,0,0\n-YPR075C (OPY2),0,0,0,0\n-YPR076W,0,0,0,0\n-YPR077C,0,0,0,0\n-YPR078C,0,0,0,0\n-YPR079W (MRL1),0,0,0,0\n-YPR080W (TEF1 EF-1%20alpha),0,0,0,0\n-YPR081C (GRS2),0,0,0,0\n-YPR082C (DIB1 SNU16),0,0,0,0\n-YPR083W (MDM36),0,0,0,0\n-YPR084W,0,0,0,0\n-YPR085C (ASA1),0,0,0,0\n-YPR086W (SUA7 SOH4),0,0,0,0\n-YPR088C (SRP54 SRH1),0,0,0,0\n-YPR089W (YPR090W),0,0,0,0\n-YPR091C,0,0,0,0\n-YPR093C (ASR1),0,0,0,0\n-YPR094W (RDS3),0,0,0,0\n-YPR095C (SYT1),0,0,0,0\n-YPR097W,0,0,0,0\n-YPR098C,0,0,0,0\n-YPR100W (MRPL51),0,0,0,0\n-YPR101W (SNT309 NTC25),0,0,0,0\n-YPR102C (RPL11A),0,0,0,0\n-YPR103W (PRE2 DOA3 PRG1 SRR2),0,0,0,0\n-YPR104C (FHL1 SPP42),0,0,0,0\n-YPR105C (COG4 COD1 SEC38 SGF1),0,0,0,0\n-YPR106W (ISR1),0,0,0,0\n-YPR107C (YTH1),0,0,0,0\n-YPR108W (RPN7),0,0,0,0\n-YPR109W,0,0,0,0\n-YPR110C (RPC40 RPC5),0,0,0,0\n-YPR111W (DBF20),0,0,0,0\n-YPR112C (MRD1),0,0,0,0\n-YPR113W (PIS1),0,0,0,0\n-YPR114W,0,0,0,0\n-YPR115W (RGC1 GCA1),0,0,0,0\n-YPR116W (RRG8),0,0,0,0\n-YPR117W,0,0,0,0\n-YPR118W (MRI1),0,0,0,0\n-YPR119W (CLB2),0,0,0,0\n-YPR120C (CLB5),0,0,0,0\n-YPR121W (THI22),0,0,0,0\n-YPR122W (AXL1 FUS5 STE22),0,0,0,0\n-YPR124W (CTR1),0,0,0,0\n-YPR125W (YLH47 MRS7),0,0,0,0\n-YPR126C,0,0,0,0\n-YPR127W,0,0,0,0\n-YPR128C (ANT1),0,0,0,0\n-YPR129W (SCD6 LSM13),0,0,0,0\n-YPR131C (NAT3 NAA20),0,0,0,0\n-YPR132W (RPS23B),0,0,0,0\n-YPR133C (SPN1 IWS1),0,0,0,0\n-YPR133W-A (TOM5 MOM8A),0,0,0,0\n-YPR134W (MSS18),0,0,0,0\n-YPR135W (CTF4 CHL15 POB1),0,0,0,0\n-YPR137W (RRP9),0,0,0,0\n-YPR138C (MEP3),0,0,0,0\n-YPR139C (VPS66),0,0,0,0\n-YPR140W (TAZ1),0,0,0,0\n-YPR141C (KAR3 OSR11),0,0,0,0\n-YPR143W (RRP15),0,0,0,0\n-YPR144C (NOC4 UTP19),0,0,0,0\n-YPR145C-A,0,0,0,0\n-YPR145W (ASN1),0,0,0,0\n-YPR147C,0,0,0,0\n-YPR148C,0,0,0,0\n-YPR149W (NCE102 NCE2),0,0,0,0\n-YPR150W,0,0,0,0\n-YPR151C (SUE1),0,0,0,0\n-YPR152C (URN1),0,0,0,0\n-YPR153W,0,0,0,0\n-YPR154W (PIN3 LSB2),0,0,0,0\n-YPR155C (NCA2),0,0,0,0\n-YPR156C (TPO3),0,0,0,0\n-YPR157W,0,0,0,0\n-YPR158W (CUR1),0,0,0,0\n-YPR159W (KRE6 CWH48),0,0,0,0\n-YPR160W (GPH1),0,0,0,0\n-YPR161C (SGV1 BUR1),0,0,0,0\n-YPR162C (ORC4),0,0,0,0\n-YPR163C (TIF3 RBL3 STM1),0,0,0,0\n-YPR164W (MMS1 RTT108 SLM6),0,0,0,0\n-YPR165W (RHO1),0,0,0,0\n-YPR166C (MRP2),0,0,0,0\n-YPR167C (MET16),0,0,0,0\n-YPR169W (JIP5),0,0,0,0\n-YPR169W-A,0,0,0,0\n-YPR170C,0,0,0,0\n-YPR170W-A,0,0,0,0\n-YPR170W-B,0,0,0,0\n-YPR171W (BSP1),0,0,0,0\n-YPR172W,0,0,0,0\n-YPR173C (VPS4 CSC1 DID6 END13 GRD13 VPL4 VPT10),0,0,0,0\n-YPR174C,0,0,0,0\n-YPR175W (DPB2),0,0,0,0\n-YPR176C (BET2),0,0,0,0\n-YPR178W (PRP4 RNA4),0,0,0,0\n-YPR179C (HDA3 PLO1),0,0,0,0\n-YPR180W (AOS1 RHC31),0,0,0,0\n-YPR181C (SEC23),0,0,0,0\n-YPR182W (SMX3),0,0,0,0\n-YPR183W (DPM1 SED3),0,0,0,0\n-YPR184W (GDB1),0,0,0,0\n-YPR185W (ATG13 APG13),0,0,0,0\n-YPR186C (PZF1 TFC2),0,0,0,0\n-YPR187W (RPO26 RPB6),0,0,0,0\n-YPR188C (MLC2),0,0,0,0\n-YPR189W (SKI3 SKI5),0,0,0,0\n-YPR190C (RPC82 RPC3),0,0,0,0\n-YPR191W (QCR2 COR2 UCR2),0,0,0,0\n-YPR192W (AQY1),0,0,0,0\n-YPR193C (HPA2),0,0,0,0\n-YPR194C (OPT2),0,0,0,0\n-YPR195C,0,0,0,0\n-YPR196W,0,0,0,0\n-YPR198W (SGE1 NOR1),0,0,0,0\n-YPR199C (ARR1 ACR1 YAP8),0,0,0,0\n-YPR201W (ARR3 ACR3),0,0,0,0\n' |
| b |
| diff -r fa06ddcae68e -r 21a0f28aea68 test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png |
| b |
| Binary file test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png has changed |
| b |
| diff -r fa06ddcae68e -r 21a0f28aea68 test-data/genes.gff --- a/test-data/genes.gff Thu Apr 11 04:01:48 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5680 +0,0 @@\n-chrM\t.\t.\t27645\t28106\t.\t+\t.\tname=Q0080 (ATP8 AAP1);bin=585;cdsStart=27665;cdsEnd=27812;proteinID=P00856;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=27645;Nagalakshmi_TTS=28106;tss=27645;tts=28106;tss_source=Nagalakshmi_2008;tts_source=Nagalakshmi_2008\n-chrM\t.\t.\t27879\t29494\t.\t+\t.\tname=Q0085 (ATP6 OLI2 OLI4 PHO1);bin=585;cdsStart=28486;cdsEnd=29266;proteinID=P00854;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=27879;Nagalakshmi_TTS=29494;tss=27879;tts=29494;tss_source=Nagalakshmi_2008;tts_source=Nagalakshmi_2008\n-chrM\t.\t.\t46675\t47014\t.\t+\t.\tname=Q0130 (OLI1 ATP9 OLI3);bin=585;cdsStart=46722;cdsEnd=46953;proteinID=P61829;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=46675;Nagalakshmi_TTS=47014;tss=46675;tts=47014;tss_source=Nagalakshmi_2008;tts_source=Nagalakshmi_2008\n-chrM\t.\t.\t79147\t80087\t.\t+\t.\tname=Q0275 (COX3 OXI2);bin=585;cdsStart=79212;cdsEnd=80022;proteinID=P00420;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=79147;Nagalakshmi_TTS=80087;tss=79147;tts=80087;tss_source=Nagalakshmi_2008;tts_source=Nagalakshmi_2008\n-chrI\t.\t.\t147536\t151218\t.\t-\t.\tname=YAL001C (TFC3 FUN24 TSV115);bin=586;cdsStart=151166;cdsEnd=147593;proteinID=P34111;Pelechano_UTR5=52;Pelechano_TSS=151218;Pelechano_UTR3=57;Pelechano_TTS=147536;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=151191;Yassour_TTS=147567;Nagalakshmi_TSS=151186;Nagalakshmi_TTS=147530;tss=151218;tts=147536;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrI\t.\t.\t143621\t147589\t.\t+\t.\tname=YAL002W (VPS8 FUN15 VPL8 VPT8);bin=586;cdsStart=143706;cdsEnd=147531;proteinID=P39702;Pelechano_UTR5=85;Pelechano_TSS=143621;Pelechano_UTR3=58;Pelechano_TTS=147589;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=143527;Yassour_TTS=147566;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=143621;tts=147589;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrI\t.\t.\t142141\t143381\t.\t+\t.\tname=YAL003W (EFB1 TEF5);bin=586;cdsStart=142173;cdsEnd=143160;proteinID=P32471;Pelechano_UTR5=32;Pelechano_TSS=142141;Pelechano_UTR3=221;Pelechano_TTS=143381;Miura_UTR5=32;Miura_TSS=142141;Miura_UTR3=66;Miura_TTS=143226;Yassour_TSS=142144;Yassour_TTS=143495;Nagalakshmi_TSS=142161;Nagalakshmi_TTS=143370;tss=142141;tts=143381;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrI\t.\t.\t140609\t141543\t.\t+\t.\tname=YAL004W;bin=586;cdsStart=140759;cdsEnd=141407;proteinID=n/a;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=140609;Yassour_TTS=141543;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=140609;tts=141543;tss_source=Yassour_2009;tts_source=Yassour_2009\n-chrI\t.\t.\t139357\t141493\t.\t-\t.\tname=YAL005C (SSA1 YG100);bin=586;cdsStart=141431;cdsEnd=139502;proteinID=P10591;Pelechano_UTR5=62;Pelechano_TSS=141493;Pelechano_UTR3=145;Pelechano_TTS=139357;Miura_UTR5=62;Miura_TSS=141493;Miura_UTR3=115;Miura_TTS=139387;Yassour_TSS=141543;Yassour_TTS=139226;Nagalakshmi_TSS=141495;Nagalakshmi_TTS=139376;tss=141493;tts=139357;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrI\t.\t.\t137552\t138414\t.\t-\t.\tname=YAL007C (ERP2);bin=586;cdsStart=138345;cdsEnd=137697;proteinID=P39704;Pelechano_UTR5=69;Pelechano_TSS=138414;Pelechano_UTR3=145;Pelechano_TTS=137552;Miura_UTR5=72;Miura_TSS=138417;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=138532;Yassour_TTS=137567;Nagalakshmi_TSS=138413;Nagalakshmi_TTS=137572;tss=138414;tts=137552;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrI\t.\t.\t136866\t137642\t.\t+\t.\tname=YAL008W (FUN14);bin=58'..b'_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t916983\t919071\t.\t-\t.\tname=YPR190C (RPC82 RPC3);bin=73;cdsStart=919041;cdsEnd=917076;proteinID=P32349;Pelechano_UTR5=30;Pelechano_TSS=919071;Pelechano_UTR3=93;Pelechano_TTS=916983;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=919130;Yassour_TTS=NA;Nagalakshmi_TSS=919084;Nagalakshmi_TTS=916984;tss=919071;tts=916983;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t919321\t920715\t.\t+\t.\tname=YPR191W (QCR2 COR2 UCR2);bin=592;cdsStart=919380;cdsEnd=920487;proteinID=P07257;Pelechano_UTR5=59;Pelechano_TSS=919321;Pelechano_UTR3=228;Pelechano_TTS=920715;Miura_UTR5=59;Miura_TSS=919321;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=919285;Yassour_TTS=920828;Nagalakshmi_TSS=919297;Nagalakshmi_TTS=920651;tss=919321;tts=920715;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t921845\t922917\t.\t+\t.\tname=YPR192W (AQY1);bin=592;cdsStart=921859;cdsEnd=922777;proteinID=D3W7A4;Pelechano_UTR5=14;Pelechano_TSS=921845;Pelechano_UTR3=140;Pelechano_TTS=922917;Miura_UTR5=28;Miura_TSS=921831;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=921493;Yassour_TTS=923376;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=921845;tts=922917;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t921059\t923831\t.\t-\t.\tname=YPR193C (HPA2);bin=592;cdsStart=923379;cdsEnd=922908;proteinID=Q06592;Pelechano_UTR5=452;Pelechano_TSS=923831;Pelechano_UTR3=1849;Pelechano_TTS=921059;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=922874;tss=923831;tts=921059;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t924143\t927232\t.\t-\t.\tname=YPR194C (OPT2);bin=592;cdsStart=926937;cdsEnd=924303;proteinID=Q06593;Pelechano_UTR5=295;Pelechano_TSS=927232;Pelechano_UTR3=160;Pelechano_TTS=924143;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=927355;Yassour_TTS=924135;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=927232;tts=924143;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t927456\t928316\t.\t-\t.\tname=YPR195C;bin=592;cdsStart=928294;cdsEnd=927964;proteinID=n/a;Pelechano_UTR5=22;Pelechano_TSS=928316;Pelechano_UTR3=508;Pelechano_TTS=927456;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=82;Miura_TTS=927882;Yassour_TSS=928631;Yassour_TTS=927360;Nagalakshmi_TSS=928305;Nagalakshmi_TTS=927801;tss=928316;tts=927456;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t931347\t933201\t.\t+\t.\tname=YPR196W;bin=592;cdsStart=931375;cdsEnd=932788;proteinID=Q06595;Pelechano_UTR5=28;Pelechano_TSS=931347;Pelechano_UTR3=413;Pelechano_TTS=933201;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=933239;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=931347;tts=933201;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t933979\t935825\t.\t+\t.\tname=YPR198W (SGE1 NOR1);bin=592;cdsStart=934033;cdsEnd=935665;proteinID=P33335;Pelechano_UTR5=54;Pelechano_TSS=933979;Pelechano_UTR3=160;Pelechano_TTS=935825;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=933993;Yassour_TTS=935838;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=935759;tss=933979;tts=935825;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t937969\t939042\t.\t-\t.\tname=YPR199C (ARR1 ACR1 YAP8);bin=592;cdsStart=939032;cdsEnd=938147;proteinID=Q06596;Pelechano_UTR5=10;Pelechano_TSS=939042;Pelechano_UTR3=178;Pelechano_TTS=937969;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=939041;Yassour_TTS=938062;Nagalakshmi_TSS=939058;Nagalakshmi_TTS=938044;tss=939042;tts=937969;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n-chrXVI\t.\t.\t939770\t942212\t.\t+\t.\tname=YPR201W (ARR3 ACR3);bin=592;cdsStart=939921;cdsEnd=941136;proteinID=Q06598;Pelechano_UTR5=151;Pelechano_TSS=939770;Pelechano_UTR3=1076;Pelechano_TTS=942212;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=939770;tts=942212;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n' |
