| Next changeset 1:f1c406f9554c (2017-01-29) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85 |
|
added:
1 2 dexseq.R dexseq.xml dexseq_count.xml dexseq_helper.py test-data (Kopie)/dexseq.gtf test-data (Kopie)/dexseq_result.tabular test-data (Kopie)/flattened.gtf test-data (Kopie)/original.gtf test-data (Kopie)/treated1fb.txt test-data (Kopie)/treated2fb.txt test-data (Kopie)/treated3fb.txt test-data (Kopie)/untreated1fb.txt test-data (Kopie)/untreated2fb.txt test-data (Kopie)/untreated3fb.txt test-data (Kopie)/untreated4fb.txt test-data/dexseq.gtf test-data/dexseq_result.tabular test-data/flattened.gtf test-data/original.gtf test-data/treated1fb.txt test-data/treated2fb.txt test-data/treated3fb.txt test-data/untreated1fb.txt test-data/untreated2fb.txt test-data/untreated3fb.txt test-data/untreated4fb.txt tool_dependencies.xml |
| b |
| diff -r 000000000000 -r 4ca0e679f21e 1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/1 Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,307 @@\n+FBgn0000003:E001\tFBgn0000003\tE001\t0.15316821713762\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3R\t2648220\t2648518\t299\t+\t0\t0\t1\t0\t0\t0\t0\tFBtr0081624\n+FBgn0000008:E001\tFBgn0000008\tE001\t0\tNA\tNA\tNA\tNA\t0.0948360378901043\t0.0743865272170741\t0.350394044304503\t2R\t18024494\t18024495\t2\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0100521\n+FBgn0000008:E002\tFBgn0000008\tE002\t0.205235479273134\t0.281215674321156\t2.21242626317474\t0.330809323479709\tNA\t0.939195295474676\t0.0476355829140882\t4.30131363355654\t2R\t18024496\t18024531\t36\t+\t0\t0\t0\t0\t0\t1\t0\tc("FBtr0071763", "FBtr0100521")\n+FBgn0000008:E003\tFBgn0000008\tE003\t0.594344937209466\t0.0968538125516843\t0.645303449176424\t0.724226040572747\tNA\t1.60132701407228\t1.05950556890012\t0.595876786352192\t2R\t18024532\t18024713\t182\t+\t0\t1\t0\t1\t1\t1\t0\tFBtr0071763\n+FBgn0000008:E004\tFBgn0000008\tE004\t0.522626439341238\t0.103462369452504\t0.101770743974669\t0.950387605331279\tNA\t1.30656104503449\t1.48745805800773\t-0.187074457480603\t2R\t18024938\t18025504\t567\t+\t1\t0\t1\t0\t1\t0\t1\tFBtr0071764\n+FBgn0000008:E005\tFBgn0000008\tE005\t1.32353144265853\t0.0459878450164219\t1.88720765333161\t0.389222613957095\tNA\t2.05783835401508\t2.5556984924881\t-0.312587983914312\t2R\t18025505\t18025756\t252\t+\t4\t1\t1\t2\t2\t0\t1\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E006\tFBgn0000008\tE006\t0.0933261680585749\t0.299122084909831\t1.8785125604006\t0.390918461072644\tNA\t0.0578623652924577\t1.03994127882261\t-4.16773295859812\t2R\t18039159\t18039200\t42\t+\t1\t0\t0\t0\t0\t0\t0\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E007\tFBgn0000008\tE007\t9.13870603970407\t0.0174582540513689\t0.663138790127846\t0.717796342965255\t0.784258967313889\t5.27086217315717\t5.83362311327364\t-0.146353214789062\t2R\t18050410\t18051199\t790\t+\t18\t8\t7\t8\t11\t11\t4\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E008\tFBgn0000008\tE008\t1.63933440281406\t0.109484103343906\t0.37069435505957\t0.830815793201498\tNA\t2.30438268043009\t2.314649547651\t-0.00641345722945448\t2R\t18052282\t18052494\t213\t+\t4\t1\t0\t0\t1\t4\t1\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E009\tFBgn0000008\tE009\t18.1387053226442\t0.012408378717531\t4.27018805855357\t0.118233472446032\t0.220525605901157\t7.87532063065209\t6.99853463703096\t0.170285781465363\t2R\t18056749\t18058222\t1474\t+\t16\t17\t15\t18\t33\t21\t10\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E010\tFBgn0000008\tE010\t12.8536495497367\t0.0232037852025063\t3.78125012010271\t0.150977409389516\t0.254504775828042\t5.97264168248932\t7.08387988878893\t-0.246170578008045\t2R\t18058283\t18059490\t1208\t+\t17\t17\t15\t9\t20\t8\t8\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E011\tFBgn0000008\tE011\t1.99928611112699\t0.0364601891575936\t2.65301612830849\t0.265402413274536\tNA\t3.16019906636034\t2.0995791205971\t0.589915283343486\t2R\t18059587\t18059757\t171\t+\t2\t0\t2\t3\t6\t1\t2\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E012\tFBgn0000008\tE012\t0.661887298226701\t0.0886117417223106\t1.92286917613052\t0.382343986227271\tNA\t1.59298610396471\t1.79969924808889\t-0.176022152675381\t2R\t18059821\t18059938\t118\t+\t3\t0\t0\t0\t2\t1\t0\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E013\tFBgn0000008\tE013\t3.91734100140517\t0.0293996888447881\t6.83620051593773\t0.0327746391939249\tNA\t4.05034478889257\t3.70647357969554\t0.127997496136844\t2R\t18060002\t18060339\t338\t+\t11\t1\t1\t5\t10\t5\t0\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E014\tFBgn0000008\tE014\t0.55498474117927\t0.0866602205345716\t1.17569168541739\t0.555522679969109\tNA\t1.58703045222552\t1.4877597658848\t0.0931882232243094\t2R\t18060340\t18060346\t7\t+\t1\t0\t1\t1\t2\t0\t0\tc("FBtr0071763", "FBtr0071764")\n+FBgn0000014:E001\tFBgn0000014\tE001\t0.298561647331709\t0.595682542318035\t0.477481494733636\t0.787619048218473\tNA\tNA\tNA\tNA\t3R\t12632936\t12633348\t413\t-\t1\t0\t0\t0\t0\t1\t0\tFBtr0306337\n+FBgn0000014:E002\tFBgn0000014\tE002\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3R\t12633349\t12635783\t2435\t-\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0083387", "FBtr0306337", "FBtr0300485", "FBtr0083388")\n+FBgn0000014:E003\tFBgn0000014\tE003\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3R\t12635854\t12636077\t224\t-\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0083387", "FBtr0306337", "FBtr0300485", "FBtr0083388"'..b'86\t0.91724524467096\tNA\tNA\tNA\tNA\t3L\t8640808\t8641002\t195\t-\t2\t1\t0\t3\t1\t1\t1\tFBtr0076599\n+FBgn0000121:E003\tFBgn0000121\tE003\t2.30524126345099\t0.0717993341520124\t4.19882575909892\t0.122528346036444\tNA\tNA\tNA\tNA\t3L\t8641070\t8642036\t967\t-\t2\t0\t1\t3\t11\t2\t1\tFBtr0076599\n+FBgn0000137:E001\tFBgn0000137\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tX\t354533\t357209\t2677\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0070075\n+FBgn0000139:E001\tFBgn0000139\tE001\t0.187795396756122\t0.28662869942016\t1.95879645587128\t0.375537018555398\tNA\t0.879924294236769\t0.212535063477741\t2.04967853146798\t3R\t20475810\t20476066\t257\t+\t0\t0\t0\t0\t0\t0\t1\tFBtr0084660\n+FBgn0000139:E002\tFBgn0000139\tE002\t1.96739811366688\t0.133921979075896\t2.6487965202692\t0.265962951457817\tNA\t2.65120798807141\t2.93475897219182\t-0.146592167088059\t3R\t20476127\t20476311\t185\t+\t4\t3\t0\t2\t7\t1\t0\tFBtr0084660\n+FBgn0000139:E003\tFBgn0000139\tE003\t3.61191788404307\t0.0548308983756597\t4.22287462031892\t0.121063835042901\tNA\t3.56858441566967\t3.96107908395784\t-0.150541605141237\t3R\t20476372\t20476716\t345\t+\t8\t4\t1\t3\t12\t1\t2\tFBtr0084660\n+FBgn0000139:E004\tFBgn0000139\tE004\t6.44700256941908\t0.0160799127779307\t5.56297415526724\t0.0619463198625985\t0.12901283905004\t4.00687137747981\t5.64469469517543\t-0.494419352705418\t3R\t20476902\t20476973\t72\t+\t14\t7\t6\t3\t10\t4\t5\tFBtr0306171\n+FBgn0000139:E005\tFBgn0000139\tE005\t13.2470390620692\t0.0198819588795418\t3.47110020589945\t0.176303188701457\t0.281132111713134\t5.95645806032007\t7.18439735682315\t-0.270412441758807\t3R\t20477139\t20477352\t214\t+\t18\t13\t14\t10\t17\t5\t18\tFBtr0084659\n+FBgn0000139:E006\tFBgn0000139\tE006\t30.3520375086607\t0.0108654430756643\t8.0810448298555\t0.0175882816342525\t0.053215826483123\t8.78271755177366\t10.4523734396129\t-0.251091261722245\t3R\t20477583\t20477963\t381\t+\t44\t29\t34\t39\t45\t15\t21\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000139:E007\tFBgn0000139\tE007\t17.4740062043893\t0.0168813732620275\t11.1280422643081\t0.00383333103382073\t0.0167530763700313\t8.02482011218845\t5.55360407829421\t0.531044722802228\t3R\t20478032\t20478312\t281\t+\t12\t5\t9\t24\t28\t24\t19\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000139:E008\tFBgn0000139\tE008\t112.43808666746\t0.00349020082049688\t2.26875223595222\t0.321622713384353\t0.457246749148839\t15.7377439052995\t15.2656264409735\t0.0439419439033773\t3R\t20478504\t20478761\t258\t+\t130\t73\t89\t133\t199\t85\t116\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000139:E009\tFBgn0000139\tE009\t96.3385782859831\t0.00642183657847803\t3.19649338344098\t0.202250815336729\t0.314021002759659\t14.7856179291691\t14.5084682007018\t0.0272993304935376\t3R\t20478820\t20479098\t279\t+\t92\t64\t93\t95\t166\t87\t94\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000140:E001\tFBgn0000140\tE001\t10.7470539964813\t0.0366854172241543\t0.13939001890347\t0.932678234577969\t0.94875889379483\t6.20586023464349\t5.88946659789097\t0.0754942287906017\t3R\t20579625\t20579777\t153\t+\t14\t9\t11\t21\t17\t5\t5\tFBtr0084692\n+FBgn0000140:E002\tFBgn0000140\tE002\t24.0938527740886\t0.00618959397365643\t18.7570601259765\t8.4519349386831e-05\t0.00076717563289585\t8.79238345032345\t7.87199695631269\t0.159524643103097\t3R\t20579850\t20580026\t177\t+\t19\t23\t22\t24\t32\t25\t21\tFBtr0084692\n+FBgn0000140:E003\tFBgn0000140\tE003\t26.5896581030249\t0.0236543543364679\t13.4606375822739\t0.00119415221231374\t0.00633535732026347\t9.06090647303951\t8.42913215137745\t0.104271286411704\t3R\t20580079\t20580291\t213\t+\t27\t25\t22\t29\t20\t32\t23\tFBtr0084692\n+FBgn0000140:E004\tFBgn0000140\tE004\t396.131203959444\t0.00799205872320755\t10.5942963619378\t0.00500584934671538\t0.0196896740970805\t23.1297257079112\t22.9569164001174\t0.0108192868221518\t3R\t20580371\t20585252\t4882\t+\t717\t355\t274\t503\t729\t250\t241\tFBtr0084692\n+FBgn0000140:E005\tFBgn0000140\tE005\t32.5533299591785\t0.0108579043041109\t5.48198106522651\t0.0645064195250201\t0.12901283905004\t9.26492586828956\t10.5148549867585\t-0.182577615669745\t3R\t20585313\t20585614\t302\t+\t51\t37\t38\t35\t47\t22\t13\tFBtr0084692\n+FBgn0000140:E006\tFBgn0000140\tE006\t29.5385944102884\t0.0121301272037325\t1.4397418800929\t0.486815080237479\t0.631254719428819\t9.2684693119714\t9.95249368626703\t-0.102726953702909\t3R\t20585679\t20586235\t557\t+\t67\t21\t26\t34\t46\t15\t22\tFBtr0084692\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e 2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2 Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,307 @@\n+FBgn0000003:E001\tFBgn0000003\tE001\t0.15316821713762\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3R\t2648220\t2648518\t299\t+\t0\t0\t1\t0\t0\t0\t0\tFBtr0081624\n+FBgn0000008:E001\tFBgn0000008\tE001\t0\tNA\tNA\tNA\tNA\t0.00180529865930859\t0.00110352032915482\t0.71012432156575\t2R\t18024494\t18024495\t2\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0100521\n+FBgn0000008:E002\tFBgn0000008\tE002\t0.205235479273134\t0.10096278259038\t0.898774886716701\t0.343110421551639\t0.875338403050321\t0.240471096378812\t0.00051821819140439\t8.85808812274094\t2R\t18024496\t18024531\t36\t+\t0\t0\t0\t0\t0\t1\t0\tc("FBtr0071763", "FBtr0100521")\n+FBgn0000008:E003\tFBgn0000008\tE003\t0.594344937209466\t0.0497242848073242\t0.560487309496096\t0.454063964795363\t0.886909987310569\t0.714213963225015\t0.307231640665086\t1.21702953797278\t2R\t18024532\t18024713\t182\t+\t0\t1\t0\t1\t1\t1\t0\tFBtr0071763\n+FBgn0000008:E004\tFBgn0000008\tE004\t0.522626439341238\t0.0510964001344879\t0.060134754086107\t0.806283082848701\t0.984471646525196\t0.475335808901208\t0.610545184627067\t-0.361150979137312\t2R\t18024938\t18025504\t567\t+\t1\t0\t1\t0\t1\t0\t1\tFBtr0071764\n+FBgn0000008:E005\tFBgn0000008\tE005\t1.32353144265853\t0.033544888378149\t0.447581692227587\t0.503485612958261\t0.915030374854578\t1.18589350280662\t1.82071437766583\t-0.618530162177662\t2R\t18025505\t18025756\t252\t+\t4\t1\t1\t2\t2\t0\t1\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E006\tFBgn0000008\tE006\t0.0933261680585749\t0.0979916935126146\t1.27827841759613\t0.25821937994891\t0.875338403050321\t0.000672771342457494\t0.302708242322453\t-8.81359598944245\t2R\t18039159\t18039200\t42\t+\t1\t0\t0\t0\t0\t0\t0\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E007\tFBgn0000008\tE007\t9.13870603970407\t0.0141325108956593\t0.712675734376205\t0.398556961507834\t0.875338403050321\t8.14729722209156\t10.0266204833643\t-0.299441975840365\t2R\t18050410\t18051199\t790\t+\t18\t8\t7\t8\t11\t11\t4\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E008\tFBgn0000008\tE008\t1.63933440281406\t0.047923510491443\t0.00265695937608257\t0.958890685444368\t0.984471646525196\t1.45564248694453\t1.50771320988272\t-0.0507059660917241\t2R\t18052282\t18052494\t213\t+\t4\t1\t0\t0\t1\t4\t1\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E009\tFBgn0000008\tE009\t18.1387053226442\t0.015647369164041\t2.25886526232591\t0.132851375230114\t0.875338403050321\t19.5445065639684\t14.9000636721322\t0.391444665930503\t2R\t18056749\t18058222\t1474\t+\t16\t17\t15\t18\t33\t21\t10\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E010\tFBgn0000008\tE010\t12.8536495497367\t0.0215900451790919\t2.78089605885198\t0.0953947831050443\t0.875338403050321\t10.6514141365433\t15.248652004024\t-0.51763672985484\t2R\t18058283\t18059490\t1208\t+\t17\t17\t15\t9\t20\t8\t8\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E011\tFBgn0000008\tE011\t1.99928611112699\t0.0285005908984633\t2.17728137604993\t0.14006168013414\t0.875338403050321\t2.83279081782886\t1.22090744534872\t1.21427023598902\t2R\t18059587\t18059757\t171\t+\t2\t0\t2\t3\t6\t1\t2\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E012\tFBgn0000008\tE012\t0.661887298226701\t0.0636367342776932\t0.0757484377954682\t0.783143887524821\t0.984471646525196\t0.709023361010478\t0.900357466728489\t-0.344664742486091\t2R\t18059821\t18059938\t118\t+\t3\t0\t0\t0\t2\t1\t0\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E013\tFBgn0000008\tE013\t3.91734100140517\t0.127923197528105\t0.290676629187701\t0.589787256358754\t0.948196435222919\t4.61734769466919\t3.6856717142009\t0.325136799373193\t2R\t18060002\t18060339\t338\t+\t11\t1\t1\t5\t10\t5\t0\tc("FBtr0071764", "FBtr0071763", "FBtr0100521")\n+FBgn0000008:E014\tFBgn0000008\tE014\t0.55498474117927\t0.0461722737752503\t0.0204925711628121\t0.886169927935646\t0.984471646525196\t0.707177320420267\t0.610621930116259\t0.211792603426508\t2R\t18060340\t18060346\t7\t+\t1\t0\t1\t1\t2\t0\t0\tc("FBtr0071763", "FBtr0071764")\n+FBgn0000014:E001\tFBgn0000014\tE001\t0.298561647331709\t0.0875181307448202\t0.500842511999075\t0.479130163486021\t0.899708711833737\t0.310032529892805\t0.234673235447371\t0.401766285517607\t3R\t12632936\t12633348\t413\t-\t1\t0\t0\t0\t0\t1\t0\tFBtr0306337\n+FBgn0000014:E002\tFBgn0000014\tE002\t0\tNA\tNA\tNA\tNA\t0.000331057184793046\t0.000148286658281537\t'..b'21:E003\tFBgn0000121\tE003\t2.30524126345099\t0.043538750357172\t3.70329152740199\t0.0543052400338495\t0.765063295665013\t2.90295913477739\t1.23440616679317\t1.23370708876375\t3L\t8641070\t8642036\t967\t-\t2\t0\t1\t3\t11\t2\t1\tFBtr0076599\n+FBgn0000137:E001\tFBgn0000137\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tX\t354533\t357209\t2677\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0070075\n+FBgn0000139:E001\tFBgn0000139\tE001\t0.187795396756122\t0.100326400857431\t0.695912882768823\t0.404160442209953\t0.875338403050321\t0.210979596643993\t0.0122505414570135\t4.10618606505055\t3R\t20475810\t20476066\t257\t+\t0\t0\t0\t0\t0\t0\t1\tFBtr0084660\n+FBgn0000139:E002\tFBgn0000139\tE002\t1.96739811366688\t0.135428011518232\t0.162834228301278\t0.686560404348099\t0.984471646525196\t1.97239281432961\t2.41089205546761\t-0.289620155561422\t3R\t20476127\t20476311\t185\t+\t4\t3\t0\t2\t7\t1\t0\tFBtr0084660\n+FBgn0000139:E003\tFBgn0000139\tE003\t3.61191788404307\t0.0987519814654319\t0.305371970085076\t0.580534113263061\t0.948196435222919\t3.5444058445605\t4.42297268013121\t-0.319472524967821\t3R\t20476372\t20476716\t345\t+\t8\t4\t1\t3\t12\t1\t2\tFBtr0084660\n+FBgn0000139:E004\tFBgn0000139\tE004\t6.44700256941908\t0.0142036296146621\t5.43914529396989\t0.0196903023446802\t0.56679248447199\t4.59269358239137\t9.36098333520745\t-1.02731955499442\t3R\t20476902\t20476973\t72\t+\t14\t7\t6\t3\t10\t4\t5\tFBtr0306171\n+FBgn0000139:E005\tFBgn0000139\tE005\t13.2470390620692\t0.017602274840644\t2.9740522118461\t0.084609672288819\t0.875338403050321\t10.5511160231273\t15.7713368519923\t-0.579909349688302\t3R\t20477139\t20477352\t214\t+\t18\t13\t14\t10\t17\t5\t18\tFBtr0084659\n+FBgn0000139:E006\tFBgn0000139\tE006\t30.3520375086607\t0.0114276033177991\t6.60344407095226\t0.0101781703493454\t0.425447520602637\t24.9862310974187\t37.5248589138266\t-0.586713344703218\t3R\t20477583\t20477963\t381\t+\t44\t29\t34\t39\t45\t15\t21\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000139:E007\tFBgn0000139\tE007\t17.4740062043893\t0.0160833635618647\t10.8194844075201\t0.00100437455135824\t0.0699714270779575\t20.3169124263052\t9.03918845465664\t1.16841601422542\t3R\t20478032\t20478312\t281\t+\t12\t5\t9\t24\t28\t24\t19\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000139:E008\tFBgn0000139\tE008\t112.43808666746\t0.0045618129130484\t1.28570707002399\t0.256840592793512\t0.875338403050321\t112.022994547703\t101.841116976382\t0.137474751703343\t3R\t20478504\t20478761\t258\t+\t130\t73\t89\t133\t199\t85\t116\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000139:E009\tFBgn0000139\tE009\t96.3385782859831\t0.0106251862216838\t0.258912769795586\t0.610868082191688\t0.963729685260772\t93.8463906621134\t88.5477019067611\t0.0838463950255508\t3R\t20478820\t20479098\t279\t+\t92\t64\t93\t95\t166\t87\t94\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000140:E001\tFBgn0000140\tE001\t10.7470539964813\t0.0234509141922009\t0.0593764089902322\t0.807484279812022\t0.984471646525196\t11.8176394234535\t10.0170015722812\t0.23849115990201\t3R\t20579625\t20579777\t153\t+\t14\t9\t11\t21\t17\t5\t5\tFBtr0084692\n+FBgn0000140:E002\tFBgn0000140\tE002\t24.0938527740886\t0.0602151860844606\t0.627706103422042\t0.428197980706108\t0.884425465013721\t26.4613550559742\t19.7455132486233\t0.42236207377132\t3R\t20579850\t20580026\t177\t+\t19\t23\t22\t24\t32\t25\t21\tFBtr0084692\n+FBgn0000140:E003\tFBgn0000140\tE003\t26.5896581030249\t0.0923257374772862\t0.159416107368031\t0.689694662252452\t0.984471646525196\t28.7037502282678\t22.5335289862472\t0.349165969113861\t3R\t20580079\t20580291\t213\t+\t27\t25\t22\t29\t20\t32\t23\tFBtr0084692\n+FBgn0000140:E004\tFBgn0000140\tE004\t396.131203959444\t0.0294658776492874\t0.119919967795425\t0.729121307118346\t0.984471646525196\t411.698323026293\t382.639789898582\t0.105600667854991\t3R\t20580371\t20585252\t4882\t+\t717\t355\t274\t503\t729\t250\t241\tFBtr0084692\n+FBgn0000140:E005\tFBgn0000140\tE005\t32.5533299591785\t0.0154869146597253\t3.6848518625651\t0.0549088489711732\t0.765063295665013\t28.8381573377971\t37.3926642609595\t-0.374776284061758\t3R\t20585313\t20585614\t302\t+\t51\t37\t38\t35\t47\t22\t13\tFBtr0084692\n+FBgn0000140:E006\tFBgn0000140\tE006\t29.5385944102884\t0.012208952369787\t0.963090136982643\t0.326409546070953\t0.875338403050321\t28.9081958706525\t32.6523000725204\t-0.175706046174373\t3R\t20585679\t20586235\t557\t+\t67\t21\t26\t34\t46\t15\t22\tFBtr0084692\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e dexseq.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dexseq.R Thu Oct 08 16:52:01 2015 -0400 |
| [ |
| @@ -0,0 +1,117 @@ +## Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +# we need that to not crash galaxy with an UTF8 error on German LC settings. +Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +library("DEXSeq") +library('getopt') +library('rjson') + + +options(stringAsfactors = FALSE, useFancyQuotes = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +#get options, using the spec as defined by the enclosed list. +#we read the options from the default: commandArgs(TRUE). +spec = matrix(c( + 'verbose', 'v', 2, "integer", + 'help', 'h', 0, "logical", + 'gtf', 'a', 1, "character", + 'outfile', 'o', 1, "character", + 'reportdir', 'r', 1, "character", + 'factors', 'f', 1, "character", + 'threads', 'p', 1, "integer", + 'fdr', 'c', 1, "double" +), byrow=TRUE, ncol=4); +opt = getopt(spec); + +# if help was asked for print a friendly message +# and exit with a non-zero error code +if ( !is.null(opt$help) ) { + cat(getopt(spec, usage=TRUE)); + q(status=1); +} + +trim <- function (x) gsub("^\\s+|\\s+$", "", x) +opt$samples <- trim(opt$samples) +opt$factors <- trim(opt$factors) + +parser <- newJSONParser() +parser$addData( opt$factors ) +factorsList <- parser$getObject() + +sampleTable<-data.frame() +countFiles<-c() +factorNames<-c() +primaryFactor<-"" +for(factor in factorsList){ + factorName<-factor[[1]] + factorNames<-append(factorNames, paste(factorName,"exon",sep=":")) + factorValuesMapList<-factor[[2]] + c = length(factorValuesMapList) + for (factorValuesMap in factorValuesMapList){ + for(files in factorValuesMap){ + for(file in files){ + if(primaryFactor == "") { + countFiles<-append(countFiles,file) + } + sampleTable[basename(file),factorName]<-paste(c,names(factorValuesMap),sep="_") + } + } + c = c-1 + } + if(primaryFactor == ""){ + primaryFactor <- factorName + } +} + +factorNames<-append(factorNames,"exon") +factorNames<-append(factorNames,"sample") +factorNames<-rev(factorNames) +formulaFullModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ ")) +factorNames <- head(factorNames,-1) +formulaReducedModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ ")) + +sampleTable +formulaFullModel +formulaReducedModel +primaryFactor +countFiles +opt$reportdir +opt$threads +getwd() + +dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= formulaFullModel, flattenedfile=opt$gtf) + +colData(dxd) +dxd <- estimateSizeFactors(dxd) +print("Estimated size factors") +sizeFactors(dxd) +BPPARAM=MulticoreParam(workers=opt$threads) +dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM) +print("Estimated dispersions") +dxd <- testForDEU(dxd, fullModel=formulaFullModel, BPPARAM=BPPARAM) +print("tested for DEU") +dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM) +print("Estimated fold changes") +res <- DEXSeqResults(dxd) +print("Results") +table(res$padj <= opt$fdr) +resSorted <- res[order(res$padj),] +head(resSorted) + +export_table <- as.data.frame(resSorted) +last_column <- ncol(export_table) +for(i in 1:nrow(export_table)) { + export_table[i,last_column] <- paste(export_table[i,last_column][[1]],collapse=", ") +} +write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE) +print("Written Results") + +if ( !is.null(opt$reportdir) ) { + save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData")) + save.image() + DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA")) + unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData")) +} +sessionInfo() |
| b |
| diff -r 000000000000 -r 4ca0e679f21e dexseq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dexseq.xml Thu Oct 08 16:52:01 2015 -0400 |
| [ |
| b'@@ -0,0 +1,192 @@\n+<tool id="dexseq" name="DEXSeq" version="1.0">\n+ <description>Determines differential exon usage from count tables</description>\n+ <requirements>\n+ <requirement type="package" version="1.14">dexseq</requirement>\n+ </requirements>\n+ <code file="dexseq_helper.py" />\n+ <stdio>\n+ <regex match="Execution halted" \n+ source="both" \n+ level="fatal" \n+ description="Execution halted." />\n+ <regex match="Input-Error 01" \n+ source="both" \n+ level="fatal" \n+ description="Error in your input parameters: Make sure you only apply factors to selected samples." />\n+ <regex match="Error in"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occured, please check your input carefully and contact your administrator." />\n+ <regex match="Error:"\n+ source="both"\n+ level="fatal"\n+ description="Error in the R script." />\n+ </stdio>\n+ <version_command>\n+ <![CDATA[\n+ echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\\$otherPkgs\\$DEXSeq\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\\$otherPkgs\\$DESeq2\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"\n+ ]]>\n+ </version_command>\n+ <command>\n+ <![CDATA[\n+ mkdir ./html_out &&\n+ #import json\n+ Rscript $__tool_directory__/dexseq.R\n+ -o "$dexseq_out"\n+ -p \\${GALAXY_SLOTS:-4}\n+ #set $temp_factor_names = list()\n+ #for $factor in $rep_factorName:\n+ #set $temp_factor = list()\n+ #set $count_files1 = list()\n+ #for $file in $factor.countFiles1:\n+ $count_files1.append(str($file))\n+ #end for\n+ $temp_factor.append( {str($factor.factorLevel1): $count_files1} )\n+\n+ #set $count_files2 = list()\n+ #for $file in $factor.countFiles2:\n+ $count_files2.append(str($file))\n+ #end for\n+ $temp_factor.append( {str($factor.factorLevel2): $count_files2} )\n+ $temp_factor_names.append([str($factor.factorName), $temp_factor])\n+ #end for\n+ -f \'#echo json.dumps(temp_factor_names)#\'\n+ -a $gtf\n+ -c $fdr_cutoff\n+\n+ #if $report:\n+ -r ./html_out\n+ &&\n+ mkdir $htmlreport.extra_files_path\n+ &&\n+ cp ./html_out/testForDEU.html $htmlreport\n+ &&\n+ cp -r ./html_out/* $htmlreport.extra_files_path\n+ #end if\n+\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>\n+ <repeat name="rep_factorName" title="Factor" min="1">\n+ <param name="factorName" type="text" value="FactorName" label="Specify a factor name" \n+ help="Only letters, numbers and underscores will be retained in this field">\n+ <sanitizer>\n+ <valid initial="string.letters,string.digits"><add value="_" /></valid>\n+ </sanitizer>\n+ </param>\n+ <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"\n+ help="Only letters, numbers and underscores will be retained in this field">\n+ <sanitizer>\n+ <valid initial="string.letters,string.digits"><add value="_" /></valid>\n+ </sanitizer>\n+ </param>\n+ <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>\n+\n+ <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify'..b'dition"/>\n+ <param name="factorLevel1" value="knockdown"/>\n+ <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>\n+ <param name="factorLevel2" value="control"/>\n+ <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>\n+ </repeat>\n+ <repeat name="rep_factorName">\n+ <param name="factorName" value="libtype"/>\n+ <param name="factorLevel1" value="singleend"/>\n+ <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>\n+ <param name="factorLevel2" value="pairedend"/>\n+ <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>\n+ </repeat>\n+ <param name="report" value="False"/>\n+ <param name="fdr_cutoff" value="0.05"/>\n+ <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+.. class:: infomark\n+\n+**What it does** \n+\n+Inference of differential exon usage in RNA-Seq.\n+\n+\n+**Inputs**\n+\n+DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.\n+DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary\n+factor that affects gene expressions. Primary factor should always be named as \'condition\'. You also input several secondary factors that might\n+influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states.\n+You need to select appropriate count table from your history for each factor level.\n+\n+The following table gives some examples of factors and their levels:\n+\n+========= ============== ===============\n+Factor Factor level 1 Factor level 2 \n+--------- -------------- ---------------\n+condition Knockdown Wildtype\n+--------- -------------- ---------------\n+treatment Treated Untreated\n+--------- -------------- ---------------\n+timePoint Day4 Day1\n+--------- -------------- ---------------\n+SeqType SingleEnd PairedEnd\n+--------- -------------- ---------------\n+Gender Female Male\n+========= ============== ===============\n+\n+*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor \'condition\' given in above table, DEXSeq computes fold changes of \'Knockdown\' samples against \'Wildtype\', i.e. the values correspond to up or down regulations of genes in Knockdown samples.\n+\n+**Output**\n+\n+DEXSeq_ generates a tabular file containing the different columns and an optional html report.\n+\n+====== ==========================================================\n+Column Description\n+------ ----------------------------------------------------------\n+ 1 Gene and exon Identifiers\n+ 2 group/gene identifier\n+ 3 feature/exon identifier\n+ 4 mean of the counts across samples in each feature/exon\n+ 5 exon dispersion estimate\n+ 6 LRT statistic\n+ 7 LRT p-value\n+ 8 BH adjusted p-values\n+ 9 exon usage coefficient factorLevel 2\n+ 10 exon usage coefficient factorLevel 1\n+ 11 relative exon usage fold changes\n+ 12 GRanges object of the coordinates of the exon/feature\n+ 13 matrix of integer counts, of each column containing a sample\n+ 14 list of transcripts overlapping with the exon\n+====== ==========================================================\n+\n+\n+.. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1101/gr.133744.111</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e dexseq_count.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dexseq_count.xml Thu Oct 08 16:52:01 2015 -0400 |
| [ |
| @@ -0,0 +1,110 @@ +<tool id="dexseq_count" name="DEXSeq-Count" version="1.0"> + <description>Prepare and count exon abundancies from RNA-seq data</description> + <requirements> + <requirement type="package" version="1.14">dexseq</requirement> + <requirement type="package" version="0.6.1">htseq</requirement> + <requirement type="package" version="0.7.7">pysam</requirement> + </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <command> + <![CDATA[ + #if $mode.mode_select == "prepare": + python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py + -r $mode.aggregate + $mode.gtffile + $flattened_gtf_out + #elif $mode.mode_select == "count": + python \$DEXSEQ_ROOT/python_scripts/dexseq_count.py + -f bam + -p $mode.paired + -s $mode.stranded + -a $mode.qual + -r $mode.order + $mode.flattened_gtf_in + $mode.bamfile + $counts_file + #end if + ]]> + </command> + <inputs> + <conditional name="mode"> + <param name="mode_select" type="select" label="Mode of operation"> + <option value="prepare">Prepare annotation</option> + <option value="count">Count reads</option> + </param> + <when value="prepare"> + <param name="gtffile" type="data" format="gff" label="GTF file"/> + <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no" + label="Aggretare genes with exons?" + help="Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored."/> + </when> + <when value="count"> + <param name="bamfile" type="data" format="bam" label="Input bam file"/> + <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/> + <param name="paired" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Is libray paired end?"/> + <param name="stranded" type="select" label="Is library strand specific?"> + <option value="no">No</option> + <option value="yes">Yes</option> + <option value="reverse">Yes, but reverse</option> + </param> + <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/> + <param name="order" type="select" label="Sorting order of alignments" help="If you generated your alignments using tophat, they are by default position sorted. Ignored for single-end data"> + <option value="pos">By position</option> + <option value="name">By name</option> + </param> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}"> + <filter>mode['mode_select'] == 'count'</filter> + </data> + <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}"> + <filter>mode['mode_select'] == 'prepare'</filter> + </data> + </outputs> + + <tests> + <test> + <param name="mode_select" value="prepare" /> + <param name="gtffile" ftype="gff" value="original.gtf"/> + <param name="aggregate" value="True"/> + <output name="flattened_gtf_out" file="flattened.gtf" ftype="gtf"/> + </test> + </tests> + + <help> + <![CDATA[ +.. class:: infomark + +**What it does** + +The main goal of this tol is to count the number of reads/fragments per exon of each gene in RNA-seq sample. In addition it also prepares your annotation gtf file compatible for counting. + + +**Inputs** + +Mode-preprare: Takes a normal gtf file as input. For example from ensembl database. +Mode-count: Inputs are flattened gtf file and BAM file. The flattened gtf file can be generated from 'prepare' mode of this tool. + +**Output** + +Mode-preprare: Flattened gtf file that contains only exons with corresponding gene ids from given gtf file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used. +Mode-count: Two column tab-delimeted file with exon ids and their read counts. + +.. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html + + ]]> + </help> + <citations> + <citation type="doi">10.1101/gr.133744.111</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 4ca0e679f21e dexseq_helper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dexseq_helper.py Thu Oct 08 16:52:01 2015 -0400 |
| [ |
| @@ -0,0 +1,41 @@ + +from galaxy.tools.parameters import DataToolParameter + +def validate_input( trans, error_map, param_values, page_param_map ): + """ + Validates the user input, before execution. + """ + factors = param_values['rep_factorName'] + factor_name_list = [] + factor_duplication = False + level_duplication = False + + for factor in factors: + # factor names should be unique + fn = factor['factorName'] + if fn in factor_name_list: + factor_duplication = True + break + factor_name_list.append( fn ) + + level_name_list = list() + factor_index_list = list() + + for level in ['factorLevel1', 'factorLevel2']: + # level names under one factor should be unique + fl = factor[level] + if fl in level_name_list: + level_duplication = True + level_name_list.append( fl ) + + if level_duplication: + error_map['rep_factorName'] = [ dict() for t in factors ] + for i in range( len( factors ) ): + error_map['rep_factorName'][i]['FactorLevel1'] = [ {'factorLevel': 'Factor levels for each factor need to be unique'} for t in [factor['factorLevel1'], factor['factorLevel2']] ] + break + + if factor_duplication: + error_map['rep_factorName'] = [ dict() for t in factors ] + for i in range( len( factors ) ): + error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique.' + |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/dexseq.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/dexseq.gtf Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,397 @@\n+2L\tdexseq_prepare_annotation.py\taggregate_gene\t378112\t387439\t.\t+\t.\tgene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t378112\t378481\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "001"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t384511\t384894\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "002"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t385701\t385746\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "003"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t386308\t386576\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "004"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t386703\t387439\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "005"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\taggregate_gene\t2156484\t2178749\t.\t-\t.\tgene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2156484\t2156791\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0077850+FBtr0077851"; exonic_part_number "001"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2156792\t2157426\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330659+FBtr0077850+FBtr0077851"; exonic_part_number "002"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2157427\t2158405\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330660+FBtr0077850+FBtr0077851+FBtr0330659"; exonic_part_number "003"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2158468\t2159245\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330660+FBtr0077850+FBtr0077851+FBtr0330659"; exonic_part_number "004"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2159312\t2160582\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330660+FBtr0077850+FBtr0077851+FBtr0330659"; exonic_part_number "005"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2161010\t2161232\t.\t-\t.\ttranscripts "FBtr0330659"; exonic_part_number "006"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2161233\t2161522\t.\t-\t.\ttranscripts "FBtr0330659+FBtr0077851"; exonic_part_number "007"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2171142\t2171198\t.\t-\t.\ttranscripts "FBtr0330658"; exonic_part_number "008"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2177847\t2178749\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330660+FBtr0077850"; exonic_part_number "009"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\taggregate_gene\t6041178\t6045970\t.\t-\t.\tgene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6041178\t6042011\t.\t-\t.\ttranscripts "FBtr0079219+FBtr0079221+FBtr0079220"; exonic_part_number "001"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6042075\t6044351\t.\t-\t.\ttranscripts "FBtr0079219+FBtr0079221+FBtr0079220"; exonic_part_number "002"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6044428\t6045526\t.\t-\t.\ttranscripts "FBtr0079219+FBtr0079221+FBtr0079220"; exonic_part_number "003"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6045527\t6045593\t.\t-\t.\ttranscripts "FBtr0079221"; exonic_part_number "004"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6045894\t6045920\t.\t-\t.\ttranscripts "FBtr0079219"; exonic_part_number "005"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6045921\t6045970\t.\t-\t.\ttranscripts "FBtr0079219+FBtr0079220"; exonic_part_number "006"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\taggregate_gene\t7014861\t7023940\t.\t-\t.\tgene_id "FBgn0000053"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t7014861\t7016374\t.\t-\t.\ttranscripts "FBtr0079431"; exonic_part_number "001"; gene_id "FBgn0000053"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t7016437\t7017486\t.\t-\t.\ttranscripts "FBtr0079431"; exonic_part_number "002"; gene_id "FBgn0000053"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t7017545\t7017966\t.\t-\t.\ttranscripts "FBtr0079431"; exonic_part_number "003"; gene_id "FBgn0000053"\n+2L\tdexseq_prepare_annotation.py\tex'..b'number "001"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15246367\t15246389\t.\t-\t.\ttranscripts "FBtr0100328+FBtr0305191"; exonic_part_number "002"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15246390\t15247200\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "003"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15247258\t15247415\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "004"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15247416\t15247421\t.\t-\t.\ttranscripts "FBtr0074015+FBtr0305196+FBtr0305191+FBtr0305193+FBtr0305192"; exonic_part_number "005"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15248260\t15248491\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "006"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15248569\t15248709\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "007"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15248788\t15248965\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "008"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15248966\t15248986\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0074015+FBtr0100328+FBtr0290064+FBtr0290063+FBtr0305191"; exonic_part_number "009"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15265545\t15265721\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "010"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15266185\t15266241\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0074015+FBtr0305194+FBtr0305196+FBtr0100328"; exonic_part_number "011"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15271594\t15271626\t.\t-\t.\ttranscripts "FBtr0305189+FBtr0074015+FBtr0100328+FBtr0290063+FBtr0305193+FBtr0100326"; exonic_part_number "012"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15272222\t15272487\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "013"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\taggregate_gene\t20065478\t20067552\t.\t-\t.\tgene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20065478\t20065681\t.\t-\t.\ttranscripts "FBtr0070025+FBtr0301931"; exonic_part_number "001"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20065962\t20065964\t.\t-\t.\ttranscripts "FBtr0301931"; exonic_part_number "002"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20066074\t20066255\t.\t-\t.\ttranscripts "FBtr0070025+FBtr0301931"; exonic_part_number "003"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20066338\t20067049\t.\t-\t.\ttranscripts "FBtr0070025+FBtr0301931"; exonic_part_number "004"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20067402\t20067506\t.\t-\t.\ttranscripts "FBtr0070025+FBtr0301931"; exonic_part_number "005"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20067507\t20067552\t.\t-\t.\ttranscripts "FBtr0070025"; exonic_part_number "006"; gene_id "FBgn0000084"\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/dexseq_result.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/dexseq_result.tabular Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,307 @@\n+FBgn0000053:E004\tFBgn0000053\tE004\t6.32535175423168\t0.0264738246817031\t12.4808978194916\t0.000411134550815063\t0.0492518704505317\t2.63422337987539\t9.85721929373845\t-1.90380303188571\t2L\t7018085\t7018148\t64\t-\t13\t7\t15\t0\t3\t3\t4\tFBtr0100353\n+FBgn0000064:E004\tFBgn0000064\tE004\t27.138007646805\t0.0317942092877562\t12.2258872107196\t0.000471309765076858\t0.0492518704505317\t16.6062937709913\t39.2893588184476\t-1.24240849858181\t3R\t22082196\t22082345\t150\t-\t74\t30\t39\t9\t25\t20\t9\tc("FBtr0085000", "FBtr0114544")\n+FBgn0000139:E007\tFBgn0000139\tE007\t17.4740062043893\t0.0160833635618647\t10.8194844075201\t0.00100437455135824\t0.0699714270779575\t20.3169124263052\t9.03918845465664\t1.16841601422542\t3R\t20478032\t20478312\t281\t+\t12\t5\t9\t24\t28\t24\t19\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000108:E006\tFBgn0000108\tE006\t0.864384408056277\t0.0406095849358183\t10.2240291607707\t0.00138622689396988\t0.0724303552099263\t0.0064298031097202\t2.13268272820952\t-8.3736790808519\tX\t465164\t465166\t3\t+\t4\t2\t1\t0\t0\t0\t0\tc("FBtr0307295", "FBtr0307293")\n+FBgn0000139:E006\tFBgn0000139\tE006\t30.3520375086607\t0.0114276033177991\t6.60344407095226\t0.0101781703493454\t0.425447520602637\t24.9862310974187\t37.5248589138266\t-0.586713344703218\t3R\t20477583\t20477963\t381\t+\t44\t29\t34\t39\t45\t15\t21\tc("FBtr0084660", "FBtr0084659", "FBtr0306171")\n+FBgn0000024:E009\tFBgn0000024\tE009\t0.979078995544713\t0.0614737893017594\t4.94673577209914\t0.0261399785022346\t0.56679248447199\t0.295119825906843\t1.49500642531607\t-2.34077893672339\t3R\t9071532\t9072376\t845\t-\t1\t2\t3\t0\t1\t0\t0\tc("FBtr0082780", "FBtr0300486")\n+FBgn0000053:E006\tFBgn0000053\tE006\t247.836023771802\t0.00378092135950294\t5.05413791743976\t0.0245672009559188\t0.56679248447199\t229.471953311261\t263.367915225463\t-0.198761765808405\t2L\t7018431\t7019080\t650\t-\t368\t279\t279\t214\t298\t171\t181\tc("FBtr0079431", "FBtr0100353")\n+FBgn0000064:E011\tFBgn0000064\tE011\t121.014747579775\t0.0362284698364635\t5.01325544112996\t0.025153962784462\t0.56679248447199\t149.76987151215\t91.4512952024606\t0.711671925160644\t3R\t22086876\t22086879\t4\t-\t154\t77\t97\t210\t219\t76\t86\tFBtr0085001\n+FBgn0000083:E008\tFBgn0000083\tE008\t148.254009682968\t0.0358197316222879\t4.88320255234424\t0.0271192576302388\t0.56679248447199\t121.238532039037\t182.493471738339\t-0.589996566865399\t3R\t16896446\t16896639\t194\t+\t317\t119\t178\t86\t149\t110\t129\tc("FBtr0089518", "FBtr0089520")\n+FBgn0000139:E004\tFBgn0000139\tE004\t6.44700256941908\t0.0142036296146621\t5.43914529396989\t0.0196903023446802\t0.56679248447199\t4.59269358239137\t9.36098333520745\t-1.02731955499442\t3R\t20476902\t20476973\t72\t+\t14\t7\t6\t3\t10\t4\t5\tFBtr0306171\n+FBgn0000100:E001\tFBgn0000100\tE001\t6.87698735532182\t0.0152843778404274\t4.4902523151994\t0.0340886460593087\t0.647684275126866\t5.84135165353717\t8.89040688980309\t-0.605947210139451\t3L\t22068967\t22069026\t60\t+\t16\t5\t9\t9\t9\t3\t3\tFBtr0334113\n+FBgn0000061:E005\tFBgn0000061\tE005\t0.374447732873272\t0.0698105105798595\t4.26069200156856\t0.0390040296560026\t0.659279933025777\t0.236860754001307\t0.609484288573047\t-1.36354985625123\t2L\t386703\t387439\t737\t+\t2\t0\t0\t0\t0\t0\t1\tFBtr0078053\n+FBgn0000121:E001\tFBgn0000121\tE001\t1.0078404227901\t0.0459551501833766\t4.17569077238689\t0.0410078427240914\t0.659279933025777\t0.529524534742667\t2.03924415875361\t-1.9452650835714\t3L\t8640361\t8640745\t385\t-\t4\t0\t1\t0\t1\t1\t1\tFBtr0076599\n+FBgn0000121:E003\tFBgn0000121\tE003\t2.30524126345099\t0.043538750357172\t3.70329152740199\t0.0543052400338495\t0.765063295665013\t2.90295913477739\t1.23440616679317\t1.23370708876375\t3L\t8641070\t8642036\t967\t-\t2\t0\t1\t3\t11\t2\t1\tFBtr0076599\n+FBgn0000140:E005\tFBgn0000140\tE005\t32.5533299591785\t0.0154869146597253\t3.6848518625651\t0.0549088489711732\t0.765063295665013\t28.8381573377971\t37.3926642609595\t-0.374776284061758\t3R\t20585313\t20585614\t302\t+\t51\t37\t38\t35\t47\t22\t13\tFBtr0084692\n+FBgn0000053:E002\tFBgn0000053\tE002\t211.729712208868\t0.00747386960650737\t3.29991336976971\t0.0692835370561524\t0.804458846929769\t229.430374547441\t191.724260042797\t0.259023502449809\t2L\t7016437\t7017486\t1050\t-\t295\t164\t223\t247\t282\t155\t176\tFBtr0079431\n+FBgn0000114:E005\tFBgn0000114\tE005\t0.441683286944607\t0.059375301501'..b'", "FBtr0300504")\n+FBgn0000099:E010\tFBgn0000099\tE010\t0\tNA\tNA\tNA\tNA\t0.000106144136324025\t0.00014469072048536\t-0.446947724582759\t2R\t1605060\t1605268\t209\t-\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0086058", "FBtr0300504")\n+FBgn0000099:E011\tFBgn0000099\tE011\t0\tNA\tNA\tNA\tNA\t0.000106144136324025\t0.00014469072048536\t-0.446947724582759\t2R\t1605269\t1605271\t3\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0086058\n+FBgn0000099:E012\tFBgn0000099\tE012\t0\tNA\tNA\tNA\tNA\t0.000106144136324025\t0.00014469072048536\t-0.446947724582759\t2R\t1613326\t1614335\t1010\t-\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0086058", "FBtr0300504")\n+FBgn0000114:E001\tFBgn0000114\tE001\t0\tNA\tNA\tNA\tNA\t0.000530857176628925\t0.000118355154570515\t2.16520122704012\t2L\t12175004\t12175420\t417\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0331998\n+FBgn0000114:E003\tFBgn0000114\tE003\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12205843\t12206130\t288\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0331646", "FBtr0080344")\n+FBgn0000114:E004\tFBgn0000114\tE004\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12222197\t12222337\t141\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0331647", "FBtr0331645")\n+FBgn0000114:E007\tFBgn0000114\tE007\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12271591\t12272084\t494\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0300567", "FBtr0331648", "FBtr0331646", "FBtr0331647", "FBtr0331644", "FBtr0331645", "FBtr0080344", "FBtr0080345", "FBtr0331998")\n+FBgn0000114:E008\tFBgn0000114\tE008\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12278837\t12278919\t83\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0300567", "FBtr0331648", "FBtr0331646", "FBtr0331647", "FBtr0331644", "FBtr0331645", "FBtr0080344", "FBtr0080345", "FBtr0331998")\n+FBgn0000114:E009\tFBgn0000114\tE009\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12282514\t12282562\t49\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0300567", "FBtr0331648", "FBtr0331646", "FBtr0331647", "FBtr0331644", "FBtr0331645", "FBtr0080344", "FBtr0080345", "FBtr0331998")\n+FBgn0000114:E013\tFBgn0000114\tE013\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12298814\t12299111\t298\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0300567", "FBtr0331648", "FBtr0331646", "FBtr0331647", "FBtr0331644", "FBtr0331645", "FBtr0080347", "FBtr0080344", "FBtr0080345", "FBtr0331998")\n+FBgn0000114:E016\tFBgn0000114\tE016\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12300610\t12300621\t12\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0331644\n+FBgn0000114:E017\tFBgn0000114\tE017\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12304446\t12304595\t150\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0300567", "FBtr0331648", "FBtr0331646", "FBtr0331647", "FBtr0331644", "FBtr0331645", "FBtr0080347", "FBtr0080344", "FBtr0080345", "FBtr0331998")\n+FBgn0000114:E018\tFBgn0000114\tE018\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12310682\t12311093\t412\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0300567", "FBtr0331648", "FBtr0331646", "FBtr0331647", "FBtr0331644", "FBtr0331645", "FBtr0080347", "FBtr0080344", "FBtr0080345", "FBtr0331998")\n+FBgn0000114:E019\tFBgn0000114\tE019\t0\tNA\tNA\tNA\tNA\t0.000165271389329436\t4.56258436126363e-05\t1.8569138572105\t2L\t12311094\t12311104\t11\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0300567", "FBtr0331648", "FBtr0331646", "FBtr0331645", "FBtr0080347", "FBtr0331998")\n+FBgn0000116:E007\tFBgn0000116\tE007\t0\tNA\tNA\tNA\tNA\t0.00011400586637056\t5.74002023085652e-05\t0.989980335847687\t3L\t9055912\t9056048\t137\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0076544\n+FBgn0000120:E001\tFBgn0000120\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18078269\t18078496\t228\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0307350", "FBtr0081030")\n+FBgn0000120:E002\tFBgn0000120\tE002\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18078916\t18079723\t808\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0307350", "FBtr0081030")\n+FBgn0000120:E003\tFBgn0000120\tE003\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18079957\t18080086\t130\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0307350", "FBtr0081030")\n+FBgn0000120:E004\tFBgn0000120\tE004\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18080147\t18080415\t269\t+\t0\t0\t0\t0\t0\t0\t0\tc("FBtr0307350", "FBtr0081030")\n+FBgn0000137:E001\tFBgn0000137\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tX\t354533\t357209\t2677\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0070075\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/flattened.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/flattened.gtf Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,257 @@\n+4\tdexseq_prepare_annotation.py\taggregate_gene\t68336\t77667\t.\t-\t.\tgene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t68336\t71088\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "001"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71142\t71239\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "002"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71240\t71306\t.\t-\t.\ttranscripts "FBtr0306168+FBtr0089178"; exonic_part_number "003"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71371\t71883\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "004"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71940\t72580\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "005"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t72643\t73010\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "006"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76457\t76916\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178"; exonic_part_number "007"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76917\t76957\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "008"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76958\t77667\t.\t-\t.\ttranscripts "FBtr0306168"; exonic_part_number "009"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\taggregate_gene\t137015\t150380\t.\t-\t.\tgene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t137015\t137256\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "001"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t137312\t139127\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "002"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t139181\t139405\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "003"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t139464\t139557\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "004"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t140514\t140838\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "005"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t141484\t142425\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "006"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t142479\t142582\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "007"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t142935\t144048\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "008"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t144411\t144518\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "009"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t149948\t150068\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "010"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t150069\t150078\t.\t-\t.\ttranscripts "FBtr0089173"; exonic_part_number "011"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t150181\t150353\t.\t-\t.\ttranscripts "FBtr0089172"; exonic_part_number "012"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t150354\t150380\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089171"; exonic_part_number "013"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\taggregate_gene\t522436\t560418\t.\t+\t.\tgene_id "FBgn0004607"\n+4\tdexseq_prepare_annotation.py\texonic_part\t522436\t522483\t.\t+\t.\ttranscripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "001"; gene_id "FBgn0004607"\n+4\tdexseq_prepare_annotation.py\texonic_part\t524477\t524764\t.\t+\t.\ttranscripts "FBtr0332913+FBtr'..b'nnotation.py\taggregate_gene\t6055\t6118\t.\t+\t.\tgene_id "FBgn0013704"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6055\t6118\t.\t+\t.\ttranscripts "FBtr0100872"; exonic_part_number "001"; gene_id "FBgn0013704"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6119\t6183\t.\t+\t.\tgene_id "FBgn0013701"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6119\t6183\t.\t+\t.\ttranscripts "FBtr0100873"; exonic_part_number "001"; gene_id "FBgn0013701"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6184\t6251\t.\t+\t.\tgene_id "FBgn0013705"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6184\t6251\t.\t+\t.\ttranscripts "FBtr0100874"; exonic_part_number "001"; gene_id "FBgn0013705"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6252\t6318\t.\t+\t.\tgene_id "FBgn0013692"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6252\t6318\t.\t+\t.\ttranscripts "FBtr0100875"; exonic_part_number "001"; gene_id "FBgn0013692"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6337\t6401\t.\t-\t.\tgene_id "FBgn0013693"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6337\t6401\t.\t-\t.\ttranscripts "FBtr0100876"; exonic_part_number "001"; gene_id "FBgn0013693"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6402\t8124\t.\t-\t.\tgene_id "FBgn0013684"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6402\t8124\t.\t-\t.\ttranscripts "FBtr0100877"; exonic_part_number "001"; gene_id "FBgn0013684"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t8140\t8205\t.\t-\t.\tgene_id "FBgn0013695"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t8140\t8205\t.\t-\t.\ttranscripts "FBtr0100878"; exonic_part_number "001"; gene_id "FBgn0013695"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9837\t9902\t.\t+\t.\tgene_id "FBgn0013707"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9837\t9902\t.\t+\t.\ttranscripts "FBtr0100881"; exonic_part_number "001"; gene_id "FBgn0013707"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9903\t9963\t.\t-\t.\tgene_id "FBgn0013702"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9903\t9963\t.\t-\t.\ttranscripts "FBtr0100882"; exonic_part_number "001"; gene_id "FBgn0013702"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9970\t10494\t.\t+\t.\tgene_id "FBgn0013685"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9970\t10494\t.\t+\t.\ttranscripts "FBtr0100883"; exonic_part_number "001"; gene_id "FBgn0013685"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t10498\t11634\t.\t+\t.\tgene_id "FBgn0013678"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t10498\t11634\t.\t+\t.\ttranscripts "FBtr0100884"; exonic_part_number "001"; gene_id "FBgn0013678"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t11637\t11702\t.\t+\t.\tgene_id "FBgn0013706"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t11637\t11702\t.\t+\t.\ttranscripts "FBtr0100885"; exonic_part_number "001"; gene_id "FBgn0013706"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t11720\t12658\t.\t-\t.\tgene_id "FBgn0013679"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t11720\t12658\t.\t-\t.\ttranscripts "FBtr0100886"; exonic_part_number "001"; gene_id "FBgn0013679"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t12669\t12733\t.\t-\t.\tgene_id "FBgn0013698"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t12669\t12733\t.\t-\t.\ttranscripts "FBtr0100887"; exonic_part_number "001"; gene_id "FBgn0013698"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t14131\t14916\t.\t-\t.\tgene_id "FBgn0013688"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t14131\t14916\t.\t-\t.\ttranscripts "FBtr0100890"; exonic_part_number "001"; gene_id "FBgn0013688"\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/original.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/original.gtf Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\n+dmel_mitochondrion_genome\ttRNA\texon\t1\t65\t.\t+\t.\tgene_id "FBgn0013696"; transcript_id "FBtr0100854"; exon_number "1"; gene_name "mt:tRNA:I"; gene_biotype "tRNA"; transcript_name "mt:tRNA:I-RA"; exon_id "FBgn0013696:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t97\t165\t.\t-\t.\tgene_id "FBgn0013703"; transcript_id "FBtr0100855"; exon_number "1"; gene_name "mt:tRNA:Q"; gene_biotype "tRNA"; transcript_name "mt:tRNA:Q-RA"; exon_id "FBgn0013703:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t171\t239\t.\t+\t.\tgene_id "FBgn0013700"; transcript_id "FBtr0100856"; exon_number "1"; gene_name "mt:tRNA:M"; gene_biotype "tRNA"; transcript_name "mt:tRNA:M-RA"; exon_id "FBgn0013700:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t1322\t1383\t.\t-\t.\tgene_id "FBgn0013690"; transcript_id "FBtr0100859"; exon_number "1"; gene_name "mt:tRNA:C"; gene_biotype "tRNA"; transcript_name "mt:tRNA:C-RA"; exon_id "FBgn0013690:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t1403\t1468\t.\t-\t.\tgene_id "FBgn0013710"; transcript_id "FBtr0100860"; exon_number "1"; gene_name "mt:tRNA:Y"; gene_biotype "tRNA"; transcript_name "mt:tRNA:Y-RA"; exon_id "FBgn0013710:1";\n+dmel_mitochondrion_genome\tprotein_coding\texon\t1474\t3009\t.\t+\t.\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA"; exon_id "FBgn0013674:1";\n+dmel_mitochondrion_genome\tprotein_coding\tCDS\t1474\t3006\t.\t+\t0\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA"; protein_id "FBpp0100176";\n+dmel_mitochondrion_genome\tprotein_coding\tstop_codon\t3007\t3009\t.\t+\t0\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA";\n+dmel_mitochondrion_genome\ttRNA\texon\t3012\t3077\t.\t+\t.\tgene_id "FBgn0013699"; transcript_id "FBtr0100862"; exon_number "1"; gene_name "mt:tRNA:L:UUR"; gene_biotype "tRNA"; transcript_name "mt:tRNA:L:UUR-RA"; exon_id "FBgn0013699:1";\n+dmel_mitochondrion_genome\tprotein_coding\texon\t3083\t3767\t.\t+\t.\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA"; exon_id "FBgn0013675:1";\n+dmel_mitochondrion_genome\tprotein_coding\tCDS\t3083\t3767\t.\t+\t0\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA"; protein_id "FBpp0100177";\n+dmel_mitochondrion_genome\tprotein_coding\tstart_codon\t3083\t3085\t.\t+\t0\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA";\n+dmel_mitochondrion_genome\ttRNA\texon\t3768\t3838\t.\t+\t.\tgene_id "FBgn0013697"; transcript_id "FBtr0100864"; exon_number "1"; gene_name "mt:tRNA:K"; gene_biotype "tRNA"; transcript_name "mt:tRNA:K-RA"; exon_id "FBgn0013697:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t3840\t3906\t.\t+\t.\tgene_id "FBgn0013691"; transcript_id "FBtr0100865"; exon_number "1"; gene_name "mt:tRNA:D"; gene_biotype "tRNA"; transcript_name "mt:tRNA:D-RA"; exon_id "FBgn0013691:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t5543\t5607\t.\t+\t.\tgene_id "FBgn0013694"; transcript_id "FBtr0100869"; exon_number "1"; gene_name "mt:tRNA:G"; gene_biotype "tRNA"; transcript_name "mt:tRNA:G-RA"; exon_id "FBgn0013694:1";\n+dmel_mitochondrion_genome\tprotein_coding\texon\t5608\t5961\t.\t+\t.\tgene_id "FBgn0013681"; transcript_id "FBtr0100870"; exon_number "1"; gene_name "mt:ND3"; gene_biotype "protein_coding"; transcript_name "mt:ND3-RA"; exon_id "FBgn0013681:1";\n+dmel_mitochondrion_genome\tprotein_coding\tCDS\t5608\t5958\t.\t+\t0\tgene_id "FBgn0013681"; transcript_id "FBtr0100870"; exon_number "1"; gene_name "mt:ND3"; gene_biotype "protein_coding"; transcript_name "mt:ND3-RA"; protein_id "FBpp0100181";\n+dmel_mitochondrion_genome\tprotein_coding\tstop_codon\t5959\t5961\t.\t+\t0\tgene_id "FBgn0013681"; transcript_id "FBt'..b'FBgn0005561:7";\n+4\tprotein_coding\tCDS\t1124161\t1124358\t.\t+\t1\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "6"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1126778\t1127223\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "7"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:8";\n+4\tprotein_coding\tCDS\t1126778\t1127223\t.\t+\t1\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "7"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1128325\t1128416\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "8"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:9";\n+4\tprotein_coding\tCDS\t1128325\t1128416\t.\t+\t2\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "8"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1128724\t1128970\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "9"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:10";\n+4\tprotein_coding\tCDS\t1128724\t1128970\t.\t+\t0\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "9"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1129100\t1129198\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "10"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:11";\n+4\tprotein_coding\tCDS\t1129100\t1129198\t.\t+\t2\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "10"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1131407\t1131514\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "11"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:15";\n+4\tprotein_coding\tCDS\t1131407\t1131514\t.\t+\t2\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "11"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1131914\t1133943\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "12"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:17";\n+4\tprotein_coding\tCDS\t1131914\t1132074\t.\t+\t2\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "12"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\tstop_codon\t1132075\t1132077\t.\t+\t0\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "12"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD";\n+4\tprotein_coding\texon\t1109444\t1109688\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "1"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE"; exon_id "FBgn0005561:1";\n+4\tprotein_coding\texon\t1112885\t1113254\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "2"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE"; exon_id "FBgn0005561:2";\n+4\tprotein_coding\tCDS\t1112912\t1113254\t.\t+\t0\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "2"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE"; protein_id "FBpp0099748";\n+4\tprotein_coding\tstart_codon\t1112912\t1112914\t.\t+\t0\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "2"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE";\n+4\tprotein_coding\texon\t1116202\t1116342\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "3"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE"; exon_id "FBgn0005561:3";\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/treated1fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/treated1fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 0 +FBgn0000008:004 1 +FBgn0000008:005 4 +FBgn0000008:006 1 +FBgn0000008:007 18 +FBgn0000008:008 4 +FBgn0000008:009 16 +FBgn0000008:010 17 +FBgn0000008:011 2 +FBgn0000008:012 3 +FBgn0000008:013 11 +FBgn0000008:014 1 +FBgn0000014:001 1 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 1 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 1 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 0 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 1564 +FBgn0000017:002 47 +FBgn0000017:003 60 +FBgn0000017:004 103 +FBgn0000017:005 296 +FBgn0000017:006 226 +FBgn0000017:007 263 +FBgn0000017:008 5 +FBgn0000017:009 623 +FBgn0000018:001 152 +FBgn0000018:002 217 +FBgn0000022:001 0 +FBgn0000024:001 2 +FBgn0000024:002 0 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 1 +FBgn0000024:006 0 +FBgn0000024:007 0 +FBgn0000024:008 0 +FBgn0000024:009 1 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 213 +FBgn0000032:003 152 +FBgn0000032:004 385 +FBgn0000032:005 42 +FBgn0000032:006 79 +FBgn0000032:007 5 +FBgn0000032:008 12 +FBgn0000032:009 54 +FBgn0000036:001 1 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 9 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 1 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 3322 +FBgn0000042:002 286 +FBgn0000042:003 53623 +FBgn0000042:004 7007 +FBgn0000042:005 119 +FBgn0000043:001 27313 +FBgn0000043:002 1145 +FBgn0000045:001 0 +FBgn0000045:002 2 +FBgn0000045:003 6 +FBgn0000046:001 1 +FBgn0000046:002 0 +FBgn0000046:003 35 +FBgn0000047:001 0 +FBgn0000047:002 7 +FBgn0000047:003 1 +FBgn0000052:001 266 +FBgn0000052:002 1005 +FBgn0000052:003 343 +FBgn0000052:004 3 +FBgn0000052:005 12 +FBgn0000052:006 18 +FBgn0000053:001 414 +FBgn0000053:002 295 +FBgn0000053:003 117 +FBgn0000053:004 13 +FBgn0000053:005 77 +FBgn0000053:006 368 +FBgn0000053:007 140 +FBgn0000053:008 179 +FBgn0000054:001 56 +FBgn0000054:002 3 +FBgn0000054:003 10 +FBgn0000054:004 66 +FBgn0000054:005 112 +FBgn0000054:006 295 +FBgn0000057:001 210 +FBgn0000057:002 303 +FBgn0000061:001 0 +FBgn0000061:002 0 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 2 +FBgn0000063:001 52 +FBgn0000063:002 156 +FBgn0000063:003 104 +FBgn0000063:004 71 +FBgn0000064:001 1709 +FBgn0000064:002 0 +FBgn0000064:003 167 +FBgn0000064:004 74 +FBgn0000064:005 746 +FBgn0000064:006 3729 +FBgn0000064:007 74 +FBgn0000064:008 33 +FBgn0000064:009 5 +FBgn0000064:010 10 +FBgn0000064:011 154 +FBgn0000071:001 0 +FBgn0000071:002 57 +FBgn0000071:003 16 +FBgn0000071:004 460 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 1 +FBgn0000075:004 1 +FBgn0000077:001 179 +FBgn0000078:001 10 +FBgn0000079:001 44 +FBgn0000083:001 36 +FBgn0000083:002 63 +FBgn0000083:003 119 +FBgn0000083:004 2447 +FBgn0000083:005 567 +FBgn0000083:006 474 +FBgn0000083:007 60 +FBgn0000083:008 317 +FBgn0000084:001 144 +FBgn0000084:002 0 +FBgn0000084:003 0 +FBgn0000084:004 767 +FBgn0000084:005 307 +FBgn0000084:006 132 +FBgn0000092:001 6 +FBgn0000092:002 7 +FBgn0000092:003 3 +FBgn0000094:001 17 +FBgn0000094:002 9 +FBgn0000097:001 1032 +FBgn0000097:002 517 +FBgn0000097:003 725 +FBgn0000097:004 72 +FBgn0000097:005 436 +FBgn0000099:001 0 +FBgn0000099:002 1 +FBgn0000099:003 1 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 16 +FBgn0000100:002 1225 +FBgn0000100:003 14672 +FBgn0000108:001 4 +FBgn0000108:002 3 +FBgn0000108:003 0 +FBgn0000108:004 4 +FBgn0000108:005 8 +FBgn0000108:006 4 +FBgn0000108:007 0 +FBgn0000108:008 5 +FBgn0000108:009 2 +FBgn0000108:010 1 +FBgn0000108:011 13 +FBgn0000109:001 68 +FBgn0000109:002 57 +FBgn0000109:003 32 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 1 +FBgn0000114:011 0 +FBgn0000114:012 1 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 88 +FBgn0000115:002 156 +FBgn0000115:003 236 +FBgn0000116:001 558 +FBgn0000116:002 0 +FBgn0000116:003 1 +FBgn0000116:004 0 +FBgn0000116:005 1 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 1892 +FBgn0000117:002 259 +FBgn0000117:003 676 +FBgn0000117:004 541 +FBgn0000117:005 4350 +FBgn0000117:006 198 +FBgn0000117:007 10 +FBgn0000117:008 53 +FBgn0000117:009 102 +FBgn0000117:010 87 +FBgn0000119:001 126 +FBgn0000119:002 55 +FBgn0000119:003 21 +FBgn0000119:004 20 +FBgn0000119:005 264 +FBgn0000119:006 31 +FBgn0000119:007 3 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 4 +FBgn0000121:002 2 +FBgn0000121:003 2 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 4 +FBgn0000139:003 8 +FBgn0000139:004 14 +FBgn0000139:005 18 +FBgn0000139:006 44 +FBgn0000139:007 12 +FBgn0000139:008 130 +FBgn0000139:009 92 +FBgn0000140:001 14 +FBgn0000140:002 19 +FBgn0000140:003 27 +FBgn0000140:004 717 +FBgn0000140:005 51 +FBgn0000140:006 67 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/treated2fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/treated2fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 1 +FBgn0000008:004 0 +FBgn0000008:005 1 +FBgn0000008:006 0 +FBgn0000008:007 8 +FBgn0000008:008 1 +FBgn0000008:009 17 +FBgn0000008:010 17 +FBgn0000008:011 0 +FBgn0000008:012 0 +FBgn0000008:013 1 +FBgn0000008:014 0 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 0 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 806 +FBgn0000017:002 29 +FBgn0000017:003 55 +FBgn0000017:004 108 +FBgn0000017:005 210 +FBgn0000017:006 135 +FBgn0000017:007 128 +FBgn0000017:008 1 +FBgn0000017:009 200 +FBgn0000018:001 41 +FBgn0000018:002 109 +FBgn0000022:001 0 +FBgn0000024:001 0 +FBgn0000024:002 1 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 1 +FBgn0000024:008 0 +FBgn0000024:009 2 +FBgn0000024:010 0 +FBgn0000024:011 1 +FBgn0000024:012 0 +FBgn0000028:001 1 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 67 +FBgn0000032:003 79 +FBgn0000032:004 165 +FBgn0000032:005 53 +FBgn0000032:006 62 +FBgn0000032:007 3 +FBgn0000032:008 11 +FBgn0000032:009 25 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 5 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 5 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 262 +FBgn0000042:002 138 +FBgn0000042:003 37301 +FBgn0000042:004 1635 +FBgn0000042:005 20 +FBgn0000043:001 15297 +FBgn0000043:002 374 +FBgn0000045:001 0 +FBgn0000045:002 3 +FBgn0000045:003 1 +FBgn0000046:001 1 +FBgn0000046:002 0 +FBgn0000046:003 16 +FBgn0000047:001 0 +FBgn0000047:002 5 +FBgn0000047:003 2 +FBgn0000052:001 187 +FBgn0000052:002 523 +FBgn0000052:003 283 +FBgn0000052:004 0 +FBgn0000052:005 2 +FBgn0000052:006 1 +FBgn0000053:001 275 +FBgn0000053:002 164 +FBgn0000053:003 77 +FBgn0000053:004 7 +FBgn0000053:005 70 +FBgn0000053:006 279 +FBgn0000053:007 123 +FBgn0000053:008 115 +FBgn0000054:001 22 +FBgn0000054:002 5 +FBgn0000054:003 5 +FBgn0000054:004 51 +FBgn0000054:005 97 +FBgn0000054:006 134 +FBgn0000057:001 129 +FBgn0000057:002 192 +FBgn0000061:001 0 +FBgn0000061:002 0 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 37 +FBgn0000063:002 89 +FBgn0000063:003 63 +FBgn0000063:004 19 +FBgn0000064:001 361 +FBgn0000064:002 7 +FBgn0000064:003 48 +FBgn0000064:004 30 +FBgn0000064:005 952 +FBgn0000064:006 2672 +FBgn0000064:007 33 +FBgn0000064:008 12 +FBgn0000064:009 2 +FBgn0000064:010 5 +FBgn0000064:011 77 +FBgn0000071:001 0 +FBgn0000071:002 24 +FBgn0000071:003 8 +FBgn0000071:004 234 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 0 +FBgn0000075:004 0 +FBgn0000077:001 85 +FBgn0000078:001 11 +FBgn0000079:001 51 +FBgn0000083:001 18 +FBgn0000083:002 24 +FBgn0000083:003 60 +FBgn0000083:004 1834 +FBgn0000083:005 413 +FBgn0000083:006 152 +FBgn0000083:007 20 +FBgn0000083:008 119 +FBgn0000084:001 41 +FBgn0000084:002 0 +FBgn0000084:003 16 +FBgn0000084:004 653 +FBgn0000084:005 96 +FBgn0000084:006 23 +FBgn0000092:001 5 +FBgn0000092:002 2 +FBgn0000092:003 0 +FBgn0000094:001 6 +FBgn0000094:002 2 +FBgn0000097:001 322 +FBgn0000097:002 327 +FBgn0000097:003 462 +FBgn0000097:004 36 +FBgn0000097:005 153 +FBgn0000099:001 0 +FBgn0000099:002 0 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 1 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 5 +FBgn0000100:002 809 +FBgn0000100:003 9830 +FBgn0000108:001 1 +FBgn0000108:002 1 +FBgn0000108:003 1 +FBgn0000108:004 2 +FBgn0000108:005 5 +FBgn0000108:006 2 +FBgn0000108:007 3 +FBgn0000108:008 8 +FBgn0000108:009 0 +FBgn0000108:010 0 +FBgn0000108:011 4 +FBgn0000109:001 10 +FBgn0000109:002 15 +FBgn0000109:003 6 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 0 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 34 +FBgn0000115:002 119 +FBgn0000115:003 140 +FBgn0000116:001 495 +FBgn0000116:002 0 +FBgn0000116:003 0 +FBgn0000116:004 0 +FBgn0000116:005 0 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 943 +FBgn0000117:002 283 +FBgn0000117:003 728 +FBgn0000117:004 507 +FBgn0000117:005 2733 +FBgn0000117:006 147 +FBgn0000117:007 5 +FBgn0000117:008 16 +FBgn0000117:009 64 +FBgn0000117:010 32 +FBgn0000119:001 62 +FBgn0000119:002 39 +FBgn0000119:003 15 +FBgn0000119:004 7 +FBgn0000119:005 142 +FBgn0000119:006 8 +FBgn0000119:007 2 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 0 +FBgn0000121:002 1 +FBgn0000121:003 0 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 3 +FBgn0000139:003 4 +FBgn0000139:004 7 +FBgn0000139:005 13 +FBgn0000139:006 29 +FBgn0000139:007 5 +FBgn0000139:008 73 +FBgn0000139:009 64 +FBgn0000140:001 9 +FBgn0000140:002 23 +FBgn0000140:003 25 +FBgn0000140:004 355 +FBgn0000140:005 37 +FBgn0000140:006 21 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/treated3fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/treated3fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 1 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 0 +FBgn0000008:004 1 +FBgn0000008:005 1 +FBgn0000008:006 0 +FBgn0000008:007 7 +FBgn0000008:008 0 +FBgn0000008:009 15 +FBgn0000008:010 15 +FBgn0000008:011 2 +FBgn0000008:012 0 +FBgn0000008:013 1 +FBgn0000008:014 1 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 1 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 875 +FBgn0000017:002 29 +FBgn0000017:003 46 +FBgn0000017:004 87 +FBgn0000017:005 261 +FBgn0000017:006 183 +FBgn0000017:007 157 +FBgn0000017:008 10 +FBgn0000017:009 211 +FBgn0000018:001 62 +FBgn0000018:002 114 +FBgn0000022:001 0 +FBgn0000024:001 0 +FBgn0000024:002 0 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 0 +FBgn0000024:008 0 +FBgn0000024:009 3 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 1 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 51 +FBgn0000032:003 102 +FBgn0000032:004 234 +FBgn0000032:005 56 +FBgn0000032:006 69 +FBgn0000032:007 0 +FBgn0000032:008 4 +FBgn0000032:009 20 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 4 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 7 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 275 +FBgn0000042:002 173 +FBgn0000042:003 41337 +FBgn0000042:004 1666 +FBgn0000042:005 29 +FBgn0000043:001 16802 +FBgn0000043:002 378 +FBgn0000045:001 0 +FBgn0000045:002 6 +FBgn0000045:003 2 +FBgn0000046:001 0 +FBgn0000046:002 0 +FBgn0000046:003 17 +FBgn0000047:001 0 +FBgn0000047:002 6 +FBgn0000047:003 1 +FBgn0000052:001 161 +FBgn0000052:002 566 +FBgn0000052:003 295 +FBgn0000052:004 2 +FBgn0000052:005 7 +FBgn0000052:006 12 +FBgn0000053:001 301 +FBgn0000053:002 223 +FBgn0000053:003 91 +FBgn0000053:004 15 +FBgn0000053:005 85 +FBgn0000053:006 279 +FBgn0000053:007 127 +FBgn0000053:008 101 +FBgn0000054:001 27 +FBgn0000054:002 4 +FBgn0000054:003 7 +FBgn0000054:004 68 +FBgn0000054:005 115 +FBgn0000054:006 161 +FBgn0000057:001 116 +FBgn0000057:002 195 +FBgn0000061:001 0 +FBgn0000061:002 0 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 25 +FBgn0000063:002 97 +FBgn0000063:003 62 +FBgn0000063:004 19 +FBgn0000064:001 542 +FBgn0000064:002 12 +FBgn0000064:003 93 +FBgn0000064:004 39 +FBgn0000064:005 1227 +FBgn0000064:006 3078 +FBgn0000064:007 39 +FBgn0000064:008 18 +FBgn0000064:009 0 +FBgn0000064:010 3 +FBgn0000064:011 97 +FBgn0000071:001 0 +FBgn0000071:002 18 +FBgn0000071:003 7 +FBgn0000071:004 286 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 0 +FBgn0000075:004 1 +FBgn0000077:001 89 +FBgn0000078:001 11 +FBgn0000079:001 53 +FBgn0000083:001 23 +FBgn0000083:002 32 +FBgn0000083:003 55 +FBgn0000083:004 2126 +FBgn0000083:005 615 +FBgn0000083:006 158 +FBgn0000083:007 15 +FBgn0000083:008 178 +FBgn0000084:001 40 +FBgn0000084:002 0 +FBgn0000084:003 13 +FBgn0000084:004 748 +FBgn0000084:005 143 +FBgn0000084:006 34 +FBgn0000092:001 3 +FBgn0000092:002 4 +FBgn0000092:003 0 +FBgn0000094:001 9 +FBgn0000094:002 0 +FBgn0000097:001 349 +FBgn0000097:002 402 +FBgn0000097:003 477 +FBgn0000097:004 37 +FBgn0000097:005 131 +FBgn0000099:001 0 +FBgn0000099:002 0 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 9 +FBgn0000100:002 496 +FBgn0000100:003 10238 +FBgn0000108:001 1 +FBgn0000108:002 0 +FBgn0000108:003 0 +FBgn0000108:004 1 +FBgn0000108:005 10 +FBgn0000108:006 1 +FBgn0000108:007 1 +FBgn0000108:008 7 +FBgn0000108:009 2 +FBgn0000108:010 1 +FBgn0000108:011 2 +FBgn0000109:001 21 +FBgn0000109:002 38 +FBgn0000109:003 19 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 1 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 2 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 41 +FBgn0000115:002 129 +FBgn0000115:003 161 +FBgn0000116:001 436 +FBgn0000116:002 0 +FBgn0000116:003 0 +FBgn0000116:004 1 +FBgn0000116:005 5 +FBgn0000116:006 1 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 1111 +FBgn0000117:002 348 +FBgn0000117:003 799 +FBgn0000117:004 690 +FBgn0000117:005 3196 +FBgn0000117:006 167 +FBgn0000117:007 2 +FBgn0000117:008 19 +FBgn0000117:009 78 +FBgn0000117:010 27 +FBgn0000119:001 49 +FBgn0000119:002 39 +FBgn0000119:003 16 +FBgn0000119:004 11 +FBgn0000119:005 176 +FBgn0000119:006 9 +FBgn0000119:007 0 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 1 +FBgn0000121:002 0 +FBgn0000121:003 1 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 0 +FBgn0000139:003 1 +FBgn0000139:004 6 +FBgn0000139:005 14 +FBgn0000139:006 34 +FBgn0000139:007 9 +FBgn0000139:008 89 +FBgn0000139:009 93 +FBgn0000140:001 11 +FBgn0000140:002 22 +FBgn0000140:003 22 +FBgn0000140:004 274 +FBgn0000140:005 38 +FBgn0000140:006 26 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/untreated1fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/untreated1fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 1 +FBgn0000008:004 0 +FBgn0000008:005 2 +FBgn0000008:006 0 +FBgn0000008:007 8 +FBgn0000008:008 0 +FBgn0000008:009 18 +FBgn0000008:010 9 +FBgn0000008:011 3 +FBgn0000008:012 0 +FBgn0000008:013 5 +FBgn0000008:014 1 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 0 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 1289 +FBgn0000017:002 36 +FBgn0000017:003 48 +FBgn0000017:004 107 +FBgn0000017:005 313 +FBgn0000017:006 182 +FBgn0000017:007 167 +FBgn0000017:008 5 +FBgn0000017:009 298 +FBgn0000018:001 106 +FBgn0000018:002 182 +FBgn0000022:001 0 +FBgn0000024:001 1 +FBgn0000024:002 0 +FBgn0000024:003 0 +FBgn0000024:004 1 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 2 +FBgn0000024:008 0 +FBgn0000024:009 0 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 112 +FBgn0000032:003 115 +FBgn0000032:004 328 +FBgn0000032:005 38 +FBgn0000032:006 80 +FBgn0000032:007 4 +FBgn0000032:008 17 +FBgn0000032:009 73 +FBgn0000036:001 1 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 5 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 1 +FBgn0000037:005 1 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 1633 +FBgn0000042:002 205 +FBgn0000042:003 47230 +FBgn0000042:004 3678 +FBgn0000042:005 45 +FBgn0000043:001 15915 +FBgn0000043:002 570 +FBgn0000045:001 0 +FBgn0000045:002 4 +FBgn0000045:003 1 +FBgn0000046:001 0 +FBgn0000046:002 0 +FBgn0000046:003 5 +FBgn0000047:001 0 +FBgn0000047:002 2 +FBgn0000047:003 4 +FBgn0000052:001 277 +FBgn0000052:002 843 +FBgn0000052:003 346 +FBgn0000052:004 2 +FBgn0000052:005 10 +FBgn0000052:006 13 +FBgn0000053:001 312 +FBgn0000053:002 247 +FBgn0000053:003 96 +FBgn0000053:004 0 +FBgn0000053:005 38 +FBgn0000053:006 214 +FBgn0000053:007 74 +FBgn0000053:008 127 +FBgn0000054:001 43 +FBgn0000054:002 10 +FBgn0000054:003 8 +FBgn0000054:004 41 +FBgn0000054:005 131 +FBgn0000054:006 246 +FBgn0000057:001 165 +FBgn0000057:002 224 +FBgn0000061:001 0 +FBgn0000061:002 0 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 46 +FBgn0000063:002 103 +FBgn0000063:003 60 +FBgn0000063:004 59 +FBgn0000064:001 439 +FBgn0000064:002 0 +FBgn0000064:003 85 +FBgn0000064:004 9 +FBgn0000064:005 542 +FBgn0000064:006 2786 +FBgn0000064:007 53 +FBgn0000064:008 10 +FBgn0000064:009 0 +FBgn0000064:010 5 +FBgn0000064:011 210 +FBgn0000071:001 0 +FBgn0000071:002 3 +FBgn0000071:003 0 +FBgn0000071:004 29 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 0 +FBgn0000075:004 0 +FBgn0000077:001 167 +FBgn0000078:001 24 +FBgn0000079:001 78 +FBgn0000083:001 30 +FBgn0000083:002 57 +FBgn0000083:003 93 +FBgn0000083:004 2309 +FBgn0000083:005 536 +FBgn0000083:006 241 +FBgn0000083:007 42 +FBgn0000083:008 86 +FBgn0000084:001 12 +FBgn0000084:002 0 +FBgn0000084:003 0 +FBgn0000084:004 799 +FBgn0000084:005 186 +FBgn0000084:006 71 +FBgn0000092:001 1 +FBgn0000092:002 2 +FBgn0000092:003 0 +FBgn0000094:001 8 +FBgn0000094:002 3 +FBgn0000097:001 473 +FBgn0000097:002 386 +FBgn0000097:003 524 +FBgn0000097:004 46 +FBgn0000097:005 240 +FBgn0000099:001 0 +FBgn0000099:002 0 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 9 +FBgn0000100:002 1366 +FBgn0000100:003 12925 +FBgn0000108:001 1 +FBgn0000108:002 0 +FBgn0000108:003 1 +FBgn0000108:004 0 +FBgn0000108:005 3 +FBgn0000108:006 0 +FBgn0000108:007 0 +FBgn0000108:008 0 +FBgn0000108:009 0 +FBgn0000108:010 2 +FBgn0000108:011 1 +FBgn0000109:001 34 +FBgn0000109:002 41 +FBgn0000109:003 38 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 0 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 72 +FBgn0000115:002 121 +FBgn0000115:003 174 +FBgn0000116:001 222 +FBgn0000116:002 0 +FBgn0000116:003 1 +FBgn0000116:004 0 +FBgn0000116:005 1 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 1063 +FBgn0000117:002 72 +FBgn0000117:003 493 +FBgn0000117:004 417 +FBgn0000117:005 3198 +FBgn0000117:006 179 +FBgn0000117:007 3 +FBgn0000117:008 22 +FBgn0000117:009 105 +FBgn0000117:010 58 +FBgn0000119:001 77 +FBgn0000119:002 62 +FBgn0000119:003 15 +FBgn0000119:004 5 +FBgn0000119:005 218 +FBgn0000119:006 13 +FBgn0000119:007 6 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 0 +FBgn0000121:002 3 +FBgn0000121:003 3 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 2 +FBgn0000139:003 3 +FBgn0000139:004 3 +FBgn0000139:005 10 +FBgn0000139:006 39 +FBgn0000139:007 24 +FBgn0000139:008 133 +FBgn0000139:009 95 +FBgn0000140:001 21 +FBgn0000140:002 24 +FBgn0000140:003 29 +FBgn0000140:004 503 +FBgn0000140:005 35 +FBgn0000140:006 34 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/untreated2fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/untreated2fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 1 +FBgn0000008:004 1 +FBgn0000008:005 2 +FBgn0000008:006 0 +FBgn0000008:007 11 +FBgn0000008:008 1 +FBgn0000008:009 33 +FBgn0000008:010 20 +FBgn0000008:011 6 +FBgn0000008:012 2 +FBgn0000008:013 10 +FBgn0000008:014 2 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 1 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 2492 +FBgn0000017:002 83 +FBgn0000017:003 132 +FBgn0000017:004 162 +FBgn0000017:005 372 +FBgn0000017:006 354 +FBgn0000017:007 345 +FBgn0000017:008 3 +FBgn0000017:009 672 +FBgn0000018:001 141 +FBgn0000018:002 242 +FBgn0000022:001 1 +FBgn0000024:001 0 +FBgn0000024:002 0 +FBgn0000024:003 1 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 1 +FBgn0000024:007 2 +FBgn0000024:008 1 +FBgn0000024:009 1 +FBgn0000024:010 0 +FBgn0000024:011 1 +FBgn0000024:012 0 +FBgn0000028:001 1 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 71 +FBgn0000032:003 182 +FBgn0000032:004 450 +FBgn0000032:005 55 +FBgn0000032:006 95 +FBgn0000032:007 7 +FBgn0000032:008 35 +FBgn0000032:009 61 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 1 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 9 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 4 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 1 +FBgn0000039:010 0 +FBgn0000042:001 3139 +FBgn0000042:002 149 +FBgn0000042:003 50144 +FBgn0000042:004 8835 +FBgn0000042:005 52 +FBgn0000043:001 20887 +FBgn0000043:002 190 +FBgn0000045:001 0 +FBgn0000045:002 4 +FBgn0000045:003 6 +FBgn0000046:001 0 +FBgn0000046:002 0 +FBgn0000046:003 33 +FBgn0000047:001 0 +FBgn0000047:002 7 +FBgn0000047:003 2 +FBgn0000052:001 264 +FBgn0000052:002 1051 +FBgn0000052:003 457 +FBgn0000052:004 5 +FBgn0000052:005 15 +FBgn0000052:006 19 +FBgn0000053:001 429 +FBgn0000053:002 282 +FBgn0000053:003 93 +FBgn0000053:004 3 +FBgn0000053:005 72 +FBgn0000053:006 298 +FBgn0000053:007 190 +FBgn0000053:008 164 +FBgn0000054:001 33 +FBgn0000054:002 8 +FBgn0000054:003 16 +FBgn0000054:004 108 +FBgn0000054:005 124 +FBgn0000054:006 299 +FBgn0000057:001 229 +FBgn0000057:002 367 +FBgn0000061:001 0 +FBgn0000061:002 1 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 50 +FBgn0000063:002 184 +FBgn0000063:003 109 +FBgn0000063:004 52 +FBgn0000064:001 682 +FBgn0000064:002 0 +FBgn0000064:003 279 +FBgn0000064:004 25 +FBgn0000064:005 790 +FBgn0000064:006 4155 +FBgn0000064:007 76 +FBgn0000064:008 21 +FBgn0000064:009 4 +FBgn0000064:010 14 +FBgn0000064:011 219 +FBgn0000071:001 0 +FBgn0000071:002 10 +FBgn0000071:003 2 +FBgn0000071:004 93 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 0 +FBgn0000075:004 2 +FBgn0000077:001 196 +FBgn0000078:001 30 +FBgn0000079:001 132 +FBgn0000083:001 22 +FBgn0000083:002 29 +FBgn0000083:003 238 +FBgn0000083:004 2810 +FBgn0000083:005 584 +FBgn0000083:006 525 +FBgn0000083:007 51 +FBgn0000083:008 149 +FBgn0000084:001 73 +FBgn0000084:002 0 +FBgn0000084:003 0 +FBgn0000084:004 1087 +FBgn0000084:005 408 +FBgn0000084:006 150 +FBgn0000092:001 4 +FBgn0000092:002 6 +FBgn0000092:003 0 +FBgn0000094:001 9 +FBgn0000094:002 8 +FBgn0000097:001 887 +FBgn0000097:002 671 +FBgn0000097:003 1052 +FBgn0000097:004 50 +FBgn0000097:005 419 +FBgn0000099:001 0 +FBgn0000099:002 1 +FBgn0000099:003 0 +FBgn0000099:004 1 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 9 +FBgn0000100:002 1073 +FBgn0000100:003 20934 +FBgn0000108:001 6 +FBgn0000108:002 1 +FBgn0000108:003 1 +FBgn0000108:004 5 +FBgn0000108:005 9 +FBgn0000108:006 0 +FBgn0000108:007 5 +FBgn0000108:008 14 +FBgn0000108:009 1 +FBgn0000108:010 1 +FBgn0000108:011 14 +FBgn0000109:001 42 +FBgn0000109:002 40 +FBgn0000109:003 29 +FBgn0000114:001 0 +FBgn0000114:002 1 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 5 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 2 +FBgn0000114:011 1 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 1 +FBgn0000114:015 1 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 99 +FBgn0000115:002 183 +FBgn0000115:003 299 +FBgn0000116:001 335 +FBgn0000116:002 1 +FBgn0000116:003 2 +FBgn0000116:004 0 +FBgn0000116:005 3 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 2137 +FBgn0000117:002 287 +FBgn0000117:003 606 +FBgn0000117:004 761 +FBgn0000117:005 4668 +FBgn0000117:006 242 +FBgn0000117:007 15 +FBgn0000117:008 31 +FBgn0000117:009 107 +FBgn0000117:010 69 +FBgn0000119:001 133 +FBgn0000119:002 84 +FBgn0000119:003 13 +FBgn0000119:004 16 +FBgn0000119:005 266 +FBgn0000119:006 22 +FBgn0000119:007 8 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 1 +FBgn0000121:002 1 +FBgn0000121:003 11 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 7 +FBgn0000139:003 12 +FBgn0000139:004 10 +FBgn0000139:005 17 +FBgn0000139:006 45 +FBgn0000139:007 28 +FBgn0000139:008 199 +FBgn0000139:009 166 +FBgn0000140:001 17 +FBgn0000140:002 32 +FBgn0000140:003 20 +FBgn0000140:004 729 +FBgn0000140:005 47 +FBgn0000140:006 46 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/untreated3fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/untreated3fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 1 +FBgn0000008:003 1 +FBgn0000008:004 0 +FBgn0000008:005 0 +FBgn0000008:006 0 +FBgn0000008:007 11 +FBgn0000008:008 4 +FBgn0000008:009 21 +FBgn0000008:010 8 +FBgn0000008:011 1 +FBgn0000008:012 1 +FBgn0000008:013 5 +FBgn0000008:014 0 +FBgn0000014:001 1 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 1 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 911 +FBgn0000017:002 48 +FBgn0000017:003 83 +FBgn0000017:004 144 +FBgn0000017:005 242 +FBgn0000017:006 208 +FBgn0000017:007 176 +FBgn0000017:008 2 +FBgn0000017:009 249 +FBgn0000018:001 37 +FBgn0000018:002 98 +FBgn0000022:001 0 +FBgn0000024:001 0 +FBgn0000024:002 1 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 0 +FBgn0000024:008 0 +FBgn0000024:009 0 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 52 +FBgn0000032:003 97 +FBgn0000032:004 197 +FBgn0000032:005 45 +FBgn0000032:006 56 +FBgn0000032:007 2 +FBgn0000032:008 5 +FBgn0000032:009 10 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 3 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 0 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 244 +FBgn0000042:002 106 +FBgn0000042:003 22833 +FBgn0000042:004 1202 +FBgn0000042:005 14 +FBgn0000043:001 8188 +FBgn0000043:002 188 +FBgn0000045:001 0 +FBgn0000045:002 0 +FBgn0000045:003 1 +FBgn0000046:001 1 +FBgn0000046:002 1 +FBgn0000046:003 12 +FBgn0000047:001 0 +FBgn0000047:002 3 +FBgn0000047:003 0 +FBgn0000052:001 124 +FBgn0000052:002 505 +FBgn0000052:003 261 +FBgn0000052:004 5 +FBgn0000052:005 2 +FBgn0000052:006 2 +FBgn0000053:001 184 +FBgn0000053:002 155 +FBgn0000053:003 65 +FBgn0000053:004 3 +FBgn0000053:005 45 +FBgn0000053:006 171 +FBgn0000053:007 88 +FBgn0000053:008 57 +FBgn0000054:001 21 +FBgn0000054:002 3 +FBgn0000054:003 9 +FBgn0000054:004 37 +FBgn0000054:005 99 +FBgn0000054:006 133 +FBgn0000057:001 94 +FBgn0000057:002 172 +FBgn0000061:001 0 +FBgn0000061:002 1 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 19 +FBgn0000063:002 71 +FBgn0000063:003 54 +FBgn0000063:004 9 +FBgn0000064:001 328 +FBgn0000064:002 10 +FBgn0000064:003 77 +FBgn0000064:004 20 +FBgn0000064:005 802 +FBgn0000064:006 2022 +FBgn0000064:007 18 +FBgn0000064:008 6 +FBgn0000064:009 0 +FBgn0000064:010 1 +FBgn0000064:011 76 +FBgn0000071:001 0 +FBgn0000071:002 5 +FBgn0000071:003 1 +FBgn0000071:004 42 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 1 +FBgn0000075:004 1 +FBgn0000077:001 70 +FBgn0000078:001 16 +FBgn0000079:001 115 +FBgn0000083:001 17 +FBgn0000083:002 26 +FBgn0000083:003 36 +FBgn0000083:004 1533 +FBgn0000083:005 399 +FBgn0000083:006 133 +FBgn0000083:007 26 +FBgn0000083:008 110 +FBgn0000084:001 50 +FBgn0000084:002 0 +FBgn0000084:003 29 +FBgn0000084:004 673 +FBgn0000084:005 128 +FBgn0000084:006 35 +FBgn0000092:001 0 +FBgn0000092:002 3 +FBgn0000092:003 1 +FBgn0000094:001 7 +FBgn0000094:002 2 +FBgn0000097:001 310 +FBgn0000097:002 348 +FBgn0000097:003 491 +FBgn0000097:004 27 +FBgn0000097:005 142 +FBgn0000099:001 0 +FBgn0000099:002 1 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 3 +FBgn0000100:002 336 +FBgn0000100:003 9117 +FBgn0000108:001 5 +FBgn0000108:002 2 +FBgn0000108:003 0 +FBgn0000108:004 2 +FBgn0000108:005 5 +FBgn0000108:006 0 +FBgn0000108:007 2 +FBgn0000108:008 8 +FBgn0000108:009 3 +FBgn0000108:010 0 +FBgn0000108:011 1 +FBgn0000109:001 19 +FBgn0000109:002 26 +FBgn0000109:003 9 +FBgn0000114:001 0 +FBgn0000114:002 1 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 0 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 33 +FBgn0000115:002 82 +FBgn0000115:003 120 +FBgn0000116:001 158 +FBgn0000116:002 0 +FBgn0000116:003 0 +FBgn0000116:004 0 +FBgn0000116:005 0 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 1 +FBgn0000117:001 670 +FBgn0000117:002 232 +FBgn0000117:003 574 +FBgn0000117:004 498 +FBgn0000117:005 2293 +FBgn0000117:006 93 +FBgn0000117:007 1 +FBgn0000117:008 11 +FBgn0000117:009 37 +FBgn0000117:010 27 +FBgn0000119:001 44 +FBgn0000119:002 29 +FBgn0000119:003 7 +FBgn0000119:004 3 +FBgn0000119:005 139 +FBgn0000119:006 14 +FBgn0000119:007 1 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 1 +FBgn0000121:002 1 +FBgn0000121:003 2 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 1 +FBgn0000139:003 1 +FBgn0000139:004 4 +FBgn0000139:005 5 +FBgn0000139:006 15 +FBgn0000139:007 24 +FBgn0000139:008 85 +FBgn0000139:009 87 +FBgn0000140:001 5 +FBgn0000140:002 25 +FBgn0000140:003 32 +FBgn0000140:004 250 +FBgn0000140:005 22 +FBgn0000140:006 15 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data (Kopie)/untreated4fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data (Kopie)/untreated4fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 0 +FBgn0000008:004 1 +FBgn0000008:005 1 +FBgn0000008:006 0 +FBgn0000008:007 4 +FBgn0000008:008 1 +FBgn0000008:009 10 +FBgn0000008:010 8 +FBgn0000008:011 2 +FBgn0000008:012 0 +FBgn0000008:013 0 +FBgn0000008:014 0 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 2 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 820 +FBgn0000017:002 28 +FBgn0000017:003 62 +FBgn0000017:004 104 +FBgn0000017:005 237 +FBgn0000017:006 152 +FBgn0000017:007 112 +FBgn0000017:008 5 +FBgn0000017:009 191 +FBgn0000018:001 57 +FBgn0000018:002 117 +FBgn0000022:001 0 +FBgn0000024:001 0 +FBgn0000024:002 0 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 0 +FBgn0000024:008 0 +FBgn0000024:009 0 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 51 +FBgn0000032:003 75 +FBgn0000032:004 204 +FBgn0000032:005 53 +FBgn0000032:006 64 +FBgn0000032:007 0 +FBgn0000032:008 6 +FBgn0000032:009 18 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 3 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 2 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 129 +FBgn0000042:002 132 +FBgn0000042:003 26327 +FBgn0000042:004 1091 +FBgn0000042:005 8 +FBgn0000043:001 9110 +FBgn0000043:002 174 +FBgn0000045:001 0 +FBgn0000045:002 1 +FBgn0000045:003 0 +FBgn0000046:001 0 +FBgn0000046:002 0 +FBgn0000046:003 12 +FBgn0000047:001 0 +FBgn0000047:002 1 +FBgn0000047:003 1 +FBgn0000052:001 191 +FBgn0000052:002 577 +FBgn0000052:003 265 +FBgn0000052:004 1 +FBgn0000052:005 2 +FBgn0000052:006 3 +FBgn0000053:001 257 +FBgn0000053:002 176 +FBgn0000053:003 64 +FBgn0000053:004 4 +FBgn0000053:005 51 +FBgn0000053:006 181 +FBgn0000053:007 68 +FBgn0000053:008 76 +FBgn0000054:001 23 +FBgn0000054:002 4 +FBgn0000054:003 8 +FBgn0000054:004 47 +FBgn0000054:005 101 +FBgn0000054:006 134 +FBgn0000057:001 122 +FBgn0000057:002 165 +FBgn0000061:001 0 +FBgn0000061:002 1 +FBgn0000061:003 0 +FBgn0000061:004 2 +FBgn0000061:005 1 +FBgn0000063:001 23 +FBgn0000063:002 66 +FBgn0000063:003 50 +FBgn0000063:004 20 +FBgn0000064:001 303 +FBgn0000064:002 12 +FBgn0000064:003 76 +FBgn0000064:004 9 +FBgn0000064:005 722 +FBgn0000064:006 2100 +FBgn0000064:007 22 +FBgn0000064:008 11 +FBgn0000064:009 0 +FBgn0000064:010 1 +FBgn0000064:011 86 +FBgn0000071:001 0 +FBgn0000071:002 3 +FBgn0000071:003 1 +FBgn0000071:004 43 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 1 +FBgn0000075:004 0 +FBgn0000077:001 92 +FBgn0000078:001 15 +FBgn0000079:001 99 +FBgn0000083:001 20 +FBgn0000083:002 27 +FBgn0000083:003 74 +FBgn0000083:004 1952 +FBgn0000083:005 524 +FBgn0000083:006 120 +FBgn0000083:007 30 +FBgn0000083:008 129 +FBgn0000084:001 45 +FBgn0000084:002 0 +FBgn0000084:003 11 +FBgn0000084:004 753 +FBgn0000084:005 138 +FBgn0000084:006 46 +FBgn0000092:001 3 +FBgn0000092:002 2 +FBgn0000092:003 2 +FBgn0000094:001 3 +FBgn0000094:002 1 +FBgn0000097:001 283 +FBgn0000097:002 286 +FBgn0000097:003 412 +FBgn0000097:004 21 +FBgn0000097:005 115 +FBgn0000099:001 0 +FBgn0000099:002 1 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 3 +FBgn0000100:002 423 +FBgn0000100:003 11258 +FBgn0000108:001 2 +FBgn0000108:002 0 +FBgn0000108:003 2 +FBgn0000108:004 1 +FBgn0000108:005 3 +FBgn0000108:006 0 +FBgn0000108:007 3 +FBgn0000108:008 7 +FBgn0000108:009 2 +FBgn0000108:010 2 +FBgn0000108:011 3 +FBgn0000109:001 25 +FBgn0000109:002 31 +FBgn0000109:003 11 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 0 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 38 +FBgn0000115:002 96 +FBgn0000115:003 136 +FBgn0000116:001 140 +FBgn0000116:002 0 +FBgn0000116:003 0 +FBgn0000116:004 0 +FBgn0000116:005 0 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 737 +FBgn0000117:002 237 +FBgn0000117:003 569 +FBgn0000117:004 535 +FBgn0000117:005 2428 +FBgn0000117:006 124 +FBgn0000117:007 3 +FBgn0000117:008 13 +FBgn0000117:009 64 +FBgn0000117:010 31 +FBgn0000119:001 57 +FBgn0000119:002 35 +FBgn0000119:003 11 +FBgn0000119:004 13 +FBgn0000119:005 168 +FBgn0000119:006 8 +FBgn0000119:007 1 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 1 +FBgn0000121:002 1 +FBgn0000121:003 1 +FBgn0000137:001 0 +FBgn0000139:001 1 +FBgn0000139:002 0 +FBgn0000139:003 2 +FBgn0000139:004 5 +FBgn0000139:005 18 +FBgn0000139:006 21 +FBgn0000139:007 19 +FBgn0000139:008 116 +FBgn0000139:009 94 +FBgn0000140:001 5 +FBgn0000140:002 21 +FBgn0000140:003 23 +FBgn0000140:004 241 +FBgn0000140:005 13 +FBgn0000140:006 22 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/dexseq.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dexseq.gtf Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,397 @@\n+2L\tdexseq_prepare_annotation.py\taggregate_gene\t378112\t387439\t.\t+\t.\tgene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t378112\t378481\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "001"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t384511\t384894\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "002"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t385701\t385746\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "003"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t386308\t386576\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "004"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t386703\t387439\t.\t+\t.\ttranscripts "FBtr0078053"; exonic_part_number "005"; gene_id "FBgn0000061"\n+2L\tdexseq_prepare_annotation.py\taggregate_gene\t2156484\t2178749\t.\t-\t.\tgene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2156484\t2156791\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0077850+FBtr0077851"; exonic_part_number "001"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2156792\t2157426\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330659+FBtr0077850+FBtr0077851"; exonic_part_number "002"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2157427\t2158405\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330660+FBtr0077850+FBtr0077851+FBtr0330659"; exonic_part_number "003"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2158468\t2159245\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330660+FBtr0077850+FBtr0077851+FBtr0330659"; exonic_part_number "004"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2159312\t2160582\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330660+FBtr0077850+FBtr0077851+FBtr0330659"; exonic_part_number "005"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2161010\t2161232\t.\t-\t.\ttranscripts "FBtr0330659"; exonic_part_number "006"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2161233\t2161522\t.\t-\t.\ttranscripts "FBtr0330659+FBtr0077851"; exonic_part_number "007"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2171142\t2171198\t.\t-\t.\ttranscripts "FBtr0330658"; exonic_part_number "008"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t2177847\t2178749\t.\t-\t.\ttranscripts "FBtr0330658+FBtr0330660+FBtr0077850"; exonic_part_number "009"; gene_id "FBgn0000097"\n+2L\tdexseq_prepare_annotation.py\taggregate_gene\t6041178\t6045970\t.\t-\t.\tgene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6041178\t6042011\t.\t-\t.\ttranscripts "FBtr0079219+FBtr0079221+FBtr0079220"; exonic_part_number "001"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6042075\t6044351\t.\t-\t.\ttranscripts "FBtr0079219+FBtr0079221+FBtr0079220"; exonic_part_number "002"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6044428\t6045526\t.\t-\t.\ttranscripts "FBtr0079219+FBtr0079221+FBtr0079220"; exonic_part_number "003"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6045527\t6045593\t.\t-\t.\ttranscripts "FBtr0079221"; exonic_part_number "004"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6045894\t6045920\t.\t-\t.\ttranscripts "FBtr0079219"; exonic_part_number "005"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t6045921\t6045970\t.\t-\t.\ttranscripts "FBtr0079219+FBtr0079220"; exonic_part_number "006"; gene_id "FBgn0000052"\n+2L\tdexseq_prepare_annotation.py\taggregate_gene\t7014861\t7023940\t.\t-\t.\tgene_id "FBgn0000053"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t7014861\t7016374\t.\t-\t.\ttranscripts "FBtr0079431"; exonic_part_number "001"; gene_id "FBgn0000053"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t7016437\t7017486\t.\t-\t.\ttranscripts "FBtr0079431"; exonic_part_number "002"; gene_id "FBgn0000053"\n+2L\tdexseq_prepare_annotation.py\texonic_part\t7017545\t7017966\t.\t-\t.\ttranscripts "FBtr0079431"; exonic_part_number "003"; gene_id "FBgn0000053"\n+2L\tdexseq_prepare_annotation.py\tex'..b'number "001"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15246367\t15246389\t.\t-\t.\ttranscripts "FBtr0100328+FBtr0305191"; exonic_part_number "002"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15246390\t15247200\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "003"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15247258\t15247415\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "004"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15247416\t15247421\t.\t-\t.\ttranscripts "FBtr0074015+FBtr0305196+FBtr0305191+FBtr0305193+FBtr0305192"; exonic_part_number "005"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15248260\t15248491\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "006"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15248569\t15248709\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "007"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15248788\t15248965\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "008"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15248966\t15248986\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0074015+FBtr0100328+FBtr0290064+FBtr0290063+FBtr0305191"; exonic_part_number "009"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15265545\t15265721\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "010"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15266185\t15266241\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0074015+FBtr0305194+FBtr0305196+FBtr0100328"; exonic_part_number "011"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15271594\t15271626\t.\t-\t.\ttranscripts "FBtr0305189+FBtr0074015+FBtr0100328+FBtr0290063+FBtr0305193+FBtr0100326"; exonic_part_number "012"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\texonic_part\t15272222\t15272487\t.\t-\t.\ttranscripts "FBtr0305195+FBtr0305189+FBtr0305196+FBtr0074015+FBtr0305194+FBtr0100328+FBtr0290063+FBtr0305191+FBtr0305190+FBtr0305193+FBtr0305192+FBtr0290064+FBtr0100326"; exonic_part_number "013"; gene_id "FBgn0000028"\n+X\tdexseq_prepare_annotation.py\taggregate_gene\t20065478\t20067552\t.\t-\t.\tgene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20065478\t20065681\t.\t-\t.\ttranscripts "FBtr0070025+FBtr0301931"; exonic_part_number "001"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20065962\t20065964\t.\t-\t.\ttranscripts "FBtr0301931"; exonic_part_number "002"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20066074\t20066255\t.\t-\t.\ttranscripts "FBtr0070025+FBtr0301931"; exonic_part_number "003"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20066338\t20067049\t.\t-\t.\ttranscripts "FBtr0070025+FBtr0301931"; exonic_part_number "004"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20067402\t20067506\t.\t-\t.\ttranscripts "FBtr0070025+FBtr0301931"; exonic_part_number "005"; gene_id "FBgn0000084"\n+X\tdexseq_prepare_annotation.py\texonic_part\t20067507\t20067552\t.\t-\t.\ttranscripts "FBtr0070025"; exonic_part_number "006"; gene_id "FBgn0000084"\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/dexseq_result.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dexseq_result.tabular Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,307 @@\n+FBgn0000064:E005\tFBgn0000064\tE005\t859.822533198768\t0.00372195558605137\t110.248504159842\t1.14773467510188e-24\t1.35432691662022e-22\t27.4026942925537\t27.8806448897375\t-0.0249461825911985\t3R\t22082655\t22082854\t200\t-\t746\t952\t1227\t542\t790\t802\t722\tFBtr0085000, FBtr0085001, FBtr0084995, FBtr0084994, FBtr0306657, FBtr0114544, FBtr0310661, FBtr0310660, FBtr0084999\n+FBgn0000042:E001\tFBgn0000042\tE001\t963.266257907235\t0.0502044280160066\t57.8426706201339\t2.7518430820889e-13\t1.62358741843245e-11\t29.1456287540252\t27.7014978680248\t0.0733155376052489\tX\t5794894\t5795046\t153\t+\t3322\t262\t275\t1633\t3139\t244\t129\tFBtr0100662, FBtr0100663, FBtr0070822\n+FBgn0000064:E002\tFBgn0000064\tE002\t7.3266084748515\t0.01707286192962\t53.7309384372156\t2.15018072623491e-12\t8.45737752319066e-11\t4.55458396475058\t4.34353926561023\t0.0684481985350057\t3R\t22080926\t22081153\t228\t-\t0\t7\t12\t0\t0\t10\t12\tFBtr0310660, FBtr0084995, FBtr0084994, FBtr0084999\n+FBgn0000084:E003\tFBgn0000084\tE003\t12.7120572355022\t0.0887912514378509\t50.3598123774543\t1.16012740873979e-11\t3.42237585578239e-10\t5.99959570586144\t6.06694051770199\t-0.0161038815249051\tX\t20066074\t20066255\t182\t-\t0\t16\t13\t0\t0\t29\t11\tFBtr0070025, FBtr0301931\n+FBgn0000042:E005\tFBgn0000042\tE005\t33.8277404051372\t0.008826686875382\t36.1644112317346\t1.40280685802709e-08\t3.31062418494392e-07\t9.58147265579643\t11.2091577033539\t-0.226358555041545\tX\t5798498\t5798821\t324\t+\t119\t20\t29\t45\t52\t14\t8\tFBtr0100662, FBtr0070823\n+FBgn0000032:E005\tFBgn0000032\tE005\t50.5080907808574\t0.00493456081981282\t35.1634122191381\t2.31399307099611e-08\t4.55085303962568e-07\t11.1453896842345\t11.6791120638017\t-0.0674835341219757\t3R\t25818551\t25818649\t99\t-\t42\t53\t56\t38\t55\t45\t53\tFBtr0085609, FBtr0085610\n+FBgn0000117:E003\tFBgn0000117\tE003\t651.648249450539\t0.00617415865170719\t33.5894584912735\t5.08325344394025e-08\t8.56891294835643e-07\t25.5863609644879\t26.3587665612206\t-0.0429078882881053\tX\t1788541\t1788813\t273\t-\t676\t728\t799\t493\t606\t574\t569\tFBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988\n+FBgn0000117:E004\tFBgn0000117\tE004\t566.705805129229\t0.00367009391373741\t30.8789228540862\t1.97118369737245e-07\t2.90749595362437e-06\t25.2478976953119\t24.8237303978564\t0.0244433312224853\tX\t1788874\t1789074\t201\t-\t541\t507\t690\t417\t761\t498\t535\tFBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988\n+FBgn0000042:E003\tFBgn0000042\tE003\t37923.6657937205\t0.0385740484752454\t28.7151085239498\t5.81558503594718e-07\t7.62487815824186e-06\t51.6463704239338\t51.5494314550159\t0.0027104476793924\tX\t5796723\t5798206\t1484\t+\t53623\t37301\t41337\t47230\t50144\t22833\t26327\tFBtr0100662, FBtr0100663, FBtr0070822, FBtr0070823\n+FBgn0000084:E006\tFBgn0000084\tE006\t59.8440945905321\t0.0201537492391107\t22.1992448368148\t1.51180310325524e-05\t0.000178392766184118\t12.7814564102042\t12.4783532683405\t0.0346246780719152\tX\t20067507\t20067552\t46\t-\t132\t23\t34\t71\t150\t35\t46\tFBtr0070025\n+FBgn0000017:E004\tFBgn0000017\tE004\t118.685044393895\t0.00902890492864188\t19.2111031647923\t6.7353776603016e-05\t0.000722522330832353\t15.8860792124228\t15.4507867306171\t0.0400828022658053\t3L\t16619373\t16619627\t255\t-\t103\t108\t87\t107\t162\t144\t104\tFBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130\n+FBgn0000042:E004\tFBgn0000042\tE004\t2902.21264539337\t0.041061850909975\t18.8599314844935\t8.02819501685372e-05\t0.00076717563289585\t36.0570377531486\t34.5088537532999\t0.0633143238060254\tX\t5798207\t5798497\t291\t+\t7007\t1635\t1666\t3678\t8835\t1202\t1091\tFBtr0100662, FBtr0100663, FBtr0070823\n+FBgn0000140:E002\tFBgn0000140\tE002\t24.0938527740886\t0.00618959397365643\t18.7570601259765\t8.4519349386831e-05\t0.00076717563289585\t8.79238345032345\t7.87199695631269\t0.159524643103097\t3R\t20579850\t20580026\t177\t+\t19\t23\t22\t24\t32\t25\t21\tFBtr0084692\n+FBgn0000117:E001\tFBgn0000117\tE001\t1110.87821042994\t0.00661398986859128\t18.1779217088585\t0.000112905332661573\t0.00095163066100469\t29.2452591928804\t29.4965680787519\t-0.0123443315343086\tX\t1785434\t1786152\t719\t-\t1892\t943\t1111\t1063\t2137\t670\t737\tFBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988\n+FBgn0000064:E011'..b'A\tNA\tNA\tNA\tNA\tNA\t2L\t12310682\t12311093\t412\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n+FBgn0000114:E019\tFBgn0000114\tE019\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12311094\t12311104\t11\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331645, FBtr0080347, FBtr0331998\n+FBgn0000116:E002\tFBgn0000116\tE002\t0.0883366573889214\t0.282766465728211\t2.01127325191983\t0.365811675448866\tNA\t1.07827840605447\t0.0146951570997782\t6.19724513023531\t3L\t9044230\t9044817\t588\t-\t0\t0\t0\t0\t1\t0\t0\tFBtr0331550, FBtr0076546\n+FBgn0000116:E003\tFBgn0000116\tE003\t0.40181652404165\t0.0974629307398967\t6.02870700146762\t0.0490775538355085\tNA\t1.87262787701226\t0.887825140243837\t1.07671677337537\t3L\t9044818\t9045001\t184\t-\t1\t0\t0\t1\t2\t0\t0\tFBtr0076546\n+FBgn0000116:E004\tFBgn0000116\tE004\t0.15316821713762\t0.296390832816979\t1.1371386880015\t0.566335090089352\tNA\t0.0201916309542209\t0.901324736307787\t-5.48021763271138\t3L\t9046620\t9046661\t42\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0331550\n+FBgn0000116:E005\tFBgn0000116\tE005\t1.25599426711867\t0.510503716927147\t0.324279389152636\t0.850322410814094\tNA\t2.0761033293771\t2.24393157600357\t-0.112150435045726\t3L\t9050643\t9050681\t39\t-\t1\t0\t5\t1\t3\t0\t0\tFBtr0076545\n+FBgn0000116:E006\tFBgn0000116\tE006\t0.15316821713762\t0.296390832816979\t1.1371386880015\t0.566335090089352\tNA\t0.0201916309542209\t0.901324736307787\t-5.48021763271138\t3L\t9055007\t9055567\t561\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0076543, FBtr0076544\n+FBgn0000116:E007\tFBgn0000116\tE007\t0\tNA\tNA\tNA\tNA\t0.0201921726660679\t0.014692887224756\t0.458678231732963\t3L\t9055912\t9056048\t137\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0076544\n+FBgn0000116:E008\tFBgn0000116\tE008\t0.205235479273134\t0.288940762923654\t3.11971830829101\t0.210165670079664\tNA\t1.11038521915022\t0.0146952088058185\t6.2395706000068\t3L\t9057564\t9057617\t54\t-\t0\t0\t0\t0\t0\t1\t0\tFBtr0112791, FBtr0076543\n+FBgn0000117:E007\tFBgn0000117\tE007\t4.5734995655629\t0.069980253920095\t3.3362555894048\t0.188599832915634\tNA\t4.25024580229025\t4.13730637770574\t0.0388544816644843\tX\t1793337\t1793413\t77\t-\t10\t5\t2\t3\t15\t1\t3\tFBtr0332583\n+FBgn0000119:E007\tFBgn0000119\tE007\t2.5085164052321\t0.026869378720391\t6.44202453635987\t0.0399146334903555\tNA\t3.59815529575842\t2.3653275825246\t0.605217453095769\t2R\t9370660\t9370723\t64\t-\t3\t2\t0\t6\t8\t1\t1\tFBtr0087702\n+FBgn0000120:E001\tFBgn0000120\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18078269\t18078496\t228\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n+FBgn0000120:E002\tFBgn0000120\tE002\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18078916\t18079723\t808\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n+FBgn0000120:E003\tFBgn0000120\tE003\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18079957\t18080086\t130\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n+FBgn0000120:E004\tFBgn0000120\tE004\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18080147\t18080415\t269\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n+FBgn0000121:E001\tFBgn0000121\tE001\t1.0078404227901\t0.0813154020717312\t4.34385793851407\t0.11395758408448\tNA\tNA\tNA\tNA\t3L\t8640361\t8640745\t385\t-\t4\t0\t1\t0\t1\t1\t1\tFBtr0076599\n+FBgn0000121:E002\tFBgn0000121\tE002\t1.2324267524932\t0.164974109301381\t0.172760800185486\t0.91724524467096\tNA\tNA\tNA\tNA\t3L\t8640808\t8641002\t195\t-\t2\t1\t0\t3\t1\t1\t1\tFBtr0076599\n+FBgn0000121:E003\tFBgn0000121\tE003\t2.30524126345099\t0.0717993341520124\t4.19882575909892\t0.122528346036444\tNA\tNA\tNA\tNA\t3L\t8641070\t8642036\t967\t-\t2\t0\t1\t3\t11\t2\t1\tFBtr0076599\n+FBgn0000137:E001\tFBgn0000137\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tX\t354533\t357209\t2677\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0070075\n+FBgn0000139:E001\tFBgn0000139\tE001\t0.187795396756122\t0.28662869942016\t1.95879645587128\t0.375537018555398\tNA\t0.879924294236769\t0.212535063477741\t2.04967853146798\t3R\t20475810\t20476066\t257\t+\t0\t0\t0\t0\t0\t0\t1\tFBtr0084660\n+FBgn0000139:E002\tFBgn0000139\tE002\t1.96739811366688\t0.133921979075896\t2.6487965202692\t0.265962951457817\tNA\t2.65120798807141\t2.93475897219182\t-0.146592167088059\t3R\t20476127\t20476311\t185\t+\t4\t3\t0\t2\t7\t1\t0\tFBtr0084660\n+FBgn0000139:E003\tFBgn0000139\tE003\t3.61191788404307\t0.0548308983756597\t4.22287462031892\t0.121063835042901\tNA\t3.56858441566967\t3.96107908395784\t-0.150541605141237\t3R\t20476372\t20476716\t345\t+\t8\t4\t1\t3\t12\t1\t2\tFBtr0084660\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/flattened.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flattened.gtf Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,257 @@\n+4\tdexseq_prepare_annotation.py\taggregate_gene\t68336\t77667\t.\t-\t.\tgene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t68336\t71088\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "001"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71142\t71239\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "002"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71240\t71306\t.\t-\t.\ttranscripts "FBtr0306168+FBtr0089178"; exonic_part_number "003"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71371\t71883\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "004"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71940\t72580\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "005"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t72643\t73010\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "006"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76457\t76916\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178"; exonic_part_number "007"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76917\t76957\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "008"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76958\t77667\t.\t-\t.\ttranscripts "FBtr0306168"; exonic_part_number "009"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\taggregate_gene\t137015\t150380\t.\t-\t.\tgene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t137015\t137256\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "001"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t137312\t139127\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "002"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t139181\t139405\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "003"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t139464\t139557\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "004"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t140514\t140838\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "005"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t141484\t142425\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "006"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t142479\t142582\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "007"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t142935\t144048\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "008"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t144411\t144518\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "009"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t149948\t150068\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "010"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t150069\t150078\t.\t-\t.\ttranscripts "FBtr0089173"; exonic_part_number "011"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t150181\t150353\t.\t-\t.\ttranscripts "FBtr0089172"; exonic_part_number "012"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\texonic_part\t150354\t150380\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089171"; exonic_part_number "013"; gene_id "FBgn0011747"\n+4\tdexseq_prepare_annotation.py\taggregate_gene\t522436\t560418\t.\t+\t.\tgene_id "FBgn0004607"\n+4\tdexseq_prepare_annotation.py\texonic_part\t522436\t522483\t.\t+\t.\ttranscripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "001"; gene_id "FBgn0004607"\n+4\tdexseq_prepare_annotation.py\texonic_part\t524477\t524764\t.\t+\t.\ttranscripts "FBtr0332913+FBtr'..b'nnotation.py\taggregate_gene\t6055\t6118\t.\t+\t.\tgene_id "FBgn0013704"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6055\t6118\t.\t+\t.\ttranscripts "FBtr0100872"; exonic_part_number "001"; gene_id "FBgn0013704"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6119\t6183\t.\t+\t.\tgene_id "FBgn0013701"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6119\t6183\t.\t+\t.\ttranscripts "FBtr0100873"; exonic_part_number "001"; gene_id "FBgn0013701"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6184\t6251\t.\t+\t.\tgene_id "FBgn0013705"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6184\t6251\t.\t+\t.\ttranscripts "FBtr0100874"; exonic_part_number "001"; gene_id "FBgn0013705"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6252\t6318\t.\t+\t.\tgene_id "FBgn0013692"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6252\t6318\t.\t+\t.\ttranscripts "FBtr0100875"; exonic_part_number "001"; gene_id "FBgn0013692"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6337\t6401\t.\t-\t.\tgene_id "FBgn0013693"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6337\t6401\t.\t-\t.\ttranscripts "FBtr0100876"; exonic_part_number "001"; gene_id "FBgn0013693"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t6402\t8124\t.\t-\t.\tgene_id "FBgn0013684"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t6402\t8124\t.\t-\t.\ttranscripts "FBtr0100877"; exonic_part_number "001"; gene_id "FBgn0013684"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t8140\t8205\t.\t-\t.\tgene_id "FBgn0013695"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t8140\t8205\t.\t-\t.\ttranscripts "FBtr0100878"; exonic_part_number "001"; gene_id "FBgn0013695"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9837\t9902\t.\t+\t.\tgene_id "FBgn0013707"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9837\t9902\t.\t+\t.\ttranscripts "FBtr0100881"; exonic_part_number "001"; gene_id "FBgn0013707"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9903\t9963\t.\t-\t.\tgene_id "FBgn0013702"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9903\t9963\t.\t-\t.\ttranscripts "FBtr0100882"; exonic_part_number "001"; gene_id "FBgn0013702"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9970\t10494\t.\t+\t.\tgene_id "FBgn0013685"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9970\t10494\t.\t+\t.\ttranscripts "FBtr0100883"; exonic_part_number "001"; gene_id "FBgn0013685"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t10498\t11634\t.\t+\t.\tgene_id "FBgn0013678"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t10498\t11634\t.\t+\t.\ttranscripts "FBtr0100884"; exonic_part_number "001"; gene_id "FBgn0013678"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t11637\t11702\t.\t+\t.\tgene_id "FBgn0013706"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t11637\t11702\t.\t+\t.\ttranscripts "FBtr0100885"; exonic_part_number "001"; gene_id "FBgn0013706"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t11720\t12658\t.\t-\t.\tgene_id "FBgn0013679"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t11720\t12658\t.\t-\t.\ttranscripts "FBtr0100886"; exonic_part_number "001"; gene_id "FBgn0013679"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t12669\t12733\t.\t-\t.\tgene_id "FBgn0013698"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t12669\t12733\t.\t-\t.\ttranscripts "FBtr0100887"; exonic_part_number "001"; gene_id "FBgn0013698"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t14131\t14916\t.\t-\t.\tgene_id "FBgn0013688"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t14131\t14916\t.\t-\t.\ttranscripts "FBtr0100890"; exonic_part_number "001"; gene_id "FBgn0013688"\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/original.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/original.gtf Thu Oct 08 16:52:01 2015 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\n+dmel_mitochondrion_genome\ttRNA\texon\t1\t65\t.\t+\t.\tgene_id "FBgn0013696"; transcript_id "FBtr0100854"; exon_number "1"; gene_name "mt:tRNA:I"; gene_biotype "tRNA"; transcript_name "mt:tRNA:I-RA"; exon_id "FBgn0013696:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t97\t165\t.\t-\t.\tgene_id "FBgn0013703"; transcript_id "FBtr0100855"; exon_number "1"; gene_name "mt:tRNA:Q"; gene_biotype "tRNA"; transcript_name "mt:tRNA:Q-RA"; exon_id "FBgn0013703:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t171\t239\t.\t+\t.\tgene_id "FBgn0013700"; transcript_id "FBtr0100856"; exon_number "1"; gene_name "mt:tRNA:M"; gene_biotype "tRNA"; transcript_name "mt:tRNA:M-RA"; exon_id "FBgn0013700:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t1322\t1383\t.\t-\t.\tgene_id "FBgn0013690"; transcript_id "FBtr0100859"; exon_number "1"; gene_name "mt:tRNA:C"; gene_biotype "tRNA"; transcript_name "mt:tRNA:C-RA"; exon_id "FBgn0013690:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t1403\t1468\t.\t-\t.\tgene_id "FBgn0013710"; transcript_id "FBtr0100860"; exon_number "1"; gene_name "mt:tRNA:Y"; gene_biotype "tRNA"; transcript_name "mt:tRNA:Y-RA"; exon_id "FBgn0013710:1";\n+dmel_mitochondrion_genome\tprotein_coding\texon\t1474\t3009\t.\t+\t.\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA"; exon_id "FBgn0013674:1";\n+dmel_mitochondrion_genome\tprotein_coding\tCDS\t1474\t3006\t.\t+\t0\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA"; protein_id "FBpp0100176";\n+dmel_mitochondrion_genome\tprotein_coding\tstop_codon\t3007\t3009\t.\t+\t0\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA";\n+dmel_mitochondrion_genome\ttRNA\texon\t3012\t3077\t.\t+\t.\tgene_id "FBgn0013699"; transcript_id "FBtr0100862"; exon_number "1"; gene_name "mt:tRNA:L:UUR"; gene_biotype "tRNA"; transcript_name "mt:tRNA:L:UUR-RA"; exon_id "FBgn0013699:1";\n+dmel_mitochondrion_genome\tprotein_coding\texon\t3083\t3767\t.\t+\t.\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA"; exon_id "FBgn0013675:1";\n+dmel_mitochondrion_genome\tprotein_coding\tCDS\t3083\t3767\t.\t+\t0\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA"; protein_id "FBpp0100177";\n+dmel_mitochondrion_genome\tprotein_coding\tstart_codon\t3083\t3085\t.\t+\t0\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA";\n+dmel_mitochondrion_genome\ttRNA\texon\t3768\t3838\t.\t+\t.\tgene_id "FBgn0013697"; transcript_id "FBtr0100864"; exon_number "1"; gene_name "mt:tRNA:K"; gene_biotype "tRNA"; transcript_name "mt:tRNA:K-RA"; exon_id "FBgn0013697:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t3840\t3906\t.\t+\t.\tgene_id "FBgn0013691"; transcript_id "FBtr0100865"; exon_number "1"; gene_name "mt:tRNA:D"; gene_biotype "tRNA"; transcript_name "mt:tRNA:D-RA"; exon_id "FBgn0013691:1";\n+dmel_mitochondrion_genome\ttRNA\texon\t5543\t5607\t.\t+\t.\tgene_id "FBgn0013694"; transcript_id "FBtr0100869"; exon_number "1"; gene_name "mt:tRNA:G"; gene_biotype "tRNA"; transcript_name "mt:tRNA:G-RA"; exon_id "FBgn0013694:1";\n+dmel_mitochondrion_genome\tprotein_coding\texon\t5608\t5961\t.\t+\t.\tgene_id "FBgn0013681"; transcript_id "FBtr0100870"; exon_number "1"; gene_name "mt:ND3"; gene_biotype "protein_coding"; transcript_name "mt:ND3-RA"; exon_id "FBgn0013681:1";\n+dmel_mitochondrion_genome\tprotein_coding\tCDS\t5608\t5958\t.\t+\t0\tgene_id "FBgn0013681"; transcript_id "FBtr0100870"; exon_number "1"; gene_name "mt:ND3"; gene_biotype "protein_coding"; transcript_name "mt:ND3-RA"; protein_id "FBpp0100181";\n+dmel_mitochondrion_genome\tprotein_coding\tstop_codon\t5959\t5961\t.\t+\t0\tgene_id "FBgn0013681"; transcript_id "FBt'..b'FBgn0005561:7";\n+4\tprotein_coding\tCDS\t1124161\t1124358\t.\t+\t1\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "6"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1126778\t1127223\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "7"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:8";\n+4\tprotein_coding\tCDS\t1126778\t1127223\t.\t+\t1\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "7"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1128325\t1128416\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "8"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:9";\n+4\tprotein_coding\tCDS\t1128325\t1128416\t.\t+\t2\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "8"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1128724\t1128970\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "9"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:10";\n+4\tprotein_coding\tCDS\t1128724\t1128970\t.\t+\t0\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "9"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1129100\t1129198\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "10"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:11";\n+4\tprotein_coding\tCDS\t1129100\t1129198\t.\t+\t2\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "10"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1131407\t1131514\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "11"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:15";\n+4\tprotein_coding\tCDS\t1131407\t1131514\t.\t+\t2\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "11"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\texon\t1131914\t1133943\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "12"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; exon_id "FBgn0005561:17";\n+4\tprotein_coding\tCDS\t1131914\t1132074\t.\t+\t2\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "12"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD"; protein_id "FBpp0099747";\n+4\tprotein_coding\tstop_codon\t1132075\t1132077\t.\t+\t0\tgene_id "FBgn0005561"; transcript_id "FBtr0100342"; exon_number "12"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RD";\n+4\tprotein_coding\texon\t1109444\t1109688\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "1"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE"; exon_id "FBgn0005561:1";\n+4\tprotein_coding\texon\t1112885\t1113254\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "2"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE"; exon_id "FBgn0005561:2";\n+4\tprotein_coding\tCDS\t1112912\t1113254\t.\t+\t0\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "2"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE"; protein_id "FBpp0099748";\n+4\tprotein_coding\tstart_codon\t1112912\t1112914\t.\t+\t0\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "2"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE";\n+4\tprotein_coding\texon\t1116202\t1116342\t.\t+\t.\tgene_id "FBgn0005561"; transcript_id "FBtr0100343"; exon_number "3"; gene_name "sv"; gene_biotype "protein_coding"; transcript_name "sv-RE"; exon_id "FBgn0005561:3";\n' |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/treated1fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treated1fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 0 +FBgn0000008:004 1 +FBgn0000008:005 4 +FBgn0000008:006 1 +FBgn0000008:007 18 +FBgn0000008:008 4 +FBgn0000008:009 16 +FBgn0000008:010 17 +FBgn0000008:011 2 +FBgn0000008:012 3 +FBgn0000008:013 11 +FBgn0000008:014 1 +FBgn0000014:001 1 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 1 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 1 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 0 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 1564 +FBgn0000017:002 47 +FBgn0000017:003 60 +FBgn0000017:004 103 +FBgn0000017:005 296 +FBgn0000017:006 226 +FBgn0000017:007 263 +FBgn0000017:008 5 +FBgn0000017:009 623 +FBgn0000018:001 152 +FBgn0000018:002 217 +FBgn0000022:001 0 +FBgn0000024:001 2 +FBgn0000024:002 0 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 1 +FBgn0000024:006 0 +FBgn0000024:007 0 +FBgn0000024:008 0 +FBgn0000024:009 1 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 213 +FBgn0000032:003 152 +FBgn0000032:004 385 +FBgn0000032:005 42 +FBgn0000032:006 79 +FBgn0000032:007 5 +FBgn0000032:008 12 +FBgn0000032:009 54 +FBgn0000036:001 1 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 9 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 1 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 3322 +FBgn0000042:002 286 +FBgn0000042:003 53623 +FBgn0000042:004 7007 +FBgn0000042:005 119 +FBgn0000043:001 27313 +FBgn0000043:002 1145 +FBgn0000045:001 0 +FBgn0000045:002 2 +FBgn0000045:003 6 +FBgn0000046:001 1 +FBgn0000046:002 0 +FBgn0000046:003 35 +FBgn0000047:001 0 +FBgn0000047:002 7 +FBgn0000047:003 1 +FBgn0000052:001 266 +FBgn0000052:002 1005 +FBgn0000052:003 343 +FBgn0000052:004 3 +FBgn0000052:005 12 +FBgn0000052:006 18 +FBgn0000053:001 414 +FBgn0000053:002 295 +FBgn0000053:003 117 +FBgn0000053:004 13 +FBgn0000053:005 77 +FBgn0000053:006 368 +FBgn0000053:007 140 +FBgn0000053:008 179 +FBgn0000054:001 56 +FBgn0000054:002 3 +FBgn0000054:003 10 +FBgn0000054:004 66 +FBgn0000054:005 112 +FBgn0000054:006 295 +FBgn0000057:001 210 +FBgn0000057:002 303 +FBgn0000061:001 0 +FBgn0000061:002 0 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 2 +FBgn0000063:001 52 +FBgn0000063:002 156 +FBgn0000063:003 104 +FBgn0000063:004 71 +FBgn0000064:001 1709 +FBgn0000064:002 0 +FBgn0000064:003 167 +FBgn0000064:004 74 +FBgn0000064:005 746 +FBgn0000064:006 3729 +FBgn0000064:007 74 +FBgn0000064:008 33 +FBgn0000064:009 5 +FBgn0000064:010 10 +FBgn0000064:011 154 +FBgn0000071:001 0 +FBgn0000071:002 57 +FBgn0000071:003 16 +FBgn0000071:004 460 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 1 +FBgn0000075:004 1 +FBgn0000077:001 179 +FBgn0000078:001 10 +FBgn0000079:001 44 +FBgn0000083:001 36 +FBgn0000083:002 63 +FBgn0000083:003 119 +FBgn0000083:004 2447 +FBgn0000083:005 567 +FBgn0000083:006 474 +FBgn0000083:007 60 +FBgn0000083:008 317 +FBgn0000084:001 144 +FBgn0000084:002 0 +FBgn0000084:003 0 +FBgn0000084:004 767 +FBgn0000084:005 307 +FBgn0000084:006 132 +FBgn0000092:001 6 +FBgn0000092:002 7 +FBgn0000092:003 3 +FBgn0000094:001 17 +FBgn0000094:002 9 +FBgn0000097:001 1032 +FBgn0000097:002 517 +FBgn0000097:003 725 +FBgn0000097:004 72 +FBgn0000097:005 436 +FBgn0000099:001 0 +FBgn0000099:002 1 +FBgn0000099:003 1 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 16 +FBgn0000100:002 1225 +FBgn0000100:003 14672 +FBgn0000108:001 4 +FBgn0000108:002 3 +FBgn0000108:003 0 +FBgn0000108:004 4 +FBgn0000108:005 8 +FBgn0000108:006 4 +FBgn0000108:007 0 +FBgn0000108:008 5 +FBgn0000108:009 2 +FBgn0000108:010 1 +FBgn0000108:011 13 +FBgn0000109:001 68 +FBgn0000109:002 57 +FBgn0000109:003 32 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 1 +FBgn0000114:011 0 +FBgn0000114:012 1 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 88 +FBgn0000115:002 156 +FBgn0000115:003 236 +FBgn0000116:001 558 +FBgn0000116:002 0 +FBgn0000116:003 1 +FBgn0000116:004 0 +FBgn0000116:005 1 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 1892 +FBgn0000117:002 259 +FBgn0000117:003 676 +FBgn0000117:004 541 +FBgn0000117:005 4350 +FBgn0000117:006 198 +FBgn0000117:007 10 +FBgn0000117:008 53 +FBgn0000117:009 102 +FBgn0000117:010 87 +FBgn0000119:001 126 +FBgn0000119:002 55 +FBgn0000119:003 21 +FBgn0000119:004 20 +FBgn0000119:005 264 +FBgn0000119:006 31 +FBgn0000119:007 3 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 4 +FBgn0000121:002 2 +FBgn0000121:003 2 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 4 +FBgn0000139:003 8 +FBgn0000139:004 14 +FBgn0000139:005 18 +FBgn0000139:006 44 +FBgn0000139:007 12 +FBgn0000139:008 130 +FBgn0000139:009 92 +FBgn0000140:001 14 +FBgn0000140:002 19 +FBgn0000140:003 27 +FBgn0000140:004 717 +FBgn0000140:005 51 +FBgn0000140:006 67 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/treated2fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treated2fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 1 +FBgn0000008:004 0 +FBgn0000008:005 1 +FBgn0000008:006 0 +FBgn0000008:007 8 +FBgn0000008:008 1 +FBgn0000008:009 17 +FBgn0000008:010 17 +FBgn0000008:011 0 +FBgn0000008:012 0 +FBgn0000008:013 1 +FBgn0000008:014 0 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 0 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 806 +FBgn0000017:002 29 +FBgn0000017:003 55 +FBgn0000017:004 108 +FBgn0000017:005 210 +FBgn0000017:006 135 +FBgn0000017:007 128 +FBgn0000017:008 1 +FBgn0000017:009 200 +FBgn0000018:001 41 +FBgn0000018:002 109 +FBgn0000022:001 0 +FBgn0000024:001 0 +FBgn0000024:002 1 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 1 +FBgn0000024:008 0 +FBgn0000024:009 2 +FBgn0000024:010 0 +FBgn0000024:011 1 +FBgn0000024:012 0 +FBgn0000028:001 1 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 67 +FBgn0000032:003 79 +FBgn0000032:004 165 +FBgn0000032:005 53 +FBgn0000032:006 62 +FBgn0000032:007 3 +FBgn0000032:008 11 +FBgn0000032:009 25 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 5 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 5 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 262 +FBgn0000042:002 138 +FBgn0000042:003 37301 +FBgn0000042:004 1635 +FBgn0000042:005 20 +FBgn0000043:001 15297 +FBgn0000043:002 374 +FBgn0000045:001 0 +FBgn0000045:002 3 +FBgn0000045:003 1 +FBgn0000046:001 1 +FBgn0000046:002 0 +FBgn0000046:003 16 +FBgn0000047:001 0 +FBgn0000047:002 5 +FBgn0000047:003 2 +FBgn0000052:001 187 +FBgn0000052:002 523 +FBgn0000052:003 283 +FBgn0000052:004 0 +FBgn0000052:005 2 +FBgn0000052:006 1 +FBgn0000053:001 275 +FBgn0000053:002 164 +FBgn0000053:003 77 +FBgn0000053:004 7 +FBgn0000053:005 70 +FBgn0000053:006 279 +FBgn0000053:007 123 +FBgn0000053:008 115 +FBgn0000054:001 22 +FBgn0000054:002 5 +FBgn0000054:003 5 +FBgn0000054:004 51 +FBgn0000054:005 97 +FBgn0000054:006 134 +FBgn0000057:001 129 +FBgn0000057:002 192 +FBgn0000061:001 0 +FBgn0000061:002 0 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 37 +FBgn0000063:002 89 +FBgn0000063:003 63 +FBgn0000063:004 19 +FBgn0000064:001 361 +FBgn0000064:002 7 +FBgn0000064:003 48 +FBgn0000064:004 30 +FBgn0000064:005 952 +FBgn0000064:006 2672 +FBgn0000064:007 33 +FBgn0000064:008 12 +FBgn0000064:009 2 +FBgn0000064:010 5 +FBgn0000064:011 77 +FBgn0000071:001 0 +FBgn0000071:002 24 +FBgn0000071:003 8 +FBgn0000071:004 234 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 0 +FBgn0000075:004 0 +FBgn0000077:001 85 +FBgn0000078:001 11 +FBgn0000079:001 51 +FBgn0000083:001 18 +FBgn0000083:002 24 +FBgn0000083:003 60 +FBgn0000083:004 1834 +FBgn0000083:005 413 +FBgn0000083:006 152 +FBgn0000083:007 20 +FBgn0000083:008 119 +FBgn0000084:001 41 +FBgn0000084:002 0 +FBgn0000084:003 16 +FBgn0000084:004 653 +FBgn0000084:005 96 +FBgn0000084:006 23 +FBgn0000092:001 5 +FBgn0000092:002 2 +FBgn0000092:003 0 +FBgn0000094:001 6 +FBgn0000094:002 2 +FBgn0000097:001 322 +FBgn0000097:002 327 +FBgn0000097:003 462 +FBgn0000097:004 36 +FBgn0000097:005 153 +FBgn0000099:001 0 +FBgn0000099:002 0 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 1 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 5 +FBgn0000100:002 809 +FBgn0000100:003 9830 +FBgn0000108:001 1 +FBgn0000108:002 1 +FBgn0000108:003 1 +FBgn0000108:004 2 +FBgn0000108:005 5 +FBgn0000108:006 2 +FBgn0000108:007 3 +FBgn0000108:008 8 +FBgn0000108:009 0 +FBgn0000108:010 0 +FBgn0000108:011 4 +FBgn0000109:001 10 +FBgn0000109:002 15 +FBgn0000109:003 6 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 0 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 34 +FBgn0000115:002 119 +FBgn0000115:003 140 +FBgn0000116:001 495 +FBgn0000116:002 0 +FBgn0000116:003 0 +FBgn0000116:004 0 +FBgn0000116:005 0 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 943 +FBgn0000117:002 283 +FBgn0000117:003 728 +FBgn0000117:004 507 +FBgn0000117:005 2733 +FBgn0000117:006 147 +FBgn0000117:007 5 +FBgn0000117:008 16 +FBgn0000117:009 64 +FBgn0000117:010 32 +FBgn0000119:001 62 +FBgn0000119:002 39 +FBgn0000119:003 15 +FBgn0000119:004 7 +FBgn0000119:005 142 +FBgn0000119:006 8 +FBgn0000119:007 2 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 0 +FBgn0000121:002 1 +FBgn0000121:003 0 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 3 +FBgn0000139:003 4 +FBgn0000139:004 7 +FBgn0000139:005 13 +FBgn0000139:006 29 +FBgn0000139:007 5 +FBgn0000139:008 73 +FBgn0000139:009 64 +FBgn0000140:001 9 +FBgn0000140:002 23 +FBgn0000140:003 25 +FBgn0000140:004 355 +FBgn0000140:005 37 +FBgn0000140:006 21 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/treated3fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treated3fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 1 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 0 +FBgn0000008:004 1 +FBgn0000008:005 1 +FBgn0000008:006 0 +FBgn0000008:007 7 +FBgn0000008:008 0 +FBgn0000008:009 15 +FBgn0000008:010 15 +FBgn0000008:011 2 +FBgn0000008:012 0 +FBgn0000008:013 1 +FBgn0000008:014 1 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 1 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 875 +FBgn0000017:002 29 +FBgn0000017:003 46 +FBgn0000017:004 87 +FBgn0000017:005 261 +FBgn0000017:006 183 +FBgn0000017:007 157 +FBgn0000017:008 10 +FBgn0000017:009 211 +FBgn0000018:001 62 +FBgn0000018:002 114 +FBgn0000022:001 0 +FBgn0000024:001 0 +FBgn0000024:002 0 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 0 +FBgn0000024:008 0 +FBgn0000024:009 3 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 1 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 51 +FBgn0000032:003 102 +FBgn0000032:004 234 +FBgn0000032:005 56 +FBgn0000032:006 69 +FBgn0000032:007 0 +FBgn0000032:008 4 +FBgn0000032:009 20 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 4 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 7 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 275 +FBgn0000042:002 173 +FBgn0000042:003 41337 +FBgn0000042:004 1666 +FBgn0000042:005 29 +FBgn0000043:001 16802 +FBgn0000043:002 378 +FBgn0000045:001 0 +FBgn0000045:002 6 +FBgn0000045:003 2 +FBgn0000046:001 0 +FBgn0000046:002 0 +FBgn0000046:003 17 +FBgn0000047:001 0 +FBgn0000047:002 6 +FBgn0000047:003 1 +FBgn0000052:001 161 +FBgn0000052:002 566 +FBgn0000052:003 295 +FBgn0000052:004 2 +FBgn0000052:005 7 +FBgn0000052:006 12 +FBgn0000053:001 301 +FBgn0000053:002 223 +FBgn0000053:003 91 +FBgn0000053:004 15 +FBgn0000053:005 85 +FBgn0000053:006 279 +FBgn0000053:007 127 +FBgn0000053:008 101 +FBgn0000054:001 27 +FBgn0000054:002 4 +FBgn0000054:003 7 +FBgn0000054:004 68 +FBgn0000054:005 115 +FBgn0000054:006 161 +FBgn0000057:001 116 +FBgn0000057:002 195 +FBgn0000061:001 0 +FBgn0000061:002 0 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 25 +FBgn0000063:002 97 +FBgn0000063:003 62 +FBgn0000063:004 19 +FBgn0000064:001 542 +FBgn0000064:002 12 +FBgn0000064:003 93 +FBgn0000064:004 39 +FBgn0000064:005 1227 +FBgn0000064:006 3078 +FBgn0000064:007 39 +FBgn0000064:008 18 +FBgn0000064:009 0 +FBgn0000064:010 3 +FBgn0000064:011 97 +FBgn0000071:001 0 +FBgn0000071:002 18 +FBgn0000071:003 7 +FBgn0000071:004 286 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 0 +FBgn0000075:004 1 +FBgn0000077:001 89 +FBgn0000078:001 11 +FBgn0000079:001 53 +FBgn0000083:001 23 +FBgn0000083:002 32 +FBgn0000083:003 55 +FBgn0000083:004 2126 +FBgn0000083:005 615 +FBgn0000083:006 158 +FBgn0000083:007 15 +FBgn0000083:008 178 +FBgn0000084:001 40 +FBgn0000084:002 0 +FBgn0000084:003 13 +FBgn0000084:004 748 +FBgn0000084:005 143 +FBgn0000084:006 34 +FBgn0000092:001 3 +FBgn0000092:002 4 +FBgn0000092:003 0 +FBgn0000094:001 9 +FBgn0000094:002 0 +FBgn0000097:001 349 +FBgn0000097:002 402 +FBgn0000097:003 477 +FBgn0000097:004 37 +FBgn0000097:005 131 +FBgn0000099:001 0 +FBgn0000099:002 0 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 9 +FBgn0000100:002 496 +FBgn0000100:003 10238 +FBgn0000108:001 1 +FBgn0000108:002 0 +FBgn0000108:003 0 +FBgn0000108:004 1 +FBgn0000108:005 10 +FBgn0000108:006 1 +FBgn0000108:007 1 +FBgn0000108:008 7 +FBgn0000108:009 2 +FBgn0000108:010 1 +FBgn0000108:011 2 +FBgn0000109:001 21 +FBgn0000109:002 38 +FBgn0000109:003 19 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 1 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 2 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 41 +FBgn0000115:002 129 +FBgn0000115:003 161 +FBgn0000116:001 436 +FBgn0000116:002 0 +FBgn0000116:003 0 +FBgn0000116:004 1 +FBgn0000116:005 5 +FBgn0000116:006 1 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 1111 +FBgn0000117:002 348 +FBgn0000117:003 799 +FBgn0000117:004 690 +FBgn0000117:005 3196 +FBgn0000117:006 167 +FBgn0000117:007 2 +FBgn0000117:008 19 +FBgn0000117:009 78 +FBgn0000117:010 27 +FBgn0000119:001 49 +FBgn0000119:002 39 +FBgn0000119:003 16 +FBgn0000119:004 11 +FBgn0000119:005 176 +FBgn0000119:006 9 +FBgn0000119:007 0 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 1 +FBgn0000121:002 0 +FBgn0000121:003 1 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 0 +FBgn0000139:003 1 +FBgn0000139:004 6 +FBgn0000139:005 14 +FBgn0000139:006 34 +FBgn0000139:007 9 +FBgn0000139:008 89 +FBgn0000139:009 93 +FBgn0000140:001 11 +FBgn0000140:002 22 +FBgn0000140:003 22 +FBgn0000140:004 274 +FBgn0000140:005 38 +FBgn0000140:006 26 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/untreated1fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/untreated1fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 1 +FBgn0000008:004 0 +FBgn0000008:005 2 +FBgn0000008:006 0 +FBgn0000008:007 8 +FBgn0000008:008 0 +FBgn0000008:009 18 +FBgn0000008:010 9 +FBgn0000008:011 3 +FBgn0000008:012 0 +FBgn0000008:013 5 +FBgn0000008:014 1 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 0 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 1289 +FBgn0000017:002 36 +FBgn0000017:003 48 +FBgn0000017:004 107 +FBgn0000017:005 313 +FBgn0000017:006 182 +FBgn0000017:007 167 +FBgn0000017:008 5 +FBgn0000017:009 298 +FBgn0000018:001 106 +FBgn0000018:002 182 +FBgn0000022:001 0 +FBgn0000024:001 1 +FBgn0000024:002 0 +FBgn0000024:003 0 +FBgn0000024:004 1 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 2 +FBgn0000024:008 0 +FBgn0000024:009 0 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 112 +FBgn0000032:003 115 +FBgn0000032:004 328 +FBgn0000032:005 38 +FBgn0000032:006 80 +FBgn0000032:007 4 +FBgn0000032:008 17 +FBgn0000032:009 73 +FBgn0000036:001 1 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 5 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 1 +FBgn0000037:005 1 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 1633 +FBgn0000042:002 205 +FBgn0000042:003 47230 +FBgn0000042:004 3678 +FBgn0000042:005 45 +FBgn0000043:001 15915 +FBgn0000043:002 570 +FBgn0000045:001 0 +FBgn0000045:002 4 +FBgn0000045:003 1 +FBgn0000046:001 0 +FBgn0000046:002 0 +FBgn0000046:003 5 +FBgn0000047:001 0 +FBgn0000047:002 2 +FBgn0000047:003 4 +FBgn0000052:001 277 +FBgn0000052:002 843 +FBgn0000052:003 346 +FBgn0000052:004 2 +FBgn0000052:005 10 +FBgn0000052:006 13 +FBgn0000053:001 312 +FBgn0000053:002 247 +FBgn0000053:003 96 +FBgn0000053:004 0 +FBgn0000053:005 38 +FBgn0000053:006 214 +FBgn0000053:007 74 +FBgn0000053:008 127 +FBgn0000054:001 43 +FBgn0000054:002 10 +FBgn0000054:003 8 +FBgn0000054:004 41 +FBgn0000054:005 131 +FBgn0000054:006 246 +FBgn0000057:001 165 +FBgn0000057:002 224 +FBgn0000061:001 0 +FBgn0000061:002 0 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 46 +FBgn0000063:002 103 +FBgn0000063:003 60 +FBgn0000063:004 59 +FBgn0000064:001 439 +FBgn0000064:002 0 +FBgn0000064:003 85 +FBgn0000064:004 9 +FBgn0000064:005 542 +FBgn0000064:006 2786 +FBgn0000064:007 53 +FBgn0000064:008 10 +FBgn0000064:009 0 +FBgn0000064:010 5 +FBgn0000064:011 210 +FBgn0000071:001 0 +FBgn0000071:002 3 +FBgn0000071:003 0 +FBgn0000071:004 29 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 0 +FBgn0000075:004 0 +FBgn0000077:001 167 +FBgn0000078:001 24 +FBgn0000079:001 78 +FBgn0000083:001 30 +FBgn0000083:002 57 +FBgn0000083:003 93 +FBgn0000083:004 2309 +FBgn0000083:005 536 +FBgn0000083:006 241 +FBgn0000083:007 42 +FBgn0000083:008 86 +FBgn0000084:001 12 +FBgn0000084:002 0 +FBgn0000084:003 0 +FBgn0000084:004 799 +FBgn0000084:005 186 +FBgn0000084:006 71 +FBgn0000092:001 1 +FBgn0000092:002 2 +FBgn0000092:003 0 +FBgn0000094:001 8 +FBgn0000094:002 3 +FBgn0000097:001 473 +FBgn0000097:002 386 +FBgn0000097:003 524 +FBgn0000097:004 46 +FBgn0000097:005 240 +FBgn0000099:001 0 +FBgn0000099:002 0 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 9 +FBgn0000100:002 1366 +FBgn0000100:003 12925 +FBgn0000108:001 1 +FBgn0000108:002 0 +FBgn0000108:003 1 +FBgn0000108:004 0 +FBgn0000108:005 3 +FBgn0000108:006 0 +FBgn0000108:007 0 +FBgn0000108:008 0 +FBgn0000108:009 0 +FBgn0000108:010 2 +FBgn0000108:011 1 +FBgn0000109:001 34 +FBgn0000109:002 41 +FBgn0000109:003 38 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 0 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 72 +FBgn0000115:002 121 +FBgn0000115:003 174 +FBgn0000116:001 222 +FBgn0000116:002 0 +FBgn0000116:003 1 +FBgn0000116:004 0 +FBgn0000116:005 1 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 1063 +FBgn0000117:002 72 +FBgn0000117:003 493 +FBgn0000117:004 417 +FBgn0000117:005 3198 +FBgn0000117:006 179 +FBgn0000117:007 3 +FBgn0000117:008 22 +FBgn0000117:009 105 +FBgn0000117:010 58 +FBgn0000119:001 77 +FBgn0000119:002 62 +FBgn0000119:003 15 +FBgn0000119:004 5 +FBgn0000119:005 218 +FBgn0000119:006 13 +FBgn0000119:007 6 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 0 +FBgn0000121:002 3 +FBgn0000121:003 3 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 2 +FBgn0000139:003 3 +FBgn0000139:004 3 +FBgn0000139:005 10 +FBgn0000139:006 39 +FBgn0000139:007 24 +FBgn0000139:008 133 +FBgn0000139:009 95 +FBgn0000140:001 21 +FBgn0000140:002 24 +FBgn0000140:003 29 +FBgn0000140:004 503 +FBgn0000140:005 35 +FBgn0000140:006 34 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/untreated2fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/untreated2fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 1 +FBgn0000008:004 1 +FBgn0000008:005 2 +FBgn0000008:006 0 +FBgn0000008:007 11 +FBgn0000008:008 1 +FBgn0000008:009 33 +FBgn0000008:010 20 +FBgn0000008:011 6 +FBgn0000008:012 2 +FBgn0000008:013 10 +FBgn0000008:014 2 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 1 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 2492 +FBgn0000017:002 83 +FBgn0000017:003 132 +FBgn0000017:004 162 +FBgn0000017:005 372 +FBgn0000017:006 354 +FBgn0000017:007 345 +FBgn0000017:008 3 +FBgn0000017:009 672 +FBgn0000018:001 141 +FBgn0000018:002 242 +FBgn0000022:001 1 +FBgn0000024:001 0 +FBgn0000024:002 0 +FBgn0000024:003 1 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 1 +FBgn0000024:007 2 +FBgn0000024:008 1 +FBgn0000024:009 1 +FBgn0000024:010 0 +FBgn0000024:011 1 +FBgn0000024:012 0 +FBgn0000028:001 1 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 71 +FBgn0000032:003 182 +FBgn0000032:004 450 +FBgn0000032:005 55 +FBgn0000032:006 95 +FBgn0000032:007 7 +FBgn0000032:008 35 +FBgn0000032:009 61 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 1 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 9 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 4 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 1 +FBgn0000039:010 0 +FBgn0000042:001 3139 +FBgn0000042:002 149 +FBgn0000042:003 50144 +FBgn0000042:004 8835 +FBgn0000042:005 52 +FBgn0000043:001 20887 +FBgn0000043:002 190 +FBgn0000045:001 0 +FBgn0000045:002 4 +FBgn0000045:003 6 +FBgn0000046:001 0 +FBgn0000046:002 0 +FBgn0000046:003 33 +FBgn0000047:001 0 +FBgn0000047:002 7 +FBgn0000047:003 2 +FBgn0000052:001 264 +FBgn0000052:002 1051 +FBgn0000052:003 457 +FBgn0000052:004 5 +FBgn0000052:005 15 +FBgn0000052:006 19 +FBgn0000053:001 429 +FBgn0000053:002 282 +FBgn0000053:003 93 +FBgn0000053:004 3 +FBgn0000053:005 72 +FBgn0000053:006 298 +FBgn0000053:007 190 +FBgn0000053:008 164 +FBgn0000054:001 33 +FBgn0000054:002 8 +FBgn0000054:003 16 +FBgn0000054:004 108 +FBgn0000054:005 124 +FBgn0000054:006 299 +FBgn0000057:001 229 +FBgn0000057:002 367 +FBgn0000061:001 0 +FBgn0000061:002 1 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 50 +FBgn0000063:002 184 +FBgn0000063:003 109 +FBgn0000063:004 52 +FBgn0000064:001 682 +FBgn0000064:002 0 +FBgn0000064:003 279 +FBgn0000064:004 25 +FBgn0000064:005 790 +FBgn0000064:006 4155 +FBgn0000064:007 76 +FBgn0000064:008 21 +FBgn0000064:009 4 +FBgn0000064:010 14 +FBgn0000064:011 219 +FBgn0000071:001 0 +FBgn0000071:002 10 +FBgn0000071:003 2 +FBgn0000071:004 93 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 0 +FBgn0000075:004 2 +FBgn0000077:001 196 +FBgn0000078:001 30 +FBgn0000079:001 132 +FBgn0000083:001 22 +FBgn0000083:002 29 +FBgn0000083:003 238 +FBgn0000083:004 2810 +FBgn0000083:005 584 +FBgn0000083:006 525 +FBgn0000083:007 51 +FBgn0000083:008 149 +FBgn0000084:001 73 +FBgn0000084:002 0 +FBgn0000084:003 0 +FBgn0000084:004 1087 +FBgn0000084:005 408 +FBgn0000084:006 150 +FBgn0000092:001 4 +FBgn0000092:002 6 +FBgn0000092:003 0 +FBgn0000094:001 9 +FBgn0000094:002 8 +FBgn0000097:001 887 +FBgn0000097:002 671 +FBgn0000097:003 1052 +FBgn0000097:004 50 +FBgn0000097:005 419 +FBgn0000099:001 0 +FBgn0000099:002 1 +FBgn0000099:003 0 +FBgn0000099:004 1 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 9 +FBgn0000100:002 1073 +FBgn0000100:003 20934 +FBgn0000108:001 6 +FBgn0000108:002 1 +FBgn0000108:003 1 +FBgn0000108:004 5 +FBgn0000108:005 9 +FBgn0000108:006 0 +FBgn0000108:007 5 +FBgn0000108:008 14 +FBgn0000108:009 1 +FBgn0000108:010 1 +FBgn0000108:011 14 +FBgn0000109:001 42 +FBgn0000109:002 40 +FBgn0000109:003 29 +FBgn0000114:001 0 +FBgn0000114:002 1 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 5 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 2 +FBgn0000114:011 1 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 1 +FBgn0000114:015 1 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 99 +FBgn0000115:002 183 +FBgn0000115:003 299 +FBgn0000116:001 335 +FBgn0000116:002 1 +FBgn0000116:003 2 +FBgn0000116:004 0 +FBgn0000116:005 3 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 2137 +FBgn0000117:002 287 +FBgn0000117:003 606 +FBgn0000117:004 761 +FBgn0000117:005 4668 +FBgn0000117:006 242 +FBgn0000117:007 15 +FBgn0000117:008 31 +FBgn0000117:009 107 +FBgn0000117:010 69 +FBgn0000119:001 133 +FBgn0000119:002 84 +FBgn0000119:003 13 +FBgn0000119:004 16 +FBgn0000119:005 266 +FBgn0000119:006 22 +FBgn0000119:007 8 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 1 +FBgn0000121:002 1 +FBgn0000121:003 11 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 7 +FBgn0000139:003 12 +FBgn0000139:004 10 +FBgn0000139:005 17 +FBgn0000139:006 45 +FBgn0000139:007 28 +FBgn0000139:008 199 +FBgn0000139:009 166 +FBgn0000140:001 17 +FBgn0000140:002 32 +FBgn0000140:003 20 +FBgn0000140:004 729 +FBgn0000140:005 47 +FBgn0000140:006 46 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/untreated3fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/untreated3fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 1 +FBgn0000008:003 1 +FBgn0000008:004 0 +FBgn0000008:005 0 +FBgn0000008:006 0 +FBgn0000008:007 11 +FBgn0000008:008 4 +FBgn0000008:009 21 +FBgn0000008:010 8 +FBgn0000008:011 1 +FBgn0000008:012 1 +FBgn0000008:013 5 +FBgn0000008:014 0 +FBgn0000014:001 1 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 1 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 911 +FBgn0000017:002 48 +FBgn0000017:003 83 +FBgn0000017:004 144 +FBgn0000017:005 242 +FBgn0000017:006 208 +FBgn0000017:007 176 +FBgn0000017:008 2 +FBgn0000017:009 249 +FBgn0000018:001 37 +FBgn0000018:002 98 +FBgn0000022:001 0 +FBgn0000024:001 0 +FBgn0000024:002 1 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 0 +FBgn0000024:008 0 +FBgn0000024:009 0 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 52 +FBgn0000032:003 97 +FBgn0000032:004 197 +FBgn0000032:005 45 +FBgn0000032:006 56 +FBgn0000032:007 2 +FBgn0000032:008 5 +FBgn0000032:009 10 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 3 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 0 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 244 +FBgn0000042:002 106 +FBgn0000042:003 22833 +FBgn0000042:004 1202 +FBgn0000042:005 14 +FBgn0000043:001 8188 +FBgn0000043:002 188 +FBgn0000045:001 0 +FBgn0000045:002 0 +FBgn0000045:003 1 +FBgn0000046:001 1 +FBgn0000046:002 1 +FBgn0000046:003 12 +FBgn0000047:001 0 +FBgn0000047:002 3 +FBgn0000047:003 0 +FBgn0000052:001 124 +FBgn0000052:002 505 +FBgn0000052:003 261 +FBgn0000052:004 5 +FBgn0000052:005 2 +FBgn0000052:006 2 +FBgn0000053:001 184 +FBgn0000053:002 155 +FBgn0000053:003 65 +FBgn0000053:004 3 +FBgn0000053:005 45 +FBgn0000053:006 171 +FBgn0000053:007 88 +FBgn0000053:008 57 +FBgn0000054:001 21 +FBgn0000054:002 3 +FBgn0000054:003 9 +FBgn0000054:004 37 +FBgn0000054:005 99 +FBgn0000054:006 133 +FBgn0000057:001 94 +FBgn0000057:002 172 +FBgn0000061:001 0 +FBgn0000061:002 1 +FBgn0000061:003 0 +FBgn0000061:004 0 +FBgn0000061:005 0 +FBgn0000063:001 19 +FBgn0000063:002 71 +FBgn0000063:003 54 +FBgn0000063:004 9 +FBgn0000064:001 328 +FBgn0000064:002 10 +FBgn0000064:003 77 +FBgn0000064:004 20 +FBgn0000064:005 802 +FBgn0000064:006 2022 +FBgn0000064:007 18 +FBgn0000064:008 6 +FBgn0000064:009 0 +FBgn0000064:010 1 +FBgn0000064:011 76 +FBgn0000071:001 0 +FBgn0000071:002 5 +FBgn0000071:003 1 +FBgn0000071:004 42 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 1 +FBgn0000075:004 1 +FBgn0000077:001 70 +FBgn0000078:001 16 +FBgn0000079:001 115 +FBgn0000083:001 17 +FBgn0000083:002 26 +FBgn0000083:003 36 +FBgn0000083:004 1533 +FBgn0000083:005 399 +FBgn0000083:006 133 +FBgn0000083:007 26 +FBgn0000083:008 110 +FBgn0000084:001 50 +FBgn0000084:002 0 +FBgn0000084:003 29 +FBgn0000084:004 673 +FBgn0000084:005 128 +FBgn0000084:006 35 +FBgn0000092:001 0 +FBgn0000092:002 3 +FBgn0000092:003 1 +FBgn0000094:001 7 +FBgn0000094:002 2 +FBgn0000097:001 310 +FBgn0000097:002 348 +FBgn0000097:003 491 +FBgn0000097:004 27 +FBgn0000097:005 142 +FBgn0000099:001 0 +FBgn0000099:002 1 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 3 +FBgn0000100:002 336 +FBgn0000100:003 9117 +FBgn0000108:001 5 +FBgn0000108:002 2 +FBgn0000108:003 0 +FBgn0000108:004 2 +FBgn0000108:005 5 +FBgn0000108:006 0 +FBgn0000108:007 2 +FBgn0000108:008 8 +FBgn0000108:009 3 +FBgn0000108:010 0 +FBgn0000108:011 1 +FBgn0000109:001 19 +FBgn0000109:002 26 +FBgn0000109:003 9 +FBgn0000114:001 0 +FBgn0000114:002 1 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 0 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 33 +FBgn0000115:002 82 +FBgn0000115:003 120 +FBgn0000116:001 158 +FBgn0000116:002 0 +FBgn0000116:003 0 +FBgn0000116:004 0 +FBgn0000116:005 0 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 1 +FBgn0000117:001 670 +FBgn0000117:002 232 +FBgn0000117:003 574 +FBgn0000117:004 498 +FBgn0000117:005 2293 +FBgn0000117:006 93 +FBgn0000117:007 1 +FBgn0000117:008 11 +FBgn0000117:009 37 +FBgn0000117:010 27 +FBgn0000119:001 44 +FBgn0000119:002 29 +FBgn0000119:003 7 +FBgn0000119:004 3 +FBgn0000119:005 139 +FBgn0000119:006 14 +FBgn0000119:007 1 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 1 +FBgn0000121:002 1 +FBgn0000121:003 2 +FBgn0000137:001 0 +FBgn0000139:001 0 +FBgn0000139:002 1 +FBgn0000139:003 1 +FBgn0000139:004 4 +FBgn0000139:005 5 +FBgn0000139:006 15 +FBgn0000139:007 24 +FBgn0000139:008 85 +FBgn0000139:009 87 +FBgn0000140:001 5 +FBgn0000140:002 25 +FBgn0000140:003 32 +FBgn0000140:004 250 +FBgn0000140:005 22 +FBgn0000140:006 15 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e test-data/untreated4fb.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/untreated4fb.txt Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,307 @@ +FBgn0000003:001 0 +FBgn0000008:001 0 +FBgn0000008:002 0 +FBgn0000008:003 0 +FBgn0000008:004 1 +FBgn0000008:005 1 +FBgn0000008:006 0 +FBgn0000008:007 4 +FBgn0000008:008 1 +FBgn0000008:009 10 +FBgn0000008:010 8 +FBgn0000008:011 2 +FBgn0000008:012 0 +FBgn0000008:013 0 +FBgn0000008:014 0 +FBgn0000014:001 0 +FBgn0000014:002 0 +FBgn0000014:003 0 +FBgn0000014:004 0 +FBgn0000014:005 0 +FBgn0000014:006 0 +FBgn0000014:007 0 +FBgn0000014:008 0 +FBgn0000014:009 0 +FBgn0000014:010 0 +FBgn0000015:001 0 +FBgn0000015:002 0 +FBgn0000015:003 0 +FBgn0000015:004 0 +FBgn0000015:005 0 +FBgn0000015:006 2 +FBgn0000015:007 0 +FBgn0000015:008 0 +FBgn0000015:009 0 +FBgn0000015:010 0 +FBgn0000015:011 0 +FBgn0000015:012 0 +FBgn0000017:001 820 +FBgn0000017:002 28 +FBgn0000017:003 62 +FBgn0000017:004 104 +FBgn0000017:005 237 +FBgn0000017:006 152 +FBgn0000017:007 112 +FBgn0000017:008 5 +FBgn0000017:009 191 +FBgn0000018:001 57 +FBgn0000018:002 117 +FBgn0000022:001 0 +FBgn0000024:001 0 +FBgn0000024:002 0 +FBgn0000024:003 0 +FBgn0000024:004 0 +FBgn0000024:005 0 +FBgn0000024:006 0 +FBgn0000024:007 0 +FBgn0000024:008 0 +FBgn0000024:009 0 +FBgn0000024:010 0 +FBgn0000024:011 0 +FBgn0000024:012 0 +FBgn0000028:001 0 +FBgn0000028:002 0 +FBgn0000028:003 0 +FBgn0000028:004 0 +FBgn0000028:005 0 +FBgn0000028:006 0 +FBgn0000028:007 0 +FBgn0000028:008 0 +FBgn0000028:009 0 +FBgn0000028:010 0 +FBgn0000028:011 0 +FBgn0000032:001 0 +FBgn0000032:002 51 +FBgn0000032:003 75 +FBgn0000032:004 204 +FBgn0000032:005 53 +FBgn0000032:006 64 +FBgn0000032:007 0 +FBgn0000032:008 6 +FBgn0000032:009 18 +FBgn0000036:001 0 +FBgn0000036:002 0 +FBgn0000036:003 0 +FBgn0000036:004 0 +FBgn0000036:005 0 +FBgn0000036:006 0 +FBgn0000036:007 0 +FBgn0000036:008 0 +FBgn0000036:009 0 +FBgn0000036:010 0 +FBgn0000037:001 3 +FBgn0000037:002 0 +FBgn0000037:003 0 +FBgn0000037:004 0 +FBgn0000037:005 2 +FBgn0000037:006 0 +FBgn0000038:001 0 +FBgn0000038:002 0 +FBgn0000038:003 0 +FBgn0000038:004 0 +FBgn0000038:005 0 +FBgn0000038:006 0 +FBgn0000038:007 0 +FBgn0000038:008 0 +FBgn0000039:001 0 +FBgn0000039:002 0 +FBgn0000039:003 0 +FBgn0000039:004 0 +FBgn0000039:005 0 +FBgn0000039:006 0 +FBgn0000039:007 0 +FBgn0000039:008 0 +FBgn0000039:009 0 +FBgn0000039:010 0 +FBgn0000042:001 129 +FBgn0000042:002 132 +FBgn0000042:003 26327 +FBgn0000042:004 1091 +FBgn0000042:005 8 +FBgn0000043:001 9110 +FBgn0000043:002 174 +FBgn0000045:001 0 +FBgn0000045:002 1 +FBgn0000045:003 0 +FBgn0000046:001 0 +FBgn0000046:002 0 +FBgn0000046:003 12 +FBgn0000047:001 0 +FBgn0000047:002 1 +FBgn0000047:003 1 +FBgn0000052:001 191 +FBgn0000052:002 577 +FBgn0000052:003 265 +FBgn0000052:004 1 +FBgn0000052:005 2 +FBgn0000052:006 3 +FBgn0000053:001 257 +FBgn0000053:002 176 +FBgn0000053:003 64 +FBgn0000053:004 4 +FBgn0000053:005 51 +FBgn0000053:006 181 +FBgn0000053:007 68 +FBgn0000053:008 76 +FBgn0000054:001 23 +FBgn0000054:002 4 +FBgn0000054:003 8 +FBgn0000054:004 47 +FBgn0000054:005 101 +FBgn0000054:006 134 +FBgn0000057:001 122 +FBgn0000057:002 165 +FBgn0000061:001 0 +FBgn0000061:002 1 +FBgn0000061:003 0 +FBgn0000061:004 2 +FBgn0000061:005 1 +FBgn0000063:001 23 +FBgn0000063:002 66 +FBgn0000063:003 50 +FBgn0000063:004 20 +FBgn0000064:001 303 +FBgn0000064:002 12 +FBgn0000064:003 76 +FBgn0000064:004 9 +FBgn0000064:005 722 +FBgn0000064:006 2100 +FBgn0000064:007 22 +FBgn0000064:008 11 +FBgn0000064:009 0 +FBgn0000064:010 1 +FBgn0000064:011 86 +FBgn0000071:001 0 +FBgn0000071:002 3 +FBgn0000071:003 1 +FBgn0000071:004 43 +FBgn0000075:001 0 +FBgn0000075:002 0 +FBgn0000075:003 1 +FBgn0000075:004 0 +FBgn0000077:001 92 +FBgn0000078:001 15 +FBgn0000079:001 99 +FBgn0000083:001 20 +FBgn0000083:002 27 +FBgn0000083:003 74 +FBgn0000083:004 1952 +FBgn0000083:005 524 +FBgn0000083:006 120 +FBgn0000083:007 30 +FBgn0000083:008 129 +FBgn0000084:001 45 +FBgn0000084:002 0 +FBgn0000084:003 11 +FBgn0000084:004 753 +FBgn0000084:005 138 +FBgn0000084:006 46 +FBgn0000092:001 3 +FBgn0000092:002 2 +FBgn0000092:003 2 +FBgn0000094:001 3 +FBgn0000094:002 1 +FBgn0000097:001 283 +FBgn0000097:002 286 +FBgn0000097:003 412 +FBgn0000097:004 21 +FBgn0000097:005 115 +FBgn0000099:001 0 +FBgn0000099:002 1 +FBgn0000099:003 0 +FBgn0000099:004 0 +FBgn0000099:005 0 +FBgn0000099:006 0 +FBgn0000099:007 0 +FBgn0000099:008 0 +FBgn0000099:009 0 +FBgn0000099:010 0 +FBgn0000099:011 0 +FBgn0000099:012 0 +FBgn0000100:001 3 +FBgn0000100:002 423 +FBgn0000100:003 11258 +FBgn0000108:001 2 +FBgn0000108:002 0 +FBgn0000108:003 2 +FBgn0000108:004 1 +FBgn0000108:005 3 +FBgn0000108:006 0 +FBgn0000108:007 3 +FBgn0000108:008 7 +FBgn0000108:009 2 +FBgn0000108:010 2 +FBgn0000108:011 3 +FBgn0000109:001 25 +FBgn0000109:002 31 +FBgn0000109:003 11 +FBgn0000114:001 0 +FBgn0000114:002 0 +FBgn0000114:003 0 +FBgn0000114:004 0 +FBgn0000114:005 0 +FBgn0000114:006 0 +FBgn0000114:007 0 +FBgn0000114:008 0 +FBgn0000114:009 0 +FBgn0000114:010 0 +FBgn0000114:011 0 +FBgn0000114:012 0 +FBgn0000114:013 0 +FBgn0000114:014 0 +FBgn0000114:015 0 +FBgn0000114:016 0 +FBgn0000114:017 0 +FBgn0000114:018 0 +FBgn0000114:019 0 +FBgn0000115:001 38 +FBgn0000115:002 96 +FBgn0000115:003 136 +FBgn0000116:001 140 +FBgn0000116:002 0 +FBgn0000116:003 0 +FBgn0000116:004 0 +FBgn0000116:005 0 +FBgn0000116:006 0 +FBgn0000116:007 0 +FBgn0000116:008 0 +FBgn0000117:001 737 +FBgn0000117:002 237 +FBgn0000117:003 569 +FBgn0000117:004 535 +FBgn0000117:005 2428 +FBgn0000117:006 124 +FBgn0000117:007 3 +FBgn0000117:008 13 +FBgn0000117:009 64 +FBgn0000117:010 31 +FBgn0000119:001 57 +FBgn0000119:002 35 +FBgn0000119:003 11 +FBgn0000119:004 13 +FBgn0000119:005 168 +FBgn0000119:006 8 +FBgn0000119:007 1 +FBgn0000120:001 0 +FBgn0000120:002 0 +FBgn0000120:003 0 +FBgn0000120:004 0 +FBgn0000121:001 1 +FBgn0000121:002 1 +FBgn0000121:003 1 +FBgn0000137:001 0 +FBgn0000139:001 1 +FBgn0000139:002 0 +FBgn0000139:003 2 +FBgn0000139:004 5 +FBgn0000139:005 18 +FBgn0000139:006 21 +FBgn0000139:007 19 +FBgn0000139:008 116 +FBgn0000139:009 94 +FBgn0000140:001 5 +FBgn0000140:002 21 +FBgn0000140:003 23 +FBgn0000140:004 241 +FBgn0000140:005 13 +FBgn0000140:006 22 |
| b |
| diff -r 000000000000 -r 4ca0e679f21e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Oct 08 16:52:01 2015 -0400 |
| b |
| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="pysam" version="0.7.7"> + <repository changeset_revision="0a5141bdf9d0" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="htseq" version="0.6.1"> + <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="dexseq" version="1.14"> + <repository changeset_revision="8db27dbccbec" name="package_dexseq_1_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |