| Previous changeset 0:4ca0e679f21e (2015-10-08) Next changeset 2:6e8b61c54ff3 (2018-01-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232 |
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modified:
dexseq.xml dexseq_count.xml dexseq_helper.py test-data/dexseq_result.tabular |
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removed:
1 2 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 tool_dependencies.xml |
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| diff -r 4ca0e679f21e -r f1c406f9554c 1 --- a/1 Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,307 +0,0 @@\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", 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|
| b |
| diff -r 4ca0e679f21e -r f1c406f9554c 2 --- a/2 Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,307 +0,0 @@\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", 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"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 4ca0e679f21e -r f1c406f9554c dexseq.xml --- a/dexseq.xml Thu Oct 08 16:52:01 2015 -0400 +++ b/dexseq.xml Sun Jan 29 06:59:35 2017 -0500 |
| [ |
| @@ -1,17 +1,19 @@ -<tool id="dexseq" name="DEXSeq" version="1.0"> +<tool id="dexseq" name="DEXSeq" version="1.20.1"> <description>Determines differential exon usage from count tables</description> <requirements> - <requirement type="package" version="1.14">dexseq</requirement> + <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="0.2.15">r-rjson</requirement> </requirements> <code file="dexseq_helper.py" /> <stdio> - <regex match="Execution halted" - source="both" - level="fatal" + <regex match="Execution halted" + source="both" + level="fatal" description="Execution halted." /> - <regex match="Input-Error 01" - source="both" - level="fatal" + <regex match="Input-Error 01" + source="both" + level="fatal" description="Error in your input parameters: Make sure you only apply factors to selected samples." /> <regex match="Error in" source="both" @@ -31,8 +33,8 @@ <![CDATA[ mkdir ./html_out && #import json - Rscript $__tool_directory__/dexseq.R - -o "$dexseq_out" + Rscript '$__tool_directory__/dexseq.R' + -o '$dexseq_out' -p \${GALAXY_SLOTS:-4} #set $temp_factor_names = list() #for $factor in $rep_factorName: @@ -57,11 +59,11 @@ #if $report: -r ./html_out && - mkdir $htmlreport.extra_files_path + mkdir '$htmlreport.extra_files_path' && cp ./html_out/testForDEU.html $htmlreport && - cp -r ./html_out/* $htmlreport.extra_files_path + cp -r ./html_out/* '$htmlreport.extra_files_path' #end if ]]> @@ -69,7 +71,7 @@ <inputs> <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/> <repeat name="rep_factorName" title="Factor" min="1"> - <param name="factorName" type="text" value="FactorName" label="Specify a factor name" + <param name="factorName" type="text" value="FactorName" label="Specify a factor name" help="Only letters, numbers and underscores will be retained in this field"> <sanitizer> <valid initial="string.letters,string.digits"><add value="_" /></valid> @@ -128,7 +130,7 @@ <![CDATA[ .. class:: infomark -**What it does** +**What it does** Inference of differential exon usage in RNA-Seq. @@ -144,7 +146,7 @@ The following table gives some examples of factors and their levels: ========= ============== =============== -Factor Factor level 1 Factor level 2 +Factor Factor level 1 Factor level 2 --------- -------------- --------------- condition Knockdown Wildtype --------- -------------- --------------- |
| b |
| diff -r 4ca0e679f21e -r f1c406f9554c dexseq_count.xml --- a/dexseq_count.xml Thu Oct 08 16:52:01 2015 -0400 +++ b/dexseq_count.xml Sun Jan 29 06:59:35 2017 -0500 |
| [ |
| @@ -1,9 +1,8 @@ -<tool id="dexseq_count" name="DEXSeq-Count" version="1.0"> +<tool id="dexseq_count" name="DEXSeq-Count" version="1.20.1"> <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> + <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement> + <requirement type="package" version="0.6.1.post1">htseq</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> @@ -16,20 +15,20 @@ <command> <![CDATA[ #if $mode.mode_select == "prepare": - python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py + dexseq_prepare_annotation.py -r $mode.aggregate - $mode.gtffile - $flattened_gtf_out + '$mode.gtffile' + '$flattened_gtf_out' #elif $mode.mode_select == "count": - python \$DEXSEQ_ROOT/python_scripts/dexseq_count.py + dexseq_count.py -f bam -p $mode.paired -s $mode.stranded -a $mode.qual -r $mode.order $mode.flattened_gtf_in - $mode.bamfile - $counts_file + '$mode.bamfile' + '$counts_file' #end if ]]> </command> @@ -42,7 +41,7 @@ <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?" + label="Aggregate 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"> @@ -85,7 +84,7 @@ <![CDATA[ .. class:: infomark -**What it does** +**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. |
| b |
| diff -r 4ca0e679f21e -r f1c406f9554c dexseq_helper.py --- a/dexseq_helper.py Thu Oct 08 16:52:01 2015 -0400 +++ b/dexseq_helper.py Sun Jan 29 06:59:35 2017 -0500 |
| [ |
| @@ -1,41 +1,36 @@ - -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.' - +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() + + 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 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/dexseq.gtf --- a/test-data (Kopie)/dexseq.gtf Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,397 +0,0 @@\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 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/dexseq_result.tabular --- a/test-data (Kopie)/dexseq_result.tabular Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,307 +0,0 @@\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 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/flattened.gtf --- a/test-data (Kopie)/flattened.gtf Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,257 +0,0 @@\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 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/original.gtf --- a/test-data (Kopie)/original.gtf Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1000 +0,0 @@\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 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/treated1fb.txt --- a/test-data (Kopie)/treated1fb.txt Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,307 +0,0 @@ -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 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| b |
| diff -r 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/treated2fb.txt --- a/test-data (Kopie)/treated2fb.txt Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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25 -FBgn0000140:004 355 -FBgn0000140:005 37 -FBgn0000140:006 21 |
| b |
| diff -r 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/treated3fb.txt --- a/test-data (Kopie)/treated3fb.txt Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,307 +0,0 @@ -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 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| b |
| diff -r 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/untreated1fb.txt --- a/test-data (Kopie)/untreated1fb.txt Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,307 +0,0 @@ -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 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| b |
| diff -r 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/untreated2fb.txt --- a/test-data (Kopie)/untreated2fb.txt Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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| b |
| diff -r 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/untreated3fb.txt --- a/test-data (Kopie)/untreated3fb.txt Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,307 +0,0 @@ -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 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| b |
| diff -r 4ca0e679f21e -r f1c406f9554c test-data (Kopie)/untreated4fb.txt --- a/test-data (Kopie)/untreated4fb.txt Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,307 +0,0 @@ -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 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-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 4ca0e679f21e -r f1c406f9554c test-data/dexseq_result.tabular --- a/test-data/dexseq_result.tabular Thu Oct 08 16:52:01 2015 -0400 +++ b/test-data/dexseq_result.tabular Sun Jan 29 06:59:35 2017 -0500 |
| b |
| b'@@ -1,134 +1,183 @@\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:E0'..b'r0076545\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+FBgn0000116:E002\tFBgn0000116\tE002\t0.0883366573889214\t0.649506832951611\t0.955102166349974\t0.620300597862845\tNA\t1.06977392668418\t0.0168077984590731\t-5.99203136858692\t3L\t9044230\t9044817\t588\t-\t0\t0\t0\t0\t1\t0\t0\tFBtr0331550, FBtr0076546\n+FBgn0000116:E004\tFBgn0000116\tE004\t0.15316821713762\t0.43977187338658\t0.328021702700227\t0.848732811933342\tNA\t0.0232213523500242\t0.90648447279086\t5.2867584097007\t3L\t9046620\t9046661\t42\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0331550\n+FBgn0000116:E006\tFBgn0000116\tE006\t0.15316821713762\t0.43977187338658\t0.328021702700227\t0.848732811933342\tNA\t0.0232213523500242\t0.90648447279086\t5.2867584097007\t3L\t9055007\t9055567\t561\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0076543, FBtr0076544\n+FBgn0000116:E007\tFBgn0000116\tE007\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3L\t9055912\t9056048\t137\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0076544\n+FBgn0000116:E008\tFBgn0000116\tE008\t0.205235479273134\t0.353436872439287\t1.98242161309956\t0.371127055796381\tNA\t1.12162424681281\t0.0168071427941747\t-6.06037114417562\t3L\t9057564\t9057617\t54\t-\t0\t0\t0\t0\t0\t1\t0\tFBtr0112791, FBtr0076543\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+FBgn0000139:E001\tFBgn0000139\tE001\t0.187795396756122\t0.374758883334333\t0.855539171390518\t0.651961618776603\tNA\t0.887149388069345\t0.0477444815800361\t-4.21577116420462\t3R\t20475810\t20476066\t257\t+\t0\t0\t0\t0\t0\t0\t1\tFBtr0084660\n' |
| b |
| diff -r 4ca0e679f21e -r f1c406f9554c tool_dependencies.xml --- a/tool_dependencies.xml Thu Oct 08 16:52:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +0,0 @@ -<?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> |