| Next changeset 1:06d9062f5430 (2018-11-28) |
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planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d |
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README.rst regtools_junctions_extract.xml test-data/Dbia3.bam test-data/Dbia3.bam.bai test-data/Dbia3_adult_males_junctions_i20_I500000.bed test-data/Dbia3_adult_males_junctions_i20_I500000_a10.bed test-data/Dbia3_adult_males_junctions_i20_I500000_a10_fixed.bed test-data/Dbia3_adult_males_junctions_i20_I500000_fixed.bed test-data/Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb.bed test-data/Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb_fixed.bed test-data/Dbia3_adult_males_junctions_i50_I50000.bed test-data/Dbia3_adult_males_junctions_i50_I50000_fixed.bed test-data/Dbia3_adult_males_shallow.bam test-data/Dbia3_adult_males_shallow.bam.bai test-data/Dbia3_i20_I500000.bed test-data/Dbia3_i20_I500000_fixed.bed tool_dependencies.xml validator.py |
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| diff -r 000000000000 -r 01ed8e112f2a README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Apr 12 17:44:58 2017 -0400 |
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| @@ -0,0 +1,10 @@ +A Galaxy Wrapper for regtools +============================= + +This is a modified Galaxy wrapper for regtools which is based on the previous wrapper written by Remi Marenco (https://github.com/remimarenco/regtools). "regtools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context" (https://regtools.readthedocs.io/en/latest/). + +This wrapper adds an validation step to check if the output files are valid BED format. The lines with invalid strand (neighter "+" or "-") will be removed. + +This wrapper creates a new 13th column to store the scores. The scores in column 4 will be changed to 1000. + +The output is BED 12+1. |
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| diff -r 000000000000 -r 01ed8e112f2a regtools_junctions_extract.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/regtools_junctions_extract.xml Wed Apr 12 17:44:58 2017 -0400 |
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| @@ -0,0 +1,138 @@ +<tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.0"> + <description>Extract splice junctions from a RNA-Seq BAM file</description> + <requirements> + <requirement type="package" version="0.3.0">regtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + ## regtools expects an indexed BAM file + ## Use symlinks to link the BAM file and its index to the working directory + ## See: https://biostar.usegalaxy.org/p/10128/ + + ln -sf '${input1}' infile.bam && + ln -sf '${input1.metadata.bam_index}' infile.bam.bai && + + regtools junctions extract + -i $min_intron_length + -I $max_intron_length + -o $output1 + #if str($advanced_options.advanced_options_selector) == "on": + -a $advanced_options.min_anchor_length + + #if str($advanced_options.region): + -r "$advanced_options.region" + #end if + #end if + infile.bam && + + python $__tool_directory__/validator.py $output1 $fixed_output + ]]></command> + <inputs> + <param name="input1" type="data" format="bam" /> + + <param name="min_intron_length" type="integer" label="Minimum intron length" value="20" min="1"> + <help>Only considers spliced RNA-Seq reads with this minimum intron length (-i)</help> + </param> + <param name="max_intron_length" type="integer" label="Maximum intron length" value="500000" min="1"> + <help>Only considers spliced RNA-Seq reads with this maximum intron length (-I)</help> + </param> + + <conditional name="advanced_options"> + <param name="advanced_options_selector" type="select" label="Advanced options"> + <option value="off" selected="true">Hide advanced options</option> + <option value="on">Display advanced options</option> + </param> + <when value="on"> + <param name="min_anchor_length" type="integer" label="Minimum anchor length" value="8" min="1"> + <help>Only report splice junctions with this minimum anchor length on both sides of the junction (-a)</help> + </param> + <param name="region" type="text" optional="true" label="Only extract junctions in this region" value=""> + <help>Only report splice junctions within this region (format = chrom:start-end) (-r)</help> + <validator type="regex" + message="Region should be in the following format: chrom:start-end">^([^:]+):(\d+)-(\d+)$</validator> + </param> + </when> + + <when value="off" /> + </conditional> + </inputs> + <outputs> + <data name="output1" format="bed" label="${tool.name} on ${on_string}: original output"/> + <data name="fixed_output" format="bed" label="${tool.name} on ${on_string}: fixed_output for HAC workflow"/> + </outputs> + <tests> + <test> + <!-- Test with default parameters --> + <param name="input1" value="Dbia3_adult_males_shallow.bam" /> + <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000.bed" /> + <output name="fixed_output" file="Dbia3_adult_males_junctions_i20_I500000_fixed.bed" /> + </test> + <test> + <!-- Test with custom intron length thresholds --> + <param name="min_intron_length" value="50" /> + <param name="max_intron_length" value="50000" /> + <param name="input1" value="Dbia3_adult_males_shallow.bam" /> + <output name="output1" file="Dbia3_adult_males_junctions_i50_I50000.bed" /> + <output name="fixed_output" file="Dbia3_adult_males_junctions_i50_I50000_fixed.bed" /> + </test> + <test> + <!-- Test with advanced option and custom anchor size --> + <param name="advanced_options_selector" value="on" /> + <param name="min_anchor_length" value="10" /> + <param name="input1" value="Dbia3_adult_males_shallow.bam" /> + <output name="output1" + file="Dbia3_adult_males_junctions_i20_I500000_a10.bed" /> + <output name="fixed_output" + file="Dbia3_adult_males_junctions_i20_I500000_a10_fixed.bed" /> + </test> + <test> + <!-- Test with advanced option and selected region --> + <param name="advanced_options_selector" value="on" /> + <param name="region" value="contig2:10000-30000" /> + <param name="input1" value="Dbia3_adult_males_shallow.bam" /> + <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb.bed" /> + <output name="fixed_output" file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb_fixed.bed"/> + </test> + <test> + <!--Test with output having invalid strand --> + <param name="input1" value="Dbia3.bam" /> + <output name="output1" file="Dbia3_i20_I500000.bed" /> + <output name="fixed_output" file="Dbia3_i20_I500000_fixed.bed" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +The `regtools junctions extract <https://regtools.readthedocs.io/en/latest/commands/junctions-extract/>`_ +tool creates a list of exon-exon junctions from spliced RNA-Seq reads within a BAM +alignment file. The format of the output BED file is similar to the ``junctions.bed`` +file produced by TopHat2. + +The extent of each BED feature corresponds to the maximum overhang of each splice +junction. The score of each BED feature corresponds to the number of spliced RNA-Seq +reads that support each junction. + +-------- + +.. class:: warningmark + +By default, the minimum intron size is **20 bp** and the maximum intron size is +**500,000 bp** so that they conform to the default intron size settings for +`HISAT2 <https://ccb.jhu.edu/software/hisat2/manual.shtml#options>`_. The minimum +intron size for the command-line version of ``regtools junctions extract`` is 70 bp. + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubregtools, + author = {Griffith Lab}, + year = {2016}, + title = {regtools}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/griffithlab/regtools}, +}</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_junctions_i20_I500000.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_adult_males_junctions_i20_I500000.bed Wed Apr 12 17:44:58 2017 -0400 |
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|
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_junctions_i20_I500000_a10.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_adult_males_junctions_i20_I500000_a10.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| b'@@ -0,0 +1,1883 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|
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_junctions_i20_I500000_a10_fixed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_adult_males_junctions_i20_I500000_a10_fixed.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| b'@@ -0,0 +1,1883 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|
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_junctions_i20_I500000_fixed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_adult_males_junctions_i20_I500000_fixed.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| b'@@ -0,0 +1,1892 @@\n+contig1\t1052\t1272\tJUNC00000001\t1000\t-\t1052\t1272\t255,0,0\t2\t65,99\t0,121\t2\n+contig1\t5287\t12663\tJUNC00000002\t1000\t-\t5287\t12663\t255,0,0\t2\t122,123\t0,7253\t16\n+contig1\t33709\t33999\tJUNC00000003\t1000\t-\t33709\t33999\t255,0,0\t2\t117,120\t0,170\t12\n+contig1\t33920\t34213\tJUNC00000004\t1000\t-\t33920\t34213\t255,0,0\t2\t124,107\t0,186\t13\n+contig1\t34498\t34796\tJUNC00000005\t1000\t-\t34498\t34796\t255,0,0\t2\t121,123\t0,175\t5\n+contig1\t35236\t35498\tJUNC00000006\t1000\t-\t35236\t35498\t255,0,0\t2\t75,115\t0,147\t4\n+contig1\t35645\t41539\tJUNC00000007\t1000\t-\t35645\t41539\t255,0,0\t2\t121,68\t0,5826\t4\n+contig1\t35751\t41273\tJUNC00000008\t1000\t-\t35751\t41273\t255,0,0\t2\t15,110\t0,5412\t1\n+contig1\t41221\t41399\tJUNC00000009\t1000\t-\t41221\t41399\t255,0,0\t2\t94,31\t0,147\t1\n+contig10\t5138\t5352\tJUNC00000010\t1000\t+\t5138\t5352\t255,0,0\t2\t47,111\t0,103\t2\n+contig10\t9381\t9565\tJUNC00000011\t1000\t+\t9381\t9565\t255,0,0\t2\t51,74\t0,110\t1\n+contig10\t25241\t27198\tJUNC00000012\t1000\t+\t25241\t27198\t255,0,0\t2\t77,120\t0,1837\t6\n+contig10\t25570\t25835\tJUNC00000013\t1000\t+\t25570\t25835\t255,0,0\t2\t97,105\t0,160\t3\n+contig10\t25711\t27200\tJUNC00000014\t1000\t+\t25711\t27200\t255,0,0\t2\t124,122\t0,1367\t24\n+contig10\t27077\t27399\tJUNC00000015\t1000\t+\t27077\t27399\t255,0,0\t2\t122,115\t0,207\t27\n+contig10\t27306\t41718\tJUNC00000016\t1000\t-\t27306\t41718\t255,0,0\t2\t124,103\t0,14309\t20\n+contig10\t27350\t29499\tJUNC00000017\t1000\t-\t27350\t29499\t255,0,0\t2\t80,45\t0,2104\t1\n+contig10\t31237\t31423\tJUNC00000020\t1000\t-\t31237\t31423\t255,0,0\t2\t49,76\t0,110\t1\n+contig10\t31624\t41718\tJUNC00000021\t1000\t-\t31624\t41718\t255,0,0\t2\t90,103\t0,9991\t9\n+contig10\t41615\t41874\tJUNC00000018\t1000\t-\t41615\t41874\t255,0,0\t2\t103,98\t0,161\t26\n+contig10\t41776\t42042\tJUNC00000022\t1000\t-\t41776\t42042\t255,0,0\t2\t98,109\t0,157\t23\n+contig10\t41936\t42196\tJUNC00000023\t1000\t-\t41936\t42196\t255,0,0\t2\t117,90\t0,170\t27\n+contig10\t41937\t42157\tJUNC00000024\t1000\t-\t41937\t42157\t255,0,0\t2\t116,12\t0,208\t3\n+contig11\t2925\t3108\tJUNC00000025\t1000\t+\t2925\t3108\t255,0,0\t2\t66,59\t0,124\t1\n+contig11\t4385\t6170\tJUNC00000026\t1000\t+\t4385\t6170\t255,0,0\t2\t93,97\t0,1688\t2\n+contig11\t4572\t4765\tJUNC00000027\t1000\t+\t4572\t4765\t255,0,0\t2\t90,40\t0,153\t2\n+contig11\t4710\t6188\tJUNC00000028\t1000\t+\t4710\t6188\t255,0,0\t2\t120,115\t0,1363\t24\n+contig11\t6077\t6402\tJUNC00000029\t1000\t+\t6077\t6402\t255,0,0\t2\t117,123\t0,202\t26\n+contig11\t6317\t20714\tJUNC00000030\t1000\t-\t6317\t20714\t255,0,0\t2\t108,104\t0,14293\t16\n+contig11\t9857\t20713\tJUNC00000032\t1000\t-\t9857\t20713\t255,0,0\t2\t66,103\t0,10753\t2\n+contig11\t10594\t20713\tJUNC00000033\t1000\t-\t10594\t20713\t255,0,0\t2\t115,103\t0,10016\t9\n+contig11\t20610\t20869\tJUNC00000031\t1000\t-\t20610\t20869\t255,0,0\t2\t103,98\t0,161\t27\n+contig11\t20771\t21049\tJUNC00000034\t1000\t-\t20771\t21049\t255,0,0\t2\t98,121\t0,157\t28\n+contig11\t20928\t21185\tJUNC00000036\t1000\t-\t20928\t21185\t255,0,0\t2\t120,45\t0,212\t3\n+contig11\t20928\t21219\tJUNC00000035\t1000\t-\t20928\t21219\t255,0,0\t2\t120,118\t0,173\t31\n+contig11\t22927\t23212\tJUNC00000037\t1000\t-\t22927\t23212\t255,0,0\t2\t116,116\t0,169\t31\n+contig11\t23104\t24161\tJUNC00000038\t1000\t-\t23104\t24161\t255,0,0\t2\t118,91\t0,966\t31\n+contig11\t24070\t24344\tJUNC00000039\t1000\t-\t24070\t24344\t255,0,0\t2\t90,124\t0,150\t26\n+contig11\t24959\t29247\tJUNC00000040\t1000\t-\t24959\t29247\t255,0,0\t2\t124,124\t0,4164\t24\n+contig11\t29173\t29665\tJUNC00000041\t1000\t-\t29173\t29665\t255,0,0\t2\t123,99\t0,393\t9\n+contig11\t29179\t29479\tJUNC00000042\t1000\t-\t29179\t29479\t255,0,0\t2\t117,123\t0,177\t20\n+contig11\t29375\t29665\tJUNC00000044\t1000\t-\t29375\t29665\t255,0,0\t2\t121,99\t0,191\t25\n+contig11\t29566\t29842\tJUNC00000043\t1000\t-\t29566\t29842\t255,0,0\t2\t99,118\t0,158\t30\n+contig11\t29781\t30287\tJUNC00000045\t1000\t-\t29781\t30287\t255,0,0\t2\t108,93\t0,413\t3\n+contig12\t797\t11710\tJUNC00000047\t1000\t-\t797\t11710\t255,0,0\t2\t123,103\t0,10810\t11\n+contig12\t1217\t1451\tJUNC00000050\t1000\t-\t1217\t1451\t255,0,0\t2\t61,112\t0,122\t5\n+contig12\t1597\t11710\tJUNC00000051\t1000\t-\t1597\t11710\t255,0,0\t2\t109,103\t0,10010\t12\n+contig12\t11600\t11866\tJUNC00000049\t1000\t-\t11600\t11866\t255,0,0\t2\t110,98\t0,168\t26\n+contig12\t11607\t11802\tJUNC00000048\t1000\t-\t11607\t11802\t255,0,0\t2\t47,34\t0,161\t1\n+contig12\t11768\t12040\tJUNC00000052\t1000\t-\t11768\t12040\t255,0,0\t2\t98,115\t0,157\t25\n+contig12\t11925\t12186\tJUNC00000'..b'9000\t255,0,0\t2\t113,118\t0,6322\t15\n+contig8\t8087\t8782\tJUNC00001885\t1000\t+\t8087\t8782\t255,0,0\t2\t48,49\t0,646\t1\n+contig8\t8733\t8910\tJUNC00001886\t1000\t+\t8733\t8910\t255,0,0\t2\t49,28\t0,149\t1\n+contig8\t9048\t9342\tJUNC00001887\t1000\t+\t9048\t9342\t255,0,0\t2\t123,106\t0,188\t23\n+contig8\t9255\t9540\tJUNC00001888\t1000\t+\t9255\t9540\t255,0,0\t2\t88,123\t0,162\t12\n+contig8\t9675\t9955\tJUNC00001889\t1000\t+\t9675\t9955\t255,0,0\t2\t104,119\t0,161\t20\n+contig8\t10231\t10532\tJUNC00001890\t1000\t+\t10231\t10532\t255,0,0\t2\t109,121\t0,180\t14\n+contig8\t10496\t15081\tJUNC00001891\t1000\t+\t10496\t15081\t255,0,0\t2\t116,122\t0,4463\t19\n+contig8\t16709\t17207\tJUNC00001892\t1000\t+\t16709\t17207\t255,0,0\t2\t123,123\t0,375\t25\n+contig8\t16726\t30543\tJUNC00001893\t1000\t+\t16726\t30543\t255,0,0\t2\t106,19\t0,13798\t1\n+contig8\t19478\t30617\tJUNC00001894\t1000\t+\t19478\t30617\t255,0,0\t2\t32,93\t0,11046\t1\n+contig8\t28726\t30591\tJUNC00001895\t1000\t+\t28726\t30591\t255,0,0\t2\t67,67\t0,1798\t2\n+contig8\t30788\t31567\tJUNC00001896\t1000\t+\t30788\t31567\t255,0,0\t2\t122,118\t0,661\t12\n+contig8\t30931\t31573\tJUNC00001897\t1000\t+\t30931\t31573\t255,0,0\t2\t48,124\t0,518\t6\n+contig8\t31515\t31813\tJUNC00001898\t1000\t+\t31515\t31813\t255,0,0\t2\t118,120\t0,178\t26\n+contig8\t31693\t31929\tJUNC00001899\t1000\t+\t31693\t31929\t255,0,0\t2\t120,60\t0,176\t2\n+contig8\t31988\t32193\tJUNC00001900\t1000\t+\t31988\t32193\t255,0,0\t2\t53,83\t0,122\t2\n+contig8\t32087\t32387\tJUNC00001901\t1000\t+\t32087\t32387\t255,0,0\t2\t116,121\t0,179\t22\n+contig8\t32101\t32286\tJUNC00001902\t1000\t+\t32101\t32286\t255,0,0\t2\t102,23\t0,162\t1\n+contig8\t33620\t33806\tJUNC00001903\t1000\t-\t33620\t33806\t255,0,0\t2\t33,92\t0,94\t1\n+contig8\t34012\t34197\tJUNC00001904\t1000\t-\t34012\t34197\t255,0,0\t2\t69,56\t0,129\t1\n+contig9\t1401\t2090\tJUNC00001905\t1000\t+\t1401\t2090\t255,0,0\t2\t55,70\t0,619\t1\n+contig9\t2558\t8995\tJUNC00001906\t1000\t+\t2558\t8995\t255,0,0\t2\t115,113\t0,6324\t20\n+contig9\t9049\t9343\tJUNC00001907\t1000\t+\t9049\t9343\t255,0,0\t2\t122,107\t0,187\t23\n+contig9\t9236\t9526\tJUNC00001908\t1000\t+\t9236\t9526\t255,0,0\t2\t107,109\t0,181\t15\n+contig9\t9655\t9959\tJUNC00001909\t1000\t+\t9655\t9959\t255,0,0\t2\t124,123\t0,181\t23\n+contig9\t9887\t10073\tJUNC00001910\t1000\t-\t9887\t10073\t255,0,0\t2\t85,40\t0,146\t1\n+contig9\t10085\t10305\tJUNC00001911\t1000\t-\t10085\t10305\t255,0,0\t2\t65,60\t0,160\t1\n+contig9\t10222\t10531\tJUNC00001912\t1000\t+\t10222\t10531\t255,0,0\t2\t118,120\t0,189\t20\n+contig9\t10492\t15079\tJUNC00001913\t1000\t+\t10492\t15079\t255,0,0\t2\t120,120\t0,4467\t22\n+contig9\t16712\t17203\tJUNC00001914\t1000\t+\t16712\t17203\t255,0,0\t2\t120,119\t0,372\t24\n+contig9\t16784\t30601\tJUNC00001915\t1000\t+\t16784\t30601\t255,0,0\t2\t48,77\t0,13740\t1\n+contig9\t30797\t31567\tJUNC00001916\t1000\t+\t30797\t31567\t255,0,0\t2\t113,118\t0,652\t10\n+contig9\t30932\t31573\tJUNC00001917\t1000\t+\t30932\t31573\t255,0,0\t2\t47,124\t0,517\t6\n+contig9\t31510\t31813\tJUNC00001918\t1000\t+\t31510\t31813\t255,0,0\t2\t123,120\t0,183\t25\n+contig9\t31719\t31915\tJUNC00001920\t1000\t+\t31719\t31915\t255,0,0\t2\t98,46\t0,150\t2\n+contig9\t31974\t32203\tJUNC00001921\t1000\t+\t31974\t32203\t255,0,0\t2\t67,93\t0,136\t4\n+contig9\t32079\t32379\tJUNC00001922\t1000\t+\t32079\t32379\t255,0,0\t2\t124,113\t0,187\t27\n+contig9\t33564\t33796\tJUNC00001923\t1000\t-\t33564\t33796\t255,0,0\t2\t89,82\t0,150\t3\n+contig9\t33963\t34238\tJUNC00001924\t1000\t-\t33963\t34238\t255,0,0\t2\t118,97\t0,178\t3\n+contig9\t35742\t36047\tJUNC00001925\t1000\t+\t35742\t36047\t255,0,0\t2\t89,36\t0,269\t1\n+contig9\t35743\t36099\tJUNC00001926\t1000\t+\t35743\t36099\t255,0,0\t2\t77,88\t0,268\t14\n+contig9\t36073\t41207\tJUNC00001927\t1000\t+\t36073\t41207\t255,0,0\t2\t122,54\t0,5080\t13\n+contig9\t36074\t40075\tJUNC00001928\t1000\t+\t36074\t40075\t255,0,0\t2\t121,47\t0,3954\t2\n+contig9\t41153\t41712\tJUNC00001930\t1000\t+\t41153\t41712\t255,0,0\t2\t54,123\t0,436\t15\n+contig9\t41162\t47759\tJUNC00001931\t1000\t+\t41162\t47759\t255,0,0\t2\t45,80\t0,6517\t1\n+contig9\t50002\t50239\tJUNC00001932\t1000\t+\t50002\t50239\t255,0,0\t2\t86,94\t0,143\t2\n+contig9\t54084\t54265\tJUNC00001933\t1000\t+\t54084\t54265\t255,0,0\t2\t115,10\t0,171\t2\n+contig9\t54404\t54669\tJUNC00001934\t1000\t+\t54404\t54669\t255,0,0\t2\t90,108\t0,157\t2\n+contig9\t55214\t55395\tJUNC00001935\t1000\t+\t55214\t55395\t255,0,0\t2\t61,64\t0,117\t1\n+contig9\t55623\t55781\tJUNC00001936\t1000\t+\t55623\t55781\t255,0,0\t2\t24,74\t0,84\t1\n+contig9\t55707\t55866\tJUNC00001937\t1000\t+\t55707\t55866\t255,0,0\t2\t74,27\t0,132\t1\n' |
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +contig2 18569 18834 JUNC00000001 3 - 18569 18834 255,0,0 2 90,122 0,143 +contig2 18590 18787 JUNC00000002 1 - 18590 18787 255,0,0 2 50,75 0,122 +contig2 18757 19041 JUNC00000003 4 - 18757 19041 255,0,0 2 120,102 0,182 +contig2 19334 19620 JUNC00000004 5 - 19334 19620 255,0,0 2 118,114 0,172 +contig2 20024 20308 JUNC00000005 8 - 20024 20308 255,0,0 2 120,92 0,192 +contig2 20566 26396 JUNC00000006 1 - 20566 26396 255,0,0 2 33,92 0,5738 +contig2 26830 27015 JUNC00000007 2 - 26830 27015 255,0,0 2 83,45 0,140 +contig2 26970 27178 JUNC00000008 1 - 26970 27178 255,0,0 2 45,58 0,150 |
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb_fixed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb_fixed.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +contig2 18569 18834 JUNC00000001 1000 - 18569 18834 255,0,0 2 90,122 0,143 3 +contig2 18590 18787 JUNC00000002 1000 - 18590 18787 255,0,0 2 50,75 0,122 1 +contig2 18757 19041 JUNC00000003 1000 - 18757 19041 255,0,0 2 120,102 0,182 4 +contig2 19334 19620 JUNC00000004 1000 - 19334 19620 255,0,0 2 118,114 0,172 5 +contig2 20024 20308 JUNC00000005 1000 - 20024 20308 255,0,0 2 120,92 0,192 8 +contig2 20566 26396 JUNC00000006 1000 - 20566 26396 255,0,0 2 33,92 0,5738 1 +contig2 26830 27015 JUNC00000007 1000 - 26830 27015 255,0,0 2 83,45 0,140 2 +contig2 26970 27178 JUNC00000008 1000 - 26970 27178 255,0,0 2 45,58 0,150 1 |
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_junctions_i50_I50000.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_adult_males_junctions_i50_I50000.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| b'@@ -0,0 +1,1878 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|
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_junctions_i50_I50000_fixed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_adult_males_junctions_i50_I50000_fixed.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| b'@@ -0,0 +1,1878 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55,0,0\t2\t88,123\t0,162\t12\n+contig8\t9675\t9955\tJUNC00001875\t1000\t+\t9675\t9955\t255,0,0\t2\t104,119\t0,161\t20\n+contig8\t10231\t10532\tJUNC00001876\t1000\t+\t10231\t10532\t255,0,0\t2\t109,121\t0,180\t14\n+contig8\t10496\t15081\tJUNC00001877\t1000\t+\t10496\t15081\t255,0,0\t2\t116,122\t0,4463\t19\n+contig8\t16709\t17207\tJUNC00001878\t1000\t+\t16709\t17207\t255,0,0\t2\t123,123\t0,375\t25\n+contig8\t16726\t30543\tJUNC00001879\t1000\t+\t16726\t30543\t255,0,0\t2\t106,19\t0,13798\t1\n+contig8\t19478\t30617\tJUNC00001880\t1000\t+\t19478\t30617\t255,0,0\t2\t32,93\t0,11046\t1\n+contig8\t28726\t30591\tJUNC00001881\t1000\t+\t28726\t30591\t255,0,0\t2\t67,67\t0,1798\t2\n+contig8\t30788\t31567\tJUNC00001882\t1000\t+\t30788\t31567\t255,0,0\t2\t122,118\t0,661\t12\n+contig8\t30931\t31573\tJUNC00001883\t1000\t+\t30931\t31573\t255,0,0\t2\t48,124\t0,518\t6\n+contig8\t31515\t31813\tJUNC00001884\t1000\t+\t31515\t31813\t255,0,0\t2\t118,120\t0,178\t26\n+contig8\t31693\t31929\tJUNC00001885\t1000\t+\t31693\t31929\t255,0,0\t2\t120,60\t0,176\t2\n+contig8\t31988\t32193\tJUNC00001886\t1000\t+\t31988\t32193\t255,0,0\t2\t53,83\t0,122\t2\n+contig8\t32087\t32387\tJUNC00001887\t1000\t+\t32087\t32387\t255,0,0\t2\t116,121\t0,179\t22\n+contig8\t32101\t32286\tJUNC00001888\t1000\t+\t32101\t32286\t255,0,0\t2\t102,23\t0,162\t1\n+contig8\t33620\t33806\tJUNC00001889\t1000\t-\t33620\t33806\t255,0,0\t2\t33,92\t0,94\t1\n+contig8\t34012\t34197\tJUNC00001890\t1000\t-\t34012\t34197\t255,0,0\t2\t69,56\t0,129\t1\n+contig9\t1401\t2090\tJUNC00001891\t1000\t+\t1401\t2090\t255,0,0\t2\t55,70\t0,619\t1\n+contig9\t2558\t8995\tJUNC00001892\t1000\t+\t2558\t8995\t255,0,0\t2\t115,113\t0,6324\t20\n+contig9\t9049\t9343\tJUNC00001893\t1000\t+\t9049\t9343\t255,0,0\t2\t122,107\t0,187\t23\n+contig9\t9236\t9526\tJUNC00001894\t1000\t+\t9236\t9526\t255,0,0\t2\t107,109\t0,181\t15\n+contig9\t9655\t9959\tJUNC00001895\t1000\t+\t9655\t9959\t255,0,0\t2\t124,123\t0,181\t23\n+contig9\t9887\t10073\tJUNC00001896\t1000\t-\t9887\t10073\t255,0,0\t2\t85,40\t0,146\t1\n+contig9\t10085\t10305\tJUNC00001897\t1000\t-\t10085\t10305\t255,0,0\t2\t65,60\t0,160\t1\n+contig9\t10222\t10531\tJUNC00001898\t1000\t+\t10222\t10531\t255,0,0\t2\t118,120\t0,189\t20\n+contig9\t10492\t15079\tJUNC00001899\t1000\t+\t10492\t15079\t255,0,0\t2\t120,120\t0,4467\t22\n+contig9\t16712\t17203\tJUNC00001900\t1000\t+\t16712\t17203\t255,0,0\t2\t120,119\t0,372\t24\n+contig9\t16784\t30601\tJUNC00001901\t1000\t+\t16784\t30601\t255,0,0\t2\t48,77\t0,13740\t1\n+contig9\t30797\t31567\tJUNC00001902\t1000\t+\t30797\t31567\t255,0,0\t2\t113,118\t0,652\t10\n+contig9\t30932\t31573\tJUNC00001903\t1000\t+\t30932\t31573\t255,0,0\t2\t47,124\t0,517\t6\n+contig9\t31510\t31813\tJUNC00001904\t1000\t+\t31510\t31813\t255,0,0\t2\t123,120\t0,183\t25\n+contig9\t31719\t31915\tJUNC00001906\t1000\t+\t31719\t31915\t255,0,0\t2\t98,46\t0,150\t2\n+contig9\t31974\t32203\tJUNC00001907\t1000\t+\t31974\t32203\t255,0,0\t2\t67,93\t0,136\t4\n+contig9\t32079\t32379\tJUNC00001908\t1000\t+\t32079\t32379\t255,0,0\t2\t124,113\t0,187\t27\n+contig9\t33564\t33796\tJUNC00001909\t1000\t-\t33564\t33796\t255,0,0\t2\t89,82\t0,150\t3\n+contig9\t33963\t34238\tJUNC00001910\t1000\t-\t33963\t34238\t255,0,0\t2\t118,97\t0,178\t3\n+contig9\t35742\t36047\tJUNC00001911\t1000\t+\t35742\t36047\t255,0,0\t2\t89,36\t0,269\t1\n+contig9\t35743\t36099\tJUNC00001912\t1000\t+\t35743\t36099\t255,0,0\t2\t77,88\t0,268\t14\n+contig9\t36073\t41207\tJUNC00001913\t1000\t+\t36073\t41207\t255,0,0\t2\t122,54\t0,5080\t13\n+contig9\t36074\t40075\tJUNC00001914\t1000\t+\t36074\t40075\t255,0,0\t2\t121,47\t0,3954\t2\n+contig9\t41153\t41712\tJUNC00001916\t1000\t+\t41153\t41712\t255,0,0\t2\t54,123\t0,436\t15\n+contig9\t41162\t47759\tJUNC00001917\t1000\t+\t41162\t47759\t255,0,0\t2\t45,80\t0,6517\t1\n+contig9\t50002\t50239\tJUNC00001918\t1000\t+\t50002\t50239\t255,0,0\t2\t86,94\t0,143\t2\n+contig9\t54084\t54265\tJUNC00001919\t1000\t+\t54084\t54265\t255,0,0\t2\t115,10\t0,171\t2\n+contig9\t54404\t54669\tJUNC00001920\t1000\t+\t54404\t54669\t255,0,0\t2\t90,108\t0,157\t2\n+contig9\t55214\t55395\tJUNC00001921\t1000\t+\t55214\t55395\t255,0,0\t2\t61,64\t0,117\t1\n+contig9\t55623\t55781\tJUNC00001922\t1000\t+\t55623\t55781\t255,0,0\t2\t24,74\t0,84\t1\n+contig9\t55707\t55866\tJUNC00001923\t1000\t+\t55707\t55866\t255,0,0\t2\t74,27\t0,132\t1\n' |
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_shallow.bam |
| b |
| Binary file test-data/Dbia3_adult_males_shallow.bam has changed |
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_adult_males_shallow.bam.bai |
| b |
| Binary file test-data/Dbia3_adult_males_shallow.bam.bai has changed |
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_i20_I500000.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_i20_I500000.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| @@ -0,0 +1,46 @@ +contig16 1808 11364 JUNC00000001 17 - 1808 11364 255,0,0 2 89,80 0,9476 +contig16 6034 6145 JUNC00000002 1 ? 6034 6145 255,0,0 2 46,44 0,67 +contig16 11374 11605 JUNC00000003 18 - 11374 11605 255,0,0 2 89,88 0,143 +contig16 11617 11783 JUNC00000004 1 - 11617 11783 255,0,0 2 65,25 0,141 +contig16 11617 11844 JUNC00000005 22 - 11617 11844 255,0,0 2 88,86 0,141 +contig16 11774 11977 JUNC00000006 13 - 11774 11977 255,0,0 2 84,56 0,147 +contig16 11806 11956 JUNC00000007 1 - 11806 11956 255,0,0 2 55,35 0,115 +contig16 11921 12673 JUNC00000008 13 - 11921 12673 255,0,0 2 54,73 0,679 +contig16 11939 17275 JUNC00000009 1 - 11939 17275 255,0,0 2 36,54 0,5282 +contig16 12090 12202 JUNC00000010 1 ? 12090 12202 255,0,0 2 26,64 0,48 +contig16 12723 17294 JUNC00000011 11 - 12723 17294 255,0,0 2 88,73 0,4498 +contig16 12782 21003 JUNC00000012 1 - 12782 21003 255,0,0 2 29,61 0,8160 +contig16 12796 21322 JUNC00000013 1 - 12796 21322 255,0,0 2 15,75 0,8451 +contig16 17251 17490 JUNC00000014 17 - 17251 17490 255,0,0 2 86,85 0,154 +contig16 17307 21307 JUNC00000015 1 - 17307 21307 255,0,0 2 30,60 0,3940 +contig16 21007 21283 JUNC00000016 1 - 21007 21283 255,0,0 2 54,36 0,240 +contig16 21250 22512 JUNC00000017 8 - 21250 22512 255,0,0 2 86,58 0,1204 +contig16 21316 23083 JUNC00000018 1 - 21316 23083 255,0,0 2 20,70 0,1697 +contig16 22206 25356 JUNC00000019 1 + 22206 25356 255,0,0 2 39,46 0,3104 +contig16 25356 26934 JUNC00000020 2 ? 25356 26934 255,0,0 2 57,48 0,1530 +contig16 27016 27178 JUNC00000021 2 + 27016 27178 255,0,0 2 33,70 0,92 +contig16 27196 34369 JUNC00000022 1 + 27196 34369 255,0,0 2 57,32 0,7141 +contig16 29103 29238 JUNC00000023 1 + 29103 29238 255,0,0 2 61,18 0,117 +contig16 29358 34416 JUNC00000024 1 + 29358 34416 255,0,0 2 11,79 0,4979 +contig16 34568 34768 JUNC00000025 3 + 34568 34768 255,0,0 2 51,84 0,116 +contig16 34573 34763 JUNC00000026 1 + 34573 34763 255,0,0 2 46,44 0,146 +contig16 34782 34954 JUNC00000027 4 + 34782 34954 255,0,0 2 53,66 0,106 +contig16 35110 42519 JUNC00000028 4 + 35110 42519 255,0,0 2 64,64 0,7345 +contig16 35119 42491 JUNC00000029 1 ? 35119 42491 255,0,0 2 56,34 0,7338 +contig16 42508 43097 JUNC00000030 6 + 42508 43097 255,0,0 2 82,65 0,524 +contig16 43273 43505 JUNC00000031 12 + 43273 43505 255,0,0 2 81,85 0,147 +contig17 1242 2504 JUNC00000032 8 - 1242 2504 255,0,0 2 86,58 0,1204 +contig17 1308 3075 JUNC00000033 1 - 1308 3075 255,0,0 2 20,70 0,1697 +contig17 2198 5348 JUNC00000034 1 + 2198 5348 255,0,0 2 39,46 0,3104 +contig17 5348 6926 JUNC00000035 2 ? 5348 6926 255,0,0 2 57,48 0,1530 +contig17 7008 7170 JUNC00000036 2 + 7008 7170 255,0,0 2 33,70 0,92 +contig17 7188 14361 JUNC00000037 1 + 7188 14361 255,0,0 2 57,32 0,7141 +contig17 9095 9230 JUNC00000038 1 + 9095 9230 255,0,0 2 61,18 0,117 +contig17 9350 14408 JUNC00000039 1 + 9350 14408 255,0,0 2 11,79 0,4979 +contig17 14560 14760 JUNC00000040 3 + 14560 14760 255,0,0 2 51,84 0,116 +contig17 14565 14755 JUNC00000041 1 + 14565 14755 255,0,0 2 46,44 0,146 +contig17 14774 14946 JUNC00000042 4 + 14774 14946 255,0,0 2 53,66 0,106 +contig17 15102 22511 JUNC00000043 4 + 15102 22511 255,0,0 2 64,64 0,7345 +contig17 15111 22483 JUNC00000044 1 ? 15111 22483 255,0,0 2 56,34 0,7338 +contig17 22500 23089 JUNC00000045 6 + 22500 23089 255,0,0 2 82,65 0,524 +contig17 23265 23497 JUNC00000046 12 + 23265 23497 255,0,0 2 81,85 0,147 |
| b |
| diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3_i20_I500000_fixed.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Dbia3_i20_I500000_fixed.bed Wed Apr 12 17:44:58 2017 -0400 |
| b |
| @@ -0,0 +1,40 @@ +contig16 1808 11364 JUNC00000001 1000 - 1808 11364 255,0,0 2 89,80 0,9476 17 +contig16 11374 11605 JUNC00000003 1000 - 11374 11605 255,0,0 2 89,88 0,143 18 +contig16 11617 11783 JUNC00000004 1000 - 11617 11783 255,0,0 2 65,25 0,141 1 +contig16 11617 11844 JUNC00000005 1000 - 11617 11844 255,0,0 2 88,86 0,141 22 +contig16 11774 11977 JUNC00000006 1000 - 11774 11977 255,0,0 2 84,56 0,147 13 +contig16 11806 11956 JUNC00000007 1000 - 11806 11956 255,0,0 2 55,35 0,115 1 +contig16 11921 12673 JUNC00000008 1000 - 11921 12673 255,0,0 2 54,73 0,679 13 +contig16 11939 17275 JUNC00000009 1000 - 11939 17275 255,0,0 2 36,54 0,5282 1 +contig16 12723 17294 JUNC00000011 1000 - 12723 17294 255,0,0 2 88,73 0,4498 11 +contig16 12782 21003 JUNC00000012 1000 - 12782 21003 255,0,0 2 29,61 0,8160 1 +contig16 12796 21322 JUNC00000013 1000 - 12796 21322 255,0,0 2 15,75 0,8451 1 +contig16 17251 17490 JUNC00000014 1000 - 17251 17490 255,0,0 2 86,85 0,154 17 +contig16 17307 21307 JUNC00000015 1000 - 17307 21307 255,0,0 2 30,60 0,3940 1 +contig16 21007 21283 JUNC00000016 1000 - 21007 21283 255,0,0 2 54,36 0,240 1 +contig16 21250 22512 JUNC00000017 1000 - 21250 22512 255,0,0 2 86,58 0,1204 8 +contig16 21316 23083 JUNC00000018 1000 - 21316 23083 255,0,0 2 20,70 0,1697 1 +contig16 22206 25356 JUNC00000019 1000 + 22206 25356 255,0,0 2 39,46 0,3104 1 +contig16 27016 27178 JUNC00000021 1000 + 27016 27178 255,0,0 2 33,70 0,92 2 +contig16 27196 34369 JUNC00000022 1000 + 27196 34369 255,0,0 2 57,32 0,7141 1 +contig16 29103 29238 JUNC00000023 1000 + 29103 29238 255,0,0 2 61,18 0,117 1 +contig16 29358 34416 JUNC00000024 1000 + 29358 34416 255,0,0 2 11,79 0,4979 1 +contig16 34568 34768 JUNC00000025 1000 + 34568 34768 255,0,0 2 51,84 0,116 3 +contig16 34573 34763 JUNC00000026 1000 + 34573 34763 255,0,0 2 46,44 0,146 1 +contig16 34782 34954 JUNC00000027 1000 + 34782 34954 255,0,0 2 53,66 0,106 4 +contig16 35110 42519 JUNC00000028 1000 + 35110 42519 255,0,0 2 64,64 0,7345 4 +contig16 42508 43097 JUNC00000030 1000 + 42508 43097 255,0,0 2 82,65 0,524 6 +contig16 43273 43505 JUNC00000031 1000 + 43273 43505 255,0,0 2 81,85 0,147 12 +contig17 1242 2504 JUNC00000032 1000 - 1242 2504 255,0,0 2 86,58 0,1204 8 +contig17 1308 3075 JUNC00000033 1000 - 1308 3075 255,0,0 2 20,70 0,1697 1 +contig17 2198 5348 JUNC00000034 1000 + 2198 5348 255,0,0 2 39,46 0,3104 1 +contig17 7008 7170 JUNC00000036 1000 + 7008 7170 255,0,0 2 33,70 0,92 2 +contig17 7188 14361 JUNC00000037 1000 + 7188 14361 255,0,0 2 57,32 0,7141 1 +contig17 9095 9230 JUNC00000038 1000 + 9095 9230 255,0,0 2 61,18 0,117 1 +contig17 9350 14408 JUNC00000039 1000 + 9350 14408 255,0,0 2 11,79 0,4979 1 +contig17 14560 14760 JUNC00000040 1000 + 14560 14760 255,0,0 2 51,84 0,116 3 +contig17 14565 14755 JUNC00000041 1000 + 14565 14755 255,0,0 2 46,44 0,146 1 +contig17 14774 14946 JUNC00000042 1000 + 14774 14946 255,0,0 2 53,66 0,106 4 +contig17 15102 22511 JUNC00000043 1000 + 15102 22511 255,0,0 2 64,64 0,7345 4 +contig17 22500 23089 JUNC00000045 1000 + 22500 23089 255,0,0 2 82,65 0,524 6 +contig17 23265 23497 JUNC00000046 1000 + 23265 23497 255,0,0 2 81,85 0,147 12 |
| b |
| diff -r 000000000000 -r 01ed8e112f2a tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 12 17:44:58 2017 -0400 |
| b |
| @@ -0,0 +1,28 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="regtools" version="0.3.0"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone --recursive https://github.com/griffithlab/regtools.git</action> + <action type="make_directory">build</action> + <action type="change_directory">build</action> + + <action type="set_environment_for_install"> + <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="cmake" version="3.2.3" /> + </repository> + </action> + <action type="shell_command">cmake ..</action> + + <action type="shell_command">make</action> + <action type="move_file"> + <source>regtools</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |
| b |
| diff -r 000000000000 -r 01ed8e112f2a validator.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/validator.py Wed Apr 12 17:44:58 2017 -0400 |
| [ |
| @@ -0,0 +1,39 @@ +import sys + +""" +Call checkAndFixBed, check the integrity of bed file. If the strand is not "+" or "-" truncate that line and report to users +create a column and move the score column to that column. +""" +def checkAndFixBed(bedfile, revised_file): +# Store the lines that have been removed + removedLines = [] +# Remove the lines with invalid strand, create a score column to store the original scores and change scores in the original score column all to 1000 + with open(revised_file, 'w') as tmp: + with open(bedfile, 'r') as f: + lines = f.readlines() + i = 1 + for line in lines: + fields = line.split() + strand = fields[5] + score = fields[4] + fields[4] = '1000' + fields.append(score) + if (strand == '+' or strand == '-'): + tmp.write('\t'.join(map(str, fields))) + tmp.write("\n") + else: + removedLines.append("line" + str(i) + ": " + line) + i = i+1 + + return removedLines + +def main(): + inputfile = str(sys.argv[1]) + outputfile = str(sys.argv[2]) + removed = checkAndFixBed(inputfile, outputfile) + if (removed != []): + print "\nRemoved invalid lines: \n" + print "\n".join(removed) + +if __name__ == "__main__": + main() |