Mercurial > repos > yating-l > regtools_junctions_extract
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Apr 12 17:44:58 2017 -0400 @@ -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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/regtools_junctions_extract.xml Wed Apr 12 17:44:58 2017 -0400 @@ -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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--- /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 @@ -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
--- /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 @@ -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
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--- /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 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 12 17:44:58 2017 -0400 @@ -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>
--- /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()