# HG changeset patch # User yating-l # Date 1492033498 14400 # Node ID 01ed8e112f2a4d09aa9f1a5c3e9a5576d5cec0e4 planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d 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 @@ -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. 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 @@ -0,0 +1,138 @@ + + Extract splice junctions from a RNA-Seq BAM file + + regtools + + + + + + + + + + Only considers spliced RNA-Seq reads with this minimum intron length (-i) + + + Only considers spliced RNA-Seq reads with this maximum intron length (-I) + + + + + + + + + + Only report splice junctions with this minimum anchor length on both sides of the junction (-a) + + + Only report splice junctions within this region (format = chrom:start-end) (-r) + ^([^:]+):(\d+)-(\d+)$ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `_ +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 `_. The minimum +intron size for the command-line version of ``regtools junctions extract`` is 70 bp. + + ]]> + + +@misc{githubregtools, + author = {Griffith Lab}, + year = {2016}, + title = {regtools}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/griffithlab/regtools}, +} + + diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3.bam Binary file test-data/Dbia3.bam has changed diff -r 000000000000 -r 01ed8e112f2a test-data/Dbia3.bam.bai Binary file test-data/Dbia3.bam.bai has changed 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 @@ -0,0 +1,1892 @@ +contig1 1052 1272 JUNC00000001 2 - 1052 1272 255,0,0 2 65,99 0,121 +contig1 5287 12663 JUNC00000002 16 - 5287 12663 255,0,0 2 122,123 0,7253 +contig1 33709 33999 JUNC00000003 12 - 33709 33999 255,0,0 2 117,120 0,170 +contig1 33920 34213 JUNC00000004 13 - 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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 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 @@ -0,0 +1,28 @@ + + + + + + git clone --recursive https://github.com/griffithlab/regtools.git + build + build + + + + + + + cmake .. + + make + + regtools + $INSTALL_DIR + + + $INSTALL_DIR + + + + + 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()