Mercurial > repos > petr-novak > re_utils
changeset 14:62fefa284036 draft
Uploaded
| author | petr-novak |
|---|---|
| date | Fri, 07 Feb 2020 06:06:47 -0500 |
| parents | f12eb3896842 |
| children | a675b4534b19 |
| files | RM_custom_search.py RM_custom_search.xml rmsk_summary_table_multiple.r |
| diffstat | 3 files changed, 16 insertions(+), 21 deletions(-) [+] |
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--- a/RM_custom_search.py Fri Feb 07 02:25:47 2020 -0500 +++ b/RM_custom_search.py Fri Feb 07 06:06:47 2020 -0500 @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/env python ''' RepeatMasker search against custom database input: - archive with sequencing data @@ -57,7 +57,7 @@ def summarizeRepeatMaskerOutput(htmlout = "summary.html"): cmd = os.path.dirname(os.path.abspath(__file__))+"/rmsk_summary_table_multiple.r" - args = [ cmd, "-f", "dir_CL*/reads.fas", "-r", "dir_CL*/reads.fas.out", "-o", "RM-custom_output_table" ] + args = [ cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", "RM-custom_output_table" ] status=subprocess.call(args) cmd = cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R" args = [cmd, htmlout]
--- a/RM_custom_search.xml Fri Feb 07 02:25:47 2020 -0500 +++ b/RM_custom_search.xml Fri Feb 07 06:06:47 2020 -0500 @@ -1,15 +1,17 @@ -<tool id="RMsearch" name="RepeatMasker custom search" version="1.0.3"> +<tool id="RMsearch2" name="RepeatMasker custom search2" version="1.0.3"> <description>Scan clustering results using RepeatMasker against custom database of repeats</description> <requirements> <requirement type="package" version="4.0.7">repeatmasker</requirement> - <requirement type="package">r-r2html</requirement> - <requirement type="package">r-getopt</requirement> - <requirement type="package">bioconductor-biostrings</requirement> + <requirement type="package" version="3.6">python</requirement> + <requirement type="package" version="2.3.2">r-r2html</requirement> + <requirement type="package" version="2.54.0">bioconductor-biostrings</requirement> </requirements> - <command interpreter="python3"> - RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html + <command> + + python3 ${__tool_directory__}/RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html; + </command> <inputs>
--- a/rmsk_summary_table_multiple.r Fri Feb 07 02:25:47 2020 -0500 +++ b/rmsk_summary_table_multiple.r Fri Feb 07 06:06:47 2020 -0500 @@ -3,19 +3,12 @@ # analysis of *.out file # input arguments: <rmsk_result.out> <reads.fas. # calculates totoal proportion of matched repetetive families and averagee score and print the table -suppressPackageStartupMessages(library(getopt)) -# INPUT ARGUMENTS: -opt = getopt(matrix(c( - 'fasta', 'f', 1, "character", - 'repeat_masker','r', 1, "character", - 'output', 'o', 1, "character", - 'help','h',0,'logical'),ncol=4,byrow=T)) +opt = list() +opt$fasta = commandArgs(T)[1] +opt$repeat_masker = commandArgs(T)[2] +opt$output = commandArgs(T)[3] -if (!is.null(opt$help)) { -cat("Usage:\n\n -f fasta file \n -r repeat masker output\n -o output files\n") -stop() -} RMfiles=system(paste("ls ",opt$repeat_masker,sep=""),intern=T) fasta=system(paste("ls ",opt$fasta,sep=""),intern=T) @@ -23,8 +16,8 @@ getsubdir=function(x){ - xx=gsub(".*/","",x) - sdir=gsub(xx,"",x,fixed=T) + xx=gsub(".*/","",x) + sdir=gsub(xx,"",x,fixed=T) sdir }