Mercurial > repos > nikos > bigwig_to_wig
changeset 16:b8e3e97e9658 draft
Uploaded
| author | nikos |
|---|---|
| date | Fri, 01 Aug 2014 08:10:27 -0400 |
| parents | 52e9cfd72b21 |
| children | 7e547e104886 |
| files | bigwig_to_wig.sh bigwig_to_wig.xml test-data/1.bigwig tool_dependencies.xml |
| diffstat | 4 files changed, 154 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwig_to_wig.sh Fri Aug 01 08:10:27 2014 -0400 @@ -0,0 +1,77 @@ +#!/bin/bash +#$Id: bigwig2wig 23 2014-01-28 12:09:22Z jens $ + +#SCRIPT CONVERTS BIGWIG FILE TO FIXED-STEP WIGGLE FORMAT FILE +#RESOLUTION IS CONTROLLED THROUGH THE BIN SIZE + +#default bin_size +bin_size=500 +mylab="wiggle file" + +#parse input +while getopts hf:b:l: myarg +do case "$myarg" in + h) echo "Usage: bigwig_correlation -f <bigwig_file> -b <bin_size>" + echo "Ex: bigwig_correlation -f <MYFILE.bw> -b 600" + exit ;; + f) bigwig_file="$OPTARG" ;; #required + l) mylab="$OPTARG" ;; #optional + b) bin_size="$OPTARG" ;; #optional + [?]) echo "Usage: bigwig_correlation -f <MYFILE.bw> -b <bin_size>" + exit 1 ;; + esac +done + +################################################### +###VALIDATE INPUT +################################################### + +#make tmp-filename to hold chromosome info +org_assembly_file=`mktemp -u` +bigWigInfo -chroms $bigwig_file | perl -ne "/^\tchr/ && print" | perl -pe "s/ +/\t/g" | cut -f2,4 > $org_assembly_file + +#check bin_size & define step_size +bin_size_mod=`expr $bin_size % 2` #determine modulus +if [ $bin_size_mod -ne 0 ]; then + echo "Chosen bin_size must be an even positive number, added +1 to bin_size" + bin_size=$(($bin_size + 1)) +fi + +if [ $bin_size -lt 100 ]; then + echo "ERROR: Chosen bin_size must be a positive number >=100" + exit 1 +fi +#set stetp size equal to bin size i.e. non-overlapping intervals +step_size=$bin_size + +################################################### +###EXTRACT DENSITIES FROM NORMALIZED BIGWIG FILES +################################################### + + +#make track definition line +echo "track type=wiggle_0 name=$mylab description=\"fixedStep format\"" + +#for each chromsome +cat $org_assembly_file | while read line; do + + cur_chr=`echo $line | cut --delimiter=" " -f1` + cur_length=`echo $line | cut --delimiter=" " -f2` + + n_bins=`echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc` + + start=1 + stop=`echo "$n_bins * $bin_size" | bc` + + #write header line for each chromosome + echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size" + + #get densities along chr in n_bins with chosen bin_size and step_size (giving overlap in bins) + nice bigWigSummary $bigwig_file $cur_chr $start $stop $n_bins | perl -pe 's/\t/\n/g' | perl -pe "s/n\/a/0/" + #gives warning if no data in/for current chromosome + +done + +#rm tmp +rm $org_assembly_file +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwig_to_wig.xml Fri Aug 01 08:10:27 2014 -0400 @@ -0,0 +1,34 @@ +<tool id="bigwig_to_wig" name="BigWig to Wig" version="1.0.0"> + <description>converter</description> + <command>bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output </command> + <requirements> + <requirement type="package">bigWigSummary</requirement> + <requirement type="package">bigWigInfo</requirement> + </requirements> + <inputs> + <param format="bigwig" name="input" type="data" label="BigWig file to convert" /> + <param name="bin_size" size="4" type="integer" value="500" label="Bin size" help="Must be an even integer > 100." /> + <param name="mylab" type="text" value="wiggle_file" label="Output file prefix" help="" /> + </inputs> + <outputs> + <data format="wig" name="output" label="${mylab}_density_bin${bin_size}.wig" /> + </outputs> + <tests> + <test> + <param name="input" value="1.bigwig" /> + <param name="bin_size" value="500" /> + <output name="output" file="1.wig" /> + <test> + </tests> + <help> + +This tool converts a **BigWig** file to fixed step **Wiggle** format. +Resolution is controlled through the bin size (the higher the size, the lower the resolution). + +The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigInfo_ and bigWigSummary_. + +.. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo +.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Aug 01 08:10:27 2014 -0400 @@ -0,0 +1,43 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bigWigSummary"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="x86_64"> + <action type="download_binary"><url_template>http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary</url_template></action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + + + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme> + </readme> + </package> + <package name="bigWigInfo"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="x86_64"> + <action type="download_binary"><url_template>http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template></action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + + + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme> + </readme> + </package> +</tool_dependency>