From 66415b36c5bfdc7ca602b2de5288c83e8a4795ef Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Tue, 24 Mar 2020 18:51:12 +0100 Subject: [PATCH] Make slurm-compatible script. --- scripts/bam2bigwig.sh | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/scripts/bam2bigwig.sh b/scripts/bam2bigwig.sh index 6c1b909..cd7a7d6 100755 --- a/scripts/bam2bigwig.sh +++ b/scripts/bam2bigwig.sh @@ -1,4 +1,4 @@ -#!/bin/dash +#!/bin/bash -l # Usage: bam2bigwig.sh <sorted.bam> <bin_file> <library_name> <orientation> <strandedness> [<normalization>] <bigwig> # <bin_file> should be a bed file representing 10 bp bins along the genome # <orientation> must be "all", "fwd" or "rev" @@ -30,7 +30,6 @@ # * python3 -> module load Python/3.6.0 # * samtools -> module load samtools/1.9 # * bedtools -> module load bedtools/2.25.0 -# * mawk -> use alias if absent # * parallel (for niceload) -> module load parallel/20170122 # * UCSC-tools (for bedGraphToBigWig) -> module load UCSC-tools/v373 @@ -66,7 +65,6 @@ error_exit () exit 1 } -mawk --version 1> /dev/null 2> /dev/null || alias mawk='awk' load_tools || error_exit "Some tools are not available" @@ -74,7 +72,7 @@ bam=${1} bin_file=${2} # Example of how to generate the bin_file from iGenome data: # cd /Genomes/C_elegans -# mawk '$1 == "@SQ" {print $2"\t0\t"$3}' Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.dict \ +# awk '$1 == "@SQ" {print $2"\t0\t"$3}' Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.dict \ # | sed 's/SN://g' | sed 's/LN://' \ # | bedops --chop 10 - \ # > Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/genome_binned_10.bed @@ -163,7 +161,7 @@ fi echo "getting chromosome bounds" genome_file="${workdir}/chrom_sizes.txt" samtools view -H ${bam} \ - | mawk '$1 == "@SQ" {print $2"\t"$3}' \ + | awk '$1 == "@SQ" {print $2"\t"$3}' \ | sed 's/SN://g' | sed 's/LN://' \ > ${genome_file} || error_exit "making ${genome_file} failed" #> ${genome_file} || cleanup && error_exit "making ${genome_file} failed" @@ -172,7 +170,7 @@ compute_coverage() { cmd="niceload --noswap bedtools genomecov -bg -split ${orient_filter} ${scaling} -ibam ${bam}" eval ${cmd} \ - | mawk '{ print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; }' | sort-bed - \ + | awk '{ print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; }' | sort-bed - \ || error_exit "compute_coverage failed" #|| cleanup && error_exit "compute_coverage failed" } -- GitLab