batch run bedtools bam2bed on accepted_hits.bam in subdirectories

README.md

bam2bed_all.sh

find

• man find
• This command is used to search for files and/or subdirectories in a directory.
• In this script, find is used to search for immediate subdirectories matching the regular expression R*.dm6. The output of find is a list of each match. These subdirectories are passed through a pipe into a push/pop loop.

pushd and popd

• Wikipedia
• These commands are used to traverse directories using a stack structure.
• In this script, they are used to cd into each subdirectory (via pushd) and return to the base directory (via popd). They are also modified to run quietly (no output).

other notes

• ${} : variable subsitution
• ${PWD##*/} : basename of pwd

tophat_batch_bam2bed.sh

#!/usr/bin/env bash

pushd () {
    command pushd "$@" > /dev/null
}

popd () {
    command popd "$@" > /dev/null
}

fn_bam="accepted_hits.bam"
fn_bed="accepted_hits.bed"
bed_dir="path/to/bam2bed"
mkdir -p bed_dir

find . -mindepth 1 -maxdepth 1 -type d -name "R*.dm6" | while read -r dir
do
  pushd "$dir"
  basedir=${PWD##*/}
  fp_bed=${bed_dir}/${basedir}_${fn_bed}
  echo "Creating ${fp_bed}"
  bedtools bamtobed -i ${fn_bam} > ${fp_bed}
  popd
done