bam 转 wig 并批量处理的方法

git clone https://github.com/Gaius-Augustus/Augustus.git
cd Augustus
make augustus

git clone https://github.com/Gaius-Augustus/Augustus.git
cd Augustus/auxprogs/bam2wig
make
./Augustus/bin/bam2wig

Usage: bam2wig [-r region] [-t trackname] <in.bam>
-----------------------------------------------------------------
 -r   Allows user to specify a target region, e.g. 'chr3L:10-250'
      This option can only be used if an index file exists
      See: samtools index
 -t   A string might be provided as track name

NOTE:File needs to be sorted by Reference ID (i.e. target name)
Use 'samtools sort <in.bam>' to such effect.

## check
samtools quickcheck SRR******.bam
## sort
samtools sort SRR******.bam -@8 -o SRR******.sorted.bam
samtools stats SRR******.sorted.bam | grep 'is sorted'
## bam2wig
bam2wig SRR******.sorted.bam > SRR6131113.wig

#!/bin/bash
SHELL_FOLDER=$(cd "$(dirname "$0")";pwd)
echo $SHELL_FOLDER/data
# cd $SHELL_FOLDER/data
data_dir=$SHELL_FOLDER/data

## get filenames
samplefile="samplenames.txt"
if [ ! -d $samplefile ]; then
        filenames=$(ls $data_dir)
        for filename in $filenames
        do
                echo $filename
        done > filenames.txt
        ### get samplenames
        grep -oP ".*?(?=\.)" filenames.txt | awk ' !x[$0]++' > samplenames.txt
else
        echo "$samplename exists!"
fi

#!/bin/bash
# 检查 env.txt 文件是否存在
if [ -f "${HOME}/env.txt" ]; then
  # 如果 env.txt 存在，则运行相应的命令
  while IFS='=' read -r key value; do
    echo "$key=$value"
    export "$key"="$value"
  done < "${HOME}/env.txt"
else
  # 运行其他命令
  echo "env.txt 文件不存在"
fi

SHELL_FOLDER=$(cd "$(dirname "$0")";pwd)
data_dir=$SHELL_FOLDER/data
results_dir=$SHELL_FOLDER/results
mkdir -p $data_dir
mkdir -p $results_dir
echo $data_dir
cd $data_dir
# samplefile=$data_dir/samplenames.txt
samplefile=$SHELL_FOLDER"/samplenames.txt"

eval "$(conda shell.bash hook)"
conda activate bulkrna

#Run
data_dir=$SHELL_FOLDER/data
data_dir_process=$SHELL_FOLDER/data_process
mkdir -p $data_dir_process

num=$(wc -l < $samplefile)
# for i in $(seq 2 2)
for i in $(seq 1 $num)
do
    echo $i
    samplename=$(sed -n "${i}p" $samplefile)
#     echo $samplename
#     cd $data_dir_process
    if [ ! -d $samplename ]; then
            echo "$samplename not completed, process in $data_dir"
            sample_file=${data_dir}/${samplename}.bam
            samtools quickcheck ${sample_file}
            echo "$samplename is checked"
            sort_file=${data_dir_process}/${samplename}.sorted.bam
            samtools sort ${sample_file} -@8 -o ${sort_file}
            samtools stats ${sort_file} | grep 'is sorted'
            Augustus/bin/bam2wig ${sort_file} > ${results_dir}/${samplename}.wig
    else
            echo "$samplename exists!"
    fi
done > run.log