如何从bash循环的输出创建表格矩阵?

时间:2018-11-21 21:33:28

标签: bash shell loops

我有一个如下所示的bashloop:

for f in sorted*.bam; do
echo "Counts for positive: " $f
bedtools coverage -a my_region.bed -b $f -bed -s
echo "Counts for negative: " $f
bedtools coverage -a my_region.bed -b $f -bed -S 
done  > >(tee total_coverage_on_each_strand.txt) 2>&1

我为$ f = 1保存为total_coverage_on_each_strand.txt的输出看起来像这样:

Counts for positive:  sorted1.bam
reverseKF898354 0   14580   my_region   0   +   200229  14347   14580   0.9840192
Counts for negative:  sorted1.bam
reverseKF898354 0   14580   my_region   0   +   305934  14320   14580   0.9821674

我想知道是否有一种方法可以将其保存在变量中,而不是执行> >(tee total_coverage_on_each_strand.txt) 2>&1。我需要在上面的for循环中做些什么,以便可以代替下面的内容?

sample  type    counts
sorted1.bam Counts for positive 200229
sorted1.bam Counts for negative 305934

0 个答案:

没有答案