How to create tabular matrix from the output of bash loop?
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I have a bashloop that looks like below:
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
The output I am saving as total_coverage_on_each_strand.txt for $f=1 looks like this:
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
I was wondering if there is a way to save this in a variable instead of doing > >(tee total_coverage_on_each_strand.txt) 2>&1. What do I need to do in above for loop so that I could get something like below instead?
sample type counts
sorted1.bam Counts for positive 200229
sorted1.bam Counts for negative 305934
bash shell loops
asked Nov 21 at 21:33
MAPK
1,619830
add a comment |
up vote
0
down vote
favorite
I have a bashloop that looks like below:
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
The output I am saving as total_coverage_on_each_strand.txt for $f=1 looks like this:
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
I was wondering if there is a way to save this in a variable instead of doing > >(tee total_coverage_on_each_strand.txt) 2>&1. What do I need to do in above for loop so that I could get something like below instead?
sample type counts
sorted1.bam Counts for positive 200229
sorted1.bam Counts for negative 305934
bash shell loops
asked Nov 21 at 21:33
MAPK
1,619830
A first step: replaceecho "Counts for positive: " $fwithecho -n "$f"
– Cyrus
Nov 21 at 21:37
Why would you write> >(tee)instead of| tee?
– Socowi
Nov 21 at 22:18
add a comment |
up vote
0
down vote
favorite
up vote
0
down vote
favorite
I have a bashloop that looks like below:
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
The output I am saving as total_coverage_on_each_strand.txt for $f=1 looks like this:
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
I was wondering if there is a way to save this in a variable instead of doing > >(tee total_coverage_on_each_strand.txt) 2>&1. What do I need to do in above for loop so that I could get something like below instead?
sample type counts
sorted1.bam Counts for positive 200229
sorted1.bam Counts for negative 305934
bash shell loops
asked Nov 21 at 21:33
MAPK
1,619830
I have a bashloop that looks like below:
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
The output I am saving as total_coverage_on_each_strand.txt for $f=1 looks like this:
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
I was wondering if there is a way to save this in a variable instead of doing > >(tee total_coverage_on_each_strand.txt) 2>&1. What do I need to do in above for loop so that I could get something like below instead?
sample type counts
sorted1.bam Counts for positive 200229
sorted1.bam Counts for negative 305934
bash shell loops
bash shell loops
asked Nov 21 at 21:33
MAPK
1,619830
asked Nov 21 at 21:33
MAPK
1,619830
asked Nov 21 at 21:33
MAPK
1,619830
asked Nov 21 at 21:33
MAPK
1,619830
asked Nov 21 at 21:33
MAPK
1,619830
1,619830
A first step: replaceecho "Counts for positive: " $fwithecho -n "$f"
– Cyrus
Nov 21 at 21:37
Why would you write> >(tee)instead of| tee?
– Socowi
Nov 21 at 22:18
add a comment |
A first step: replaceecho "Counts for positive: " $fwithecho -n "$f"
– Cyrus
Nov 21 at 21:37
Why would you write> >(tee)instead of| tee?
– Socowi
Nov 21 at 22:18
A first step: replace
echo "Counts for positive: " $f with echo -n "$f"– Cyrus
Nov 21 at 21:37
A first step: replace
echo "Counts for positive: " $f with echo -n "$f"– Cyrus
Nov 21 at 21:37
Why would you write
> >(tee) instead of | tee?– Socowi
Nov 21 at 22:18
Why would you write
> >(tee) instead of | tee?– Socowi
Nov 21 at 22:18
add a comment |
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A first step: replace
echo "Counts for positive: " $fwithecho -n "$f"– Cyrus
Nov 21 at 21:37
Why would you write
> >(tee)instead of| tee?– Socowi
Nov 21 at 22:18