How can I use a for loop to run a command over several files with unique output files? The...
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How can I use a for loop to run a command over several files with unique output files?
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I need to run a command with the below syntax for 1000 files in a directory and save the output to a unique file for each iteration.
command universalinputfile variableinputfile > outputfile
for example
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_1rndb > motifoutput/output_1
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_2rndb > motifoutput/output_2
I've tried using the below for loop without success.
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_$irndb > motifoutput/output_$i
done
I've also tried the for loop with the "for file in /dir" format without success.
How can I do this?
linux bash
edited 14 mins ago
Stephen Harris
27.5k35383
asked 16 mins ago
begginer_bioinformaticsbegginer_bioinformatics
1
New contributor
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |
I need to run a command with the below syntax for 1000 files in a directory and save the output to a unique file for each iteration.
command universalinputfile variableinputfile > outputfile
for example
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_1rndb > motifoutput/output_1
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_2rndb > motifoutput/output_2
I've tried using the below for loop without success.
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_$irndb > motifoutput/output_$i
done
I've also tried the for loop with the "for file in /dir" format without success.
How can I do this?
linux bash
edited 14 mins ago
Stephen Harris
27.5k35383
asked 16 mins ago
begginer_bioinformaticsbegginer_bioinformatics
1
New contributor
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Do you wantrandomseq_${i}rndbto scope the variable${i}?
– Stephen Harris
13 mins ago
Yes exactly. Each input file is named "randomseq_irndb" where i is a number 1 through 1000. I want to run the MotifPSSM command on all 1000 files and have a unique output file for each.
– begginer_bioinformatics
10 mins ago
Try yourforloop with${i}rndb. Your script had$irndbwhich is totally different; it's looking for a variable calledirndbinstead of a variableifollowed byrndb
– Stephen Harris
9 mins ago
add a comment |
I need to run a command with the below syntax for 1000 files in a directory and save the output to a unique file for each iteration.
command universalinputfile variableinputfile > outputfile
for example
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_1rndb > motifoutput/output_1
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_2rndb > motifoutput/output_2
I've tried using the below for loop without success.
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_$irndb > motifoutput/output_$i
done
I've also tried the for loop with the "for file in /dir" format without success.
How can I do this?
linux bash
edited 14 mins ago
Stephen Harris
27.5k35383
asked 16 mins ago
begginer_bioinformaticsbegginer_bioinformatics
1
New contributor
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
I need to run a command with the below syntax for 1000 files in a directory and save the output to a unique file for each iteration.
command universalinputfile variableinputfile > outputfile
for example
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_1rndb > motifoutput/output_1
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_2rndb > motifoutput/output_2
I've tried using the below for loop without success.
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_$irndb > motifoutput/output_$i
done
I've also tried the for loop with the "for file in /dir" format without success.
How can I do this?
linux bash
linux bash
edited 14 mins ago
Stephen Harris
27.5k35383
asked 16 mins ago
begginer_bioinformaticsbegginer_bioinformatics
1
New contributor
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited 14 mins ago
Stephen Harris
27.5k35383
asked 16 mins ago
begginer_bioinformaticsbegginer_bioinformatics
1
New contributor
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited 14 mins ago
Stephen Harris
27.5k35383
edited 14 mins ago
Stephen Harris
27.5k35383
edited 14 mins ago
Stephen Harris
27.5k35383
27.5k35383
asked 16 mins ago
begginer_bioinformaticsbegginer_bioinformatics
1
New contributor
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 16 mins ago
begginer_bioinformaticsbegginer_bioinformatics
1
asked 16 mins ago
begginer_bioinformaticsbegginer_bioinformatics
1
1
New contributor
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
begginer_bioinformatics is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Do you wantrandomseq_${i}rndbto scope the variable${i}?
– Stephen Harris
13 mins ago
Yes exactly. Each input file is named "randomseq_irndb" where i is a number 1 through 1000. I want to run the MotifPSSM command on all 1000 files and have a unique output file for each.
– begginer_bioinformatics
10 mins ago
Try yourforloop with${i}rndb. Your script had$irndbwhich is totally different; it's looking for a variable calledirndbinstead of a variableifollowed byrndb
– Stephen Harris
9 mins ago
add a comment |
Do you wantrandomseq_${i}rndbto scope the variable${i}?
– Stephen Harris
13 mins ago
Yes exactly. Each input file is named "randomseq_irndb" where i is a number 1 through 1000. I want to run the MotifPSSM command on all 1000 files and have a unique output file for each.
– begginer_bioinformatics
10 mins ago
Try yourforloop with${i}rndb. Your script had$irndbwhich is totally different; it's looking for a variable calledirndbinstead of a variableifollowed byrndb
– Stephen Harris
9 mins ago
Do you want
randomseq_${i}rndb to scope the variable ${i} ?– Stephen Harris
13 mins ago
Do you want
randomseq_${i}rndb to scope the variable ${i} ?– Stephen Harris
13 mins ago
Yes exactly. Each input file is named "randomseq_irndb" where i is a number 1 through 1000. I want to run the MotifPSSM command on all 1000 files and have a unique output file for each.
– begginer_bioinformatics
10 mins ago
Yes exactly. Each input file is named "randomseq_irndb" where i is a number 1 through 1000. I want to run the MotifPSSM command on all 1000 files and have a unique output file for each.
– begginer_bioinformatics
10 mins ago
Try your
for loop with ${i}rndb. Your script had $irndb which is totally different; it's looking for a variable called irndb instead of a variable i followed by rndb– Stephen Harris
9 mins ago
Try your
for loop with ${i}rndb. Your script had $irndb which is totally different; it's looking for a variable called irndb instead of a variable i followed by rndb– Stephen Harris
9 mins ago
add a comment |
1 Answer
1
active
oldest
votes
$irndb is read as a single variable called irndb. You can change the parse to use just i as the variable name with ${i}rndb:
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_${i}rndb > motifoutput/output_$i
done
The for loop itself was fine, including the brace expansion {1..1000}, so you don't need to change that.
answered 7 mins ago
Michael HomerMichael Homer
50.9k8141178
add a comment |
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votes
$irndb is read as a single variable called irndb. You can change the parse to use just i as the variable name with ${i}rndb:
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_${i}rndb > motifoutput/output_$i
done
The for loop itself was fine, including the brace expansion {1..1000}, so you don't need to change that.
answered 7 mins ago
Michael HomerMichael Homer
50.9k8141178
add a comment |
$irndb is read as a single variable called irndb. You can change the parse to use just i as the variable name with ${i}rndb:
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_${i}rndb > motifoutput/output_$i
done
The for loop itself was fine, including the brace expansion {1..1000}, so you don't need to change that.
answered 7 mins ago
Michael HomerMichael Homer
50.9k8141178
add a comment |
$irndb is read as a single variable called irndb. You can change the parse to use just i as the variable name with ${i}rndb:
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_${i}rndb > motifoutput/output_$i
done
The for loop itself was fine, including the brace expansion {1..1000}, so you don't need to change that.
answered 7 mins ago
Michael HomerMichael Homer
50.9k8141178
$irndb is read as a single variable called irndb. You can change the parse to use just i as the variable name with ${i}rndb:
for i in {1..1000}
do
MotifPSSM ../source/FruR-DPInteract.txt genrand/randomseq_${i}rndb > motifoutput/output_$i
done
The for loop itself was fine, including the brace expansion {1..1000}, so you don't need to change that.
answered 7 mins ago
Michael HomerMichael Homer
50.9k8141178
answered 7 mins ago
Michael HomerMichael Homer
50.9k8141178
answered 7 mins ago
Michael HomerMichael Homer
50.9k8141178
answered 7 mins ago
Michael HomerMichael Homer
50.9k8141178
50.9k8141178
add a comment |
add a comment |
begginer_bioinformatics is a new contributor. Be nice, and check out our Code of Conduct.
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Do you want
randomseq_${i}rndbto scope the variable${i}?– Stephen Harris
13 mins ago
Yes exactly. Each input file is named "randomseq_irndb" where i is a number 1 through 1000. I want to run the MotifPSSM command on all 1000 files and have a unique output file for each.
– begginer_bioinformatics
10 mins ago
Try your
forloop with${i}rndb. Your script had$irndbwhich is totally different; it's looking for a variable calledirndbinstead of a variableifollowed byrndb– Stephen Harris
9 mins ago