Creating a function that reads off an input list of files
I am in the process of writing bioinformatics pipelines.
These pipelines take in input files and pass them through multiple packages.
Say there is a list of files that goes file1, file2, file3... file n, and for each I want to apply a function that goes function1 -file 1| function 2 | function 3 > file 1.output but want to do it for the whole list of files using a for loop, and allocate file names to the output files accordingly, what commands and syntax should I use?
pipe function loop-device
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Nov 13 '15 at 16:12
Ankur Chakravarthy
1032
add a comment |
I am in the process of writing bioinformatics pipelines.
These pipelines take in input files and pass them through multiple packages.
Say there is a list of files that goes file1, file2, file3... file n, and for each I want to apply a function that goes function1 -file 1| function 2 | function 3 > file 1.output but want to do it for the whole list of files using a for loop, and allocate file names to the output files accordingly, what commands and syntax should I use?
pipe function loop-device
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Nov 13 '15 at 16:12
Ankur Chakravarthy
1032
add a comment |
I am in the process of writing bioinformatics pipelines.
These pipelines take in input files and pass them through multiple packages.
Say there is a list of files that goes file1, file2, file3... file n, and for each I want to apply a function that goes function1 -file 1| function 2 | function 3 > file 1.output but want to do it for the whole list of files using a for loop, and allocate file names to the output files accordingly, what commands and syntax should I use?
pipe function loop-device
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Nov 13 '15 at 16:12
Ankur Chakravarthy
1032
I am in the process of writing bioinformatics pipelines.
These pipelines take in input files and pass them through multiple packages.
Say there is a list of files that goes file1, file2, file3... file n, and for each I want to apply a function that goes function1 -file 1| function 2 | function 3 > file 1.output but want to do it for the whole list of files using a for loop, and allocate file names to the output files accordingly, what commands and syntax should I use?
pipe function loop-device
pipe function loop-device
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Nov 13 '15 at 16:12
Ankur Chakravarthy
1032
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Nov 13 '15 at 16:12
Ankur Chakravarthy
1032
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
39.2k1479130
asked Nov 13 '15 at 16:12
Ankur Chakravarthy
1032
asked Nov 13 '15 at 16:12
Ankur Chakravarthy
1032
asked Nov 13 '15 at 16:12
Ankur Chakravarthy
1032
1032
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
According to the information in your question, this should do what you requested:
for i in file1 file2 file3 file4 fileN
do
function1 "$i"| function2 | function3 > "$i".output
done
answered Nov 13 '15 at 16:16
RobertL
4,808624
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
According to the information in your question, this should do what you requested:
for i in file1 file2 file3 file4 fileN
do
function1 "$i"| function2 | function3 > "$i".output
done
answered Nov 13 '15 at 16:16
RobertL
4,808624
add a comment |
According to the information in your question, this should do what you requested:
for i in file1 file2 file3 file4 fileN
do
function1 "$i"| function2 | function3 > "$i".output
done
answered Nov 13 '15 at 16:16
RobertL
4,808624
add a comment |
According to the information in your question, this should do what you requested:
for i in file1 file2 file3 file4 fileN
do
function1 "$i"| function2 | function3 > "$i".output
done
answered Nov 13 '15 at 16:16
RobertL
4,808624
According to the information in your question, this should do what you requested:
for i in file1 file2 file3 file4 fileN
do
function1 "$i"| function2 | function3 > "$i".output
done
answered Nov 13 '15 at 16:16
RobertL
4,808624
answered Nov 13 '15 at 16:16
RobertL
4,808624
answered Nov 13 '15 at 16:16
RobertL
4,808624
answered Nov 13 '15 at 16:16
RobertL
4,808624
4,808624
add a comment |
add a comment |
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