Complex nested for loop in directory
I have two sets of files in two separate directories organized as such:
#first directory
/direc1/files
file0.num1.tar.gz
file0.num2.tar.gz
file0.num3.tar.gz
file0.num4.tar.gz
.
.
.
file0.22.tar.gz
#second directory
/directory2/files
textfile.num1.tar.gz
textfile.num2.tar.gz
textfile.num3.tar.gz
textfile.num4.tar.gz
.
.
.
textfile.num22.tar.gz
In the first directory, I have 242 files in total. In the second directory I have 22 files.
I have written a simple nested for loop that uses script.py, as shown below. This loop works, but it has a caveat.
for z in `seq 0 10`; do
for i in `seq 1 22`; do python script.py --l2 --bfile ../directory2/textfile.num${i}.tar.gz --secondfile file${z}.num${i} --out file${z}.${i} --print-snps;done;done
If you notice, I have hardcoded file. Is there a way to run this without having to type in the filename?
The mapping logic is simple - files with the same "num" in the filename must map to one another. So:
file0.num1.tar.gz, file1.num1.tar.gz ... file10.num1.tar.gz must map to textfile.num1.tar.gz. And as a second example.
file0.num2.tar.gz, file1.num2.tar.gz ... file10.num2.tar.gz must map to textfile.num2.tar.gz
My loop is accomplishing this already, but I want to be able to write it without having to write file in the loop.
UPDATE:
I have gotten flagged for posting a duplicate question (I asked a somewhat similar question here: Nested for Loop In Directory). My previous question asked how I can use variables instead of filenames to run a loop. This question asks how I can use variables given that my loop runs on two separate directories .
linux shell directory variable
edited Dec 17 at 18:36
Kusalananda
121k16229372
asked Dec 15 at 23:48
Workhorse
1104
add a comment |
I have two sets of files in two separate directories organized as such:
#first directory
/direc1/files
file0.num1.tar.gz
file0.num2.tar.gz
file0.num3.tar.gz
file0.num4.tar.gz
.
.
.
file0.22.tar.gz
#second directory
/directory2/files
textfile.num1.tar.gz
textfile.num2.tar.gz
textfile.num3.tar.gz
textfile.num4.tar.gz
.
.
.
textfile.num22.tar.gz
In the first directory, I have 242 files in total. In the second directory I have 22 files.
I have written a simple nested for loop that uses script.py, as shown below. This loop works, but it has a caveat.
for z in `seq 0 10`; do
for i in `seq 1 22`; do python script.py --l2 --bfile ../directory2/textfile.num${i}.tar.gz --secondfile file${z}.num${i} --out file${z}.${i} --print-snps;done;done
If you notice, I have hardcoded file. Is there a way to run this without having to type in the filename?
The mapping logic is simple - files with the same "num" in the filename must map to one another. So:
file0.num1.tar.gz, file1.num1.tar.gz ... file10.num1.tar.gz must map to textfile.num1.tar.gz. And as a second example.
file0.num2.tar.gz, file1.num2.tar.gz ... file10.num2.tar.gz must map to textfile.num2.tar.gz
My loop is accomplishing this already, but I want to be able to write it without having to write file in the loop.
UPDATE:
I have gotten flagged for posting a duplicate question (I asked a somewhat similar question here: Nested for Loop In Directory). My previous question asked how I can use variables instead of filenames to run a loop. This question asks how I can use variables given that my loop runs on two separate directories .
linux shell directory variable
edited Dec 17 at 18:36
Kusalananda
121k16229372
asked Dec 15 at 23:48
Workhorse
1104
add a comment |
I have two sets of files in two separate directories organized as such:
#first directory
/direc1/files
file0.num1.tar.gz
file0.num2.tar.gz
file0.num3.tar.gz
file0.num4.tar.gz
.
.
.
file0.22.tar.gz
#second directory
/directory2/files
textfile.num1.tar.gz
textfile.num2.tar.gz
textfile.num3.tar.gz
textfile.num4.tar.gz
.
.
.
textfile.num22.tar.gz
In the first directory, I have 242 files in total. In the second directory I have 22 files.
I have written a simple nested for loop that uses script.py, as shown below. This loop works, but it has a caveat.
for z in `seq 0 10`; do
for i in `seq 1 22`; do python script.py --l2 --bfile ../directory2/textfile.num${i}.tar.gz --secondfile file${z}.num${i} --out file${z}.${i} --print-snps;done;done
If you notice, I have hardcoded file. Is there a way to run this without having to type in the filename?
The mapping logic is simple - files with the same "num" in the filename must map to one another. So:
file0.num1.tar.gz, file1.num1.tar.gz ... file10.num1.tar.gz must map to textfile.num1.tar.gz. And as a second example.
file0.num2.tar.gz, file1.num2.tar.gz ... file10.num2.tar.gz must map to textfile.num2.tar.gz
My loop is accomplishing this already, but I want to be able to write it without having to write file in the loop.
UPDATE:
I have gotten flagged for posting a duplicate question (I asked a somewhat similar question here: Nested for Loop In Directory). My previous question asked how I can use variables instead of filenames to run a loop. This question asks how I can use variables given that my loop runs on two separate directories .
linux shell directory variable
edited Dec 17 at 18:36
Kusalananda
121k16229372
asked Dec 15 at 23:48
Workhorse
1104
I have two sets of files in two separate directories organized as such:
#first directory
/direc1/files
file0.num1.tar.gz
file0.num2.tar.gz
file0.num3.tar.gz
file0.num4.tar.gz
.
.
.
file0.22.tar.gz
#second directory
/directory2/files
textfile.num1.tar.gz
textfile.num2.tar.gz
textfile.num3.tar.gz
textfile.num4.tar.gz
.
.
.
textfile.num22.tar.gz
In the first directory, I have 242 files in total. In the second directory I have 22 files.
I have written a simple nested for loop that uses script.py, as shown below. This loop works, but it has a caveat.
for z in `seq 0 10`; do
for i in `seq 1 22`; do python script.py --l2 --bfile ../directory2/textfile.num${i}.tar.gz --secondfile file${z}.num${i} --out file${z}.${i} --print-snps;done;done
If you notice, I have hardcoded file. Is there a way to run this without having to type in the filename?
The mapping logic is simple - files with the same "num" in the filename must map to one another. So:
file0.num1.tar.gz, file1.num1.tar.gz ... file10.num1.tar.gz must map to textfile.num1.tar.gz. And as a second example.
file0.num2.tar.gz, file1.num2.tar.gz ... file10.num2.tar.gz must map to textfile.num2.tar.gz
My loop is accomplishing this already, but I want to be able to write it without having to write file in the loop.
UPDATE:
I have gotten flagged for posting a duplicate question (I asked a somewhat similar question here: Nested for Loop In Directory). My previous question asked how I can use variables instead of filenames to run a loop. This question asks how I can use variables given that my loop runs on two separate directories .
linux shell directory variable
linux shell directory variable
edited Dec 17 at 18:36
Kusalananda
121k16229372
asked Dec 15 at 23:48
Workhorse
1104
edited Dec 17 at 18:36
Kusalananda
121k16229372
asked Dec 15 at 23:48
Workhorse
1104
edited Dec 17 at 18:36
Kusalananda
121k16229372
edited Dec 17 at 18:36
Kusalananda
121k16229372
edited Dec 17 at 18:36
Kusalananda
121k16229372
121k16229372
asked Dec 15 at 23:48
Workhorse
1104
asked Dec 15 at 23:48
Workhorse
1104
asked Dec 15 at 23:48
Workhorse
1104
1104
add a comment |
add a comment |
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