bash script split file names
0
I have the following bash script:
#!/bin/bash
for r in $(find . -name "*.fastq");
do
cat <<EOF
#qsub <<EOF
#!/bin/bash -l
#PBS -N $r
EOF
done
Unfortunately, all filename get split:
> sh cFiltering_pbs.sh
#qsub <<EOF
#!/bin/bash -l
#PBS -N ./76A
#qsub <<EOF
#!/bin/bash -l
#PBS -N Paired.fastq
#qsub <<EOF
#!/bin/bash -l
#PBS -N ./104A
#qsub <<EOF
#!/bin/bash -l
#PBS -N Paired.fastq
Here is the find output:
find . -name "*.fastq"
./76A Paired.fastq
./104A Paired.fastq
What did I miss?
bash
asked 3 hours ago
user977828user977828
3471516
add a comment |
0
I have the following bash script:
#!/bin/bash
for r in $(find . -name "*.fastq");
do
cat <<EOF
#qsub <<EOF
#!/bin/bash -l
#PBS -N $r
EOF
done
Unfortunately, all filename get split:
> sh cFiltering_pbs.sh
#qsub <<EOF
#!/bin/bash -l
#PBS -N ./76A
#qsub <<EOF
#!/bin/bash -l
#PBS -N Paired.fastq
#qsub <<EOF
#!/bin/bash -l
#PBS -N ./104A
#qsub <<EOF
#!/bin/bash -l
#PBS -N Paired.fastq
Here is the find output:
find . -name "*.fastq"
./76A Paired.fastq
./104A Paired.fastq
What did I miss?
bash
asked 3 hours ago
user977828user977828
3471516
5
for r in $(find . -name "*.fastq");is pretty bad...
– don_crissti
3 hours ago
1
Are all yourfastqfiles in the same directory?
– roaima
3 hours ago
yes, they're all in the same directory. I solved it with this unix.stackexchange.com/a/9499/34872
– user977828
2 hours ago
That's a poor solution for your situation
– roaima
2 hours ago
2
see: Why does my shell script choke on whitespace or other special characters? and Recursively iterate through files in a directory and also mywiki.wooledge.org/WordSplitting
– ilkkachu
2 hours ago
add a comment |
0
0
0
I have the following bash script:
#!/bin/bash
for r in $(find . -name "*.fastq");
do
cat <<EOF
#qsub <<EOF
#!/bin/bash -l
#PBS -N $r
EOF
done
Unfortunately, all filename get split:
> sh cFiltering_pbs.sh
#qsub <<EOF
#!/bin/bash -l
#PBS -N ./76A
#qsub <<EOF
#!/bin/bash -l
#PBS -N Paired.fastq
#qsub <<EOF
#!/bin/bash -l
#PBS -N ./104A
#qsub <<EOF
#!/bin/bash -l
#PBS -N Paired.fastq
Here is the find output:
find . -name "*.fastq"
./76A Paired.fastq
./104A Paired.fastq
What did I miss?
bash
asked 3 hours ago
user977828user977828
3471516
I have the following bash script:
#!/bin/bash
for r in $(find . -name "*.fastq");
do
cat <<EOF
#qsub <<EOF
#!/bin/bash -l
#PBS -N $r
EOF
done
Unfortunately, all filename get split:
> sh cFiltering_pbs.sh
#qsub <<EOF
#!/bin/bash -l
#PBS -N ./76A
#qsub <<EOF
#!/bin/bash -l
#PBS -N Paired.fastq
#qsub <<EOF
#!/bin/bash -l
#PBS -N ./104A
#qsub <<EOF
#!/bin/bash -l
#PBS -N Paired.fastq
Here is the find output:
find . -name "*.fastq"
./76A Paired.fastq
./104A Paired.fastq
What did I miss?
bash
bash
asked 3 hours ago
user977828user977828
3471516
asked 3 hours ago
user977828user977828
3471516
asked 3 hours ago
user977828user977828
3471516
asked 3 hours ago
user977828user977828
3471516
asked 3 hours ago
user977828user977828
3471516
3471516
5
for r in $(find . -name "*.fastq");is pretty bad...
– don_crissti
3 hours ago
1
Are all yourfastqfiles in the same directory?
– roaima
3 hours ago
yes, they're all in the same directory. I solved it with this unix.stackexchange.com/a/9499/34872
– user977828
2 hours ago
That's a poor solution for your situation
– roaima
2 hours ago
2
see: Why does my shell script choke on whitespace or other special characters? and Recursively iterate through files in a directory and also mywiki.wooledge.org/WordSplitting
– ilkkachu
2 hours ago
add a comment |
5
for r in $(find . -name "*.fastq");is pretty bad...
– don_crissti
3 hours ago
1
Are all yourfastqfiles in the same directory?
– roaima
3 hours ago
yes, they're all in the same directory. I solved it with this unix.stackexchange.com/a/9499/34872
– user977828
2 hours ago
That's a poor solution for your situation
– roaima
2 hours ago
2
see: Why does my shell script choke on whitespace or other special characters? and Recursively iterate through files in a directory and also mywiki.wooledge.org/WordSplitting
– ilkkachu
2 hours ago
5
5
for r in $(find . -name "*.fastq"); is pretty bad...– don_crissti
3 hours ago
for r in $(find . -name "*.fastq"); is pretty bad...– don_crissti
3 hours ago
1
1
Are all your
fastq files in the same directory?– roaima
3 hours ago
Are all your
fastq files in the same directory?– roaima
3 hours ago
yes, they're all in the same directory. I solved it with this unix.stackexchange.com/a/9499/34872
– user977828
2 hours ago
yes, they're all in the same directory. I solved it with this unix.stackexchange.com/a/9499/34872
– user977828
2 hours ago
That's a poor solution for your situation
– roaima
2 hours ago
That's a poor solution for your situation
– roaima
2 hours ago
2
2
see: Why does my shell script choke on whitespace or other special characters? and Recursively iterate through files in a directory and also mywiki.wooledge.org/WordSplitting
– ilkkachu
2 hours ago
see: Why does my shell script choke on whitespace or other special characters? and Recursively iterate through files in a directory and also mywiki.wooledge.org/WordSplitting
– ilkkachu
2 hours ago
add a comment |
1 Answer
1
active
oldest
votes
1
Instead of using find you can simply loop through the files themselves. Notice that I have double-quoted "$r"; you need to do that to keep the space in the filenames intact and unparsed by the shell.
for r in *.fastq
do
# Stuff using "$r"...
:
done
answered 2 hours ago
roaimaroaima
43.4k553116
add a comment |
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1 Answer
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1
Instead of using find you can simply loop through the files themselves. Notice that I have double-quoted "$r"; you need to do that to keep the space in the filenames intact and unparsed by the shell.
for r in *.fastq
do
# Stuff using "$r"...
:
done
answered 2 hours ago
roaimaroaima
43.4k553116
add a comment |
1
Instead of using find you can simply loop through the files themselves. Notice that I have double-quoted "$r"; you need to do that to keep the space in the filenames intact and unparsed by the shell.
for r in *.fastq
do
# Stuff using "$r"...
:
done
answered 2 hours ago
roaimaroaima
43.4k553116
add a comment |
1
1
1
Instead of using find you can simply loop through the files themselves. Notice that I have double-quoted "$r"; you need to do that to keep the space in the filenames intact and unparsed by the shell.
for r in *.fastq
do
# Stuff using "$r"...
:
done
answered 2 hours ago
roaimaroaima
43.4k553116
Instead of using find you can simply loop through the files themselves. Notice that I have double-quoted "$r"; you need to do that to keep the space in the filenames intact and unparsed by the shell.
for r in *.fastq
do
# Stuff using "$r"...
:
done
answered 2 hours ago
roaimaroaima
43.4k553116
answered 2 hours ago
roaimaroaima
43.4k553116
answered 2 hours ago
roaimaroaima
43.4k553116
answered 2 hours ago
roaimaroaima
43.4k553116
43.4k553116
add a comment |
add a comment |
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5
for r in $(find . -name "*.fastq");is pretty bad...– don_crissti
3 hours ago
1
Are all your
fastqfiles in the same directory?– roaima
3 hours ago
yes, they're all in the same directory. I solved it with this unix.stackexchange.com/a/9499/34872
– user977828
2 hours ago
That's a poor solution for your situation
– roaima
2 hours ago
2
see: Why does my shell script choke on whitespace or other special characters? and Recursively iterate through files in a directory and also mywiki.wooledge.org/WordSplitting
– ilkkachu
2 hours ago