How to replace letters in lines in fasta file using bash loops?
I want to change all n in the sequence into -, but I don't know how to make my bash script not change the n that show up in sequence names. I'm not experienced with sed or regex to make sure my bash script reads only the lines that do not start with >, as that indicates the header.
Example file:
>Name_with_nnn
nnnatgcnnnatttg
>Name2_with_nnn
atgggnnnnGGtnnn
At the same time I want to convert all lowercase letters into uppercase, only in the sequence lines. I don't even know how to begin using sed, I find it really tricky to understand.
Expected output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
So after I created my sequence files I tried to continue my script with:
while IFS= read -r line
do
if [[ $line == ">"* ]]
then
echo "Ignoring header line: $line"
else
echo "Converting to uppercase and then N-to-gaps"
# sed or tr?? do call $line or do I call $OUTFILE? so confused..
fi
done
bash sed
edited Jan 3 at 18:49
Benjamin W.
21.6k135257
asked Jan 3 at 18:27
DNAngelDNAngel
1491110
add a comment |
I want to change all n in the sequence into -, but I don't know how to make my bash script not change the n that show up in sequence names. I'm not experienced with sed or regex to make sure my bash script reads only the lines that do not start with >, as that indicates the header.
Example file:
>Name_with_nnn
nnnatgcnnnatttg
>Name2_with_nnn
atgggnnnnGGtnnn
At the same time I want to convert all lowercase letters into uppercase, only in the sequence lines. I don't even know how to begin using sed, I find it really tricky to understand.
Expected output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
So after I created my sequence files I tried to continue my script with:
while IFS= read -r line
do
if [[ $line == ">"* ]]
then
echo "Ignoring header line: $line"
else
echo "Converting to uppercase and then N-to-gaps"
# sed or tr?? do call $line or do I call $OUTFILE? so confused..
fi
done
bash sed
edited Jan 3 at 18:49
Benjamin W.
21.6k135257
asked Jan 3 at 18:27
DNAngelDNAngel
1491110
add a comment |
I want to change all n in the sequence into -, but I don't know how to make my bash script not change the n that show up in sequence names. I'm not experienced with sed or regex to make sure my bash script reads only the lines that do not start with >, as that indicates the header.
Example file:
>Name_with_nnn
nnnatgcnnnatttg
>Name2_with_nnn
atgggnnnnGGtnnn
At the same time I want to convert all lowercase letters into uppercase, only in the sequence lines. I don't even know how to begin using sed, I find it really tricky to understand.
Expected output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
So after I created my sequence files I tried to continue my script with:
while IFS= read -r line
do
if [[ $line == ">"* ]]
then
echo "Ignoring header line: $line"
else
echo "Converting to uppercase and then N-to-gaps"
# sed or tr?? do call $line or do I call $OUTFILE? so confused..
fi
done
bash sed
edited Jan 3 at 18:49
Benjamin W.
21.6k135257
asked Jan 3 at 18:27
DNAngelDNAngel
1491110
I want to change all n in the sequence into -, but I don't know how to make my bash script not change the n that show up in sequence names. I'm not experienced with sed or regex to make sure my bash script reads only the lines that do not start with >, as that indicates the header.
Example file:
>Name_with_nnn
nnnatgcnnnatttg
>Name2_with_nnn
atgggnnnnGGtnnn
At the same time I want to convert all lowercase letters into uppercase, only in the sequence lines. I don't even know how to begin using sed, I find it really tricky to understand.
Expected output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
So after I created my sequence files I tried to continue my script with:
while IFS= read -r line
do
if [[ $line == ">"* ]]
then
echo "Ignoring header line: $line"
else
echo "Converting to uppercase and then N-to-gaps"
# sed or tr?? do call $line or do I call $OUTFILE? so confused..
fi
done
bash sed
bash sed
edited Jan 3 at 18:49
Benjamin W.
21.6k135257
asked Jan 3 at 18:27
DNAngelDNAngel
1491110
edited Jan 3 at 18:49
Benjamin W.
21.6k135257
asked Jan 3 at 18:27
DNAngelDNAngel
1491110
edited Jan 3 at 18:49
Benjamin W.
21.6k135257
edited Jan 3 at 18:49
Benjamin W.
21.6k135257
edited Jan 3 at 18:49
Benjamin W.
21.6k135257
21.6k135257
asked Jan 3 at 18:27
DNAngelDNAngel
1491110
asked Jan 3 at 18:27
DNAngelDNAngel
1491110
asked Jan 3 at 18:27
DNAngelDNAngel
1491110
1491110
add a comment |
add a comment |
4 Answers
4
active
oldest
votes
You can resolve this with sed with below line:
sed -i "/^>/! {s/n/-/g; s/(.*)/U1/g}" text.txt
And your output would be:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:38
Cedric ZoppoloCedric Zoppolo
1,36211529
@DNAngel be aware I updated the script as converting to uppercase was missing.
– Cedric Zoppolo
Jan 3 at 18:55
1
@CedricZoppolo Not only uppercase, you updatedstart with>too, might be worth mentioning.
– Tiw
Jan 3 at 19:05
@Tiw is correct. I also updated to ensure only lines not starting with>will be converted. I was missing^character in order to get the lines starting with>and not lines containing such character in any part of line.
– Cedric Zoppolo
Jan 3 at 19:12
add a comment |
You may use this simple gnu sed:
sed '/^>/!{s/n/-/g; s/.*/U&/;}' file
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:35
anubhavaanubhava
534k48332409
add a comment |
In pure Bash, likely quite slow for larger inputs:
while IFS= read -r line; do
case $line in
'>'*)
printf '%sn' "$line"
;;
*)
line=${line//n/-}
printf '%sn' "${line^^}"
;;
esac
done < infile
This uses a case statement with pattern matching to test if a line starts with > or not; to modify the lines, parameter expansions are used. The ${parameter^^} expansion requires Bash 4.0 or newer.
answered Jan 3 at 18:58
Benjamin W.Benjamin W.
21.6k135257
add a comment |
How about awk ?
awk '/^[^>]/{gsub("n","-");print toupper($0);next;}1' data
Output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
However, sed can do it too (GNU sed):
sed -E '/^[^>]/{s/n/-/g;s/(.*)/U1/g;}' data
It's the same as:
sed -E '/^>/!{s/n/-/g;s/(.*)/U1/g;}' data
If you want to change in place, you can add -i switch to sed.
answered Jan 3 at 18:29
TiwTiw
4,35461630
add a comment |
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4 Answers
4
active
oldest
votes
4 Answers
4
active
oldest
votes
active
oldest
votes
active
oldest
votes
You can resolve this with sed with below line:
sed -i "/^>/! {s/n/-/g; s/(.*)/U1/g}" text.txt
And your output would be:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:38
Cedric ZoppoloCedric Zoppolo
1,36211529
@DNAngel be aware I updated the script as converting to uppercase was missing.
– Cedric Zoppolo
Jan 3 at 18:55
1
@CedricZoppolo Not only uppercase, you updatedstart with>too, might be worth mentioning.
– Tiw
Jan 3 at 19:05
@Tiw is correct. I also updated to ensure only lines not starting with>will be converted. I was missing^character in order to get the lines starting with>and not lines containing such character in any part of line.
– Cedric Zoppolo
Jan 3 at 19:12
add a comment |
You can resolve this with sed with below line:
sed -i "/^>/! {s/n/-/g; s/(.*)/U1/g}" text.txt
And your output would be:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:38
Cedric ZoppoloCedric Zoppolo
1,36211529
@DNAngel be aware I updated the script as converting to uppercase was missing.
– Cedric Zoppolo
Jan 3 at 18:55
1
@CedricZoppolo Not only uppercase, you updatedstart with>too, might be worth mentioning.
– Tiw
Jan 3 at 19:05
@Tiw is correct. I also updated to ensure only lines not starting with>will be converted. I was missing^character in order to get the lines starting with>and not lines containing such character in any part of line.
– Cedric Zoppolo
Jan 3 at 19:12
add a comment |
You can resolve this with sed with below line:
sed -i "/^>/! {s/n/-/g; s/(.*)/U1/g}" text.txt
And your output would be:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:38
Cedric ZoppoloCedric Zoppolo
1,36211529
You can resolve this with sed with below line:
sed -i "/^>/! {s/n/-/g; s/(.*)/U1/g}" text.txt
And your output would be:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:38
Cedric ZoppoloCedric Zoppolo
1,36211529
edited Jan 3 at 18:59
answered Jan 3 at 18:38
Cedric ZoppoloCedric Zoppolo
1,36211529
answered Jan 3 at 18:38
Cedric ZoppoloCedric Zoppolo
1,36211529
answered Jan 3 at 18:38
Cedric ZoppoloCedric Zoppolo
1,36211529
1,36211529
@DNAngel be aware I updated the script as converting to uppercase was missing.
– Cedric Zoppolo
Jan 3 at 18:55
1
@CedricZoppolo Not only uppercase, you updatedstart with>too, might be worth mentioning.
– Tiw
Jan 3 at 19:05
@Tiw is correct. I also updated to ensure only lines not starting with>will be converted. I was missing^character in order to get the lines starting with>and not lines containing such character in any part of line.
– Cedric Zoppolo
Jan 3 at 19:12
add a comment |
@DNAngel be aware I updated the script as converting to uppercase was missing.
– Cedric Zoppolo
Jan 3 at 18:55
1
@CedricZoppolo Not only uppercase, you updatedstart with>too, might be worth mentioning.
– Tiw
Jan 3 at 19:05
@Tiw is correct. I also updated to ensure only lines not starting with>will be converted. I was missing^character in order to get the lines starting with>and not lines containing such character in any part of line.
– Cedric Zoppolo
Jan 3 at 19:12
@DNAngel be aware I updated the script as converting to uppercase was missing.
– Cedric Zoppolo
Jan 3 at 18:55
@DNAngel be aware I updated the script as converting to uppercase was missing.
– Cedric Zoppolo
Jan 3 at 18:55
1
1
@CedricZoppolo Not only uppercase, you updated
start with > too, might be worth mentioning.– Tiw
Jan 3 at 19:05
@CedricZoppolo Not only uppercase, you updated
start with > too, might be worth mentioning.– Tiw
Jan 3 at 19:05
@Tiw is correct. I also updated to ensure only lines not starting with
> will be converted. I was missing ^ character in order to get the lines starting with > and not lines containing such character in any part of line.– Cedric Zoppolo
Jan 3 at 19:12
@Tiw is correct. I also updated to ensure only lines not starting with
> will be converted. I was missing ^ character in order to get the lines starting with > and not lines containing such character in any part of line.– Cedric Zoppolo
Jan 3 at 19:12
add a comment |
You may use this simple gnu sed:
sed '/^>/!{s/n/-/g; s/.*/U&/;}' file
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:35
anubhavaanubhava
534k48332409
add a comment |
You may use this simple gnu sed:
sed '/^>/!{s/n/-/g; s/.*/U&/;}' file
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:35
anubhavaanubhava
534k48332409
add a comment |
You may use this simple gnu sed:
sed '/^>/!{s/n/-/g; s/.*/U&/;}' file
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:35
anubhavaanubhava
534k48332409
You may use this simple gnu sed:
sed '/^>/!{s/n/-/g; s/.*/U&/;}' file
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
answered Jan 3 at 18:35
anubhavaanubhava
534k48332409
answered Jan 3 at 18:35
anubhavaanubhava
534k48332409
answered Jan 3 at 18:35
anubhavaanubhava
534k48332409
answered Jan 3 at 18:35
anubhavaanubhava
534k48332409
534k48332409
add a comment |
add a comment |
In pure Bash, likely quite slow for larger inputs:
while IFS= read -r line; do
case $line in
'>'*)
printf '%sn' "$line"
;;
*)
line=${line//n/-}
printf '%sn' "${line^^}"
;;
esac
done < infile
This uses a case statement with pattern matching to test if a line starts with > or not; to modify the lines, parameter expansions are used. The ${parameter^^} expansion requires Bash 4.0 or newer.
answered Jan 3 at 18:58
Benjamin W.Benjamin W.
21.6k135257
add a comment |
In pure Bash, likely quite slow for larger inputs:
while IFS= read -r line; do
case $line in
'>'*)
printf '%sn' "$line"
;;
*)
line=${line//n/-}
printf '%sn' "${line^^}"
;;
esac
done < infile
This uses a case statement with pattern matching to test if a line starts with > or not; to modify the lines, parameter expansions are used. The ${parameter^^} expansion requires Bash 4.0 or newer.
answered Jan 3 at 18:58
Benjamin W.Benjamin W.
21.6k135257
add a comment |
In pure Bash, likely quite slow for larger inputs:
while IFS= read -r line; do
case $line in
'>'*)
printf '%sn' "$line"
;;
*)
line=${line//n/-}
printf '%sn' "${line^^}"
;;
esac
done < infile
This uses a case statement with pattern matching to test if a line starts with > or not; to modify the lines, parameter expansions are used. The ${parameter^^} expansion requires Bash 4.0 or newer.
answered Jan 3 at 18:58
Benjamin W.Benjamin W.
21.6k135257
In pure Bash, likely quite slow for larger inputs:
while IFS= read -r line; do
case $line in
'>'*)
printf '%sn' "$line"
;;
*)
line=${line//n/-}
printf '%sn' "${line^^}"
;;
esac
done < infile
This uses a case statement with pattern matching to test if a line starts with > or not; to modify the lines, parameter expansions are used. The ${parameter^^} expansion requires Bash 4.0 or newer.
answered Jan 3 at 18:58
Benjamin W.Benjamin W.
21.6k135257
answered Jan 3 at 18:58
Benjamin W.Benjamin W.
21.6k135257
answered Jan 3 at 18:58
Benjamin W.Benjamin W.
21.6k135257
answered Jan 3 at 18:58
Benjamin W.Benjamin W.
21.6k135257
21.6k135257
add a comment |
add a comment |
How about awk ?
awk '/^[^>]/{gsub("n","-");print toupper($0);next;}1' data
Output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
However, sed can do it too (GNU sed):
sed -E '/^[^>]/{s/n/-/g;s/(.*)/U1/g;}' data
It's the same as:
sed -E '/^>/!{s/n/-/g;s/(.*)/U1/g;}' data
If you want to change in place, you can add -i switch to sed.
answered Jan 3 at 18:29
TiwTiw
4,35461630
add a comment |
How about awk ?
awk '/^[^>]/{gsub("n","-");print toupper($0);next;}1' data
Output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
However, sed can do it too (GNU sed):
sed -E '/^[^>]/{s/n/-/g;s/(.*)/U1/g;}' data
It's the same as:
sed -E '/^>/!{s/n/-/g;s/(.*)/U1/g;}' data
If you want to change in place, you can add -i switch to sed.
answered Jan 3 at 18:29
TiwTiw
4,35461630
add a comment |
How about awk ?
awk '/^[^>]/{gsub("n","-");print toupper($0);next;}1' data
Output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
However, sed can do it too (GNU sed):
sed -E '/^[^>]/{s/n/-/g;s/(.*)/U1/g;}' data
It's the same as:
sed -E '/^>/!{s/n/-/g;s/(.*)/U1/g;}' data
If you want to change in place, you can add -i switch to sed.
answered Jan 3 at 18:29
TiwTiw
4,35461630
How about awk ?
awk '/^[^>]/{gsub("n","-");print toupper($0);next;}1' data
Output:
>Name_with_nnn
---ATGC---ATTTG
>Name2_with_nnn
ATGGG----GGT---
However, sed can do it too (GNU sed):
sed -E '/^[^>]/{s/n/-/g;s/(.*)/U1/g;}' data
It's the same as:
sed -E '/^>/!{s/n/-/g;s/(.*)/U1/g;}' data
If you want to change in place, you can add -i switch to sed.
answered Jan 3 at 18:29
TiwTiw
4,35461630
edited Jan 3 at 18:52
answered Jan 3 at 18:29
TiwTiw
4,35461630
answered Jan 3 at 18:29
TiwTiw
4,35461630
answered Jan 3 at 18:29
TiwTiw
4,35461630
4,35461630
add a comment |
add a comment |
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