sed or awk: remove numbers after a symbol
I would like to remove just the numbers and "_" after ">" symbol, for example:
>1_CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>2_R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>3000_N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
Expected Results:
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
I used sed "s/>[0-9][_]//g" but it removed ">" as well.
awk sed delete
asked Dec 13 at 21:40
Paul
1037
add a comment |
I would like to remove just the numbers and "_" after ">" symbol, for example:
>1_CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>2_R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>3000_N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
Expected Results:
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
I used sed "s/>[0-9][_]//g" but it removed ">" as well.
awk sed delete
asked Dec 13 at 21:40
Paul
1037
add a comment |
I would like to remove just the numbers and "_" after ">" symbol, for example:
>1_CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>2_R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>3000_N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
Expected Results:
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
I used sed "s/>[0-9][_]//g" but it removed ">" as well.
awk sed delete
asked Dec 13 at 21:40
Paul
1037
I would like to remove just the numbers and "_" after ">" symbol, for example:
>1_CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>2_R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>3000_N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
Expected Results:
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
I used sed "s/>[0-9][_]//g" but it removed ">" as well.
awk sed delete
awk sed delete
asked Dec 13 at 21:40
Paul
1037
asked Dec 13 at 21:40
Paul
1037
asked Dec 13 at 21:40
Paul
1037
asked Dec 13 at 21:40
Paul
1037
asked Dec 13 at 21:40
Paul
1037
1037
add a comment |
add a comment |
3 Answers
3
active
oldest
votes
Just a slight modification from your sed command:
sed 's/^>[0-9]+[_]/>/g'
the s is the sed substitute command, it searches for the string on the left hand side and replaces it with the string on the right hand side. Instead of replacing it with nothing you can replace it with the > character that you would like to keep.
^ is used to specify that the match should only start at the beginning of a newline
Additionally the * is being used to match more than a single digit.
answered Dec 13 at 21:43
Jesse_b
11.7k23064
thanks. I tried so many options, but not this one.
– Paul
Dec 13 at 21:47
3
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
Dec 13 at 21:56
add a comment |
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered Dec 14 at 0:58
Claes Wikner
13713
add a comment |
command:sed 's/^>[0-9]{1,9}_/>/g' filename
output
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 15 hours ago
Praveen Kumar BS
1,176138
add a comment |
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3 Answers
3
active
oldest
votes
3 Answers
3
active
oldest
votes
active
oldest
votes
active
oldest
votes
Just a slight modification from your sed command:
sed 's/^>[0-9]+[_]/>/g'
the s is the sed substitute command, it searches for the string on the left hand side and replaces it with the string on the right hand side. Instead of replacing it with nothing you can replace it with the > character that you would like to keep.
^ is used to specify that the match should only start at the beginning of a newline
Additionally the * is being used to match more than a single digit.
answered Dec 13 at 21:43
Jesse_b
11.7k23064
thanks. I tried so many options, but not this one.
– Paul
Dec 13 at 21:47
3
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
Dec 13 at 21:56
add a comment |
Just a slight modification from your sed command:
sed 's/^>[0-9]+[_]/>/g'
the s is the sed substitute command, it searches for the string on the left hand side and replaces it with the string on the right hand side. Instead of replacing it with nothing you can replace it with the > character that you would like to keep.
^ is used to specify that the match should only start at the beginning of a newline
Additionally the * is being used to match more than a single digit.
answered Dec 13 at 21:43
Jesse_b
11.7k23064
thanks. I tried so many options, but not this one.
– Paul
Dec 13 at 21:47
3
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
Dec 13 at 21:56
add a comment |
Just a slight modification from your sed command:
sed 's/^>[0-9]+[_]/>/g'
the s is the sed substitute command, it searches for the string on the left hand side and replaces it with the string on the right hand side. Instead of replacing it with nothing you can replace it with the > character that you would like to keep.
^ is used to specify that the match should only start at the beginning of a newline
Additionally the * is being used to match more than a single digit.
answered Dec 13 at 21:43
Jesse_b
11.7k23064
Just a slight modification from your sed command:
sed 's/^>[0-9]+[_]/>/g'
the s is the sed substitute command, it searches for the string on the left hand side and replaces it with the string on the right hand side. Instead of replacing it with nothing you can replace it with the > character that you would like to keep.
^ is used to specify that the match should only start at the beginning of a newline
Additionally the * is being used to match more than a single digit.
answered Dec 13 at 21:43
Jesse_b
11.7k23064
edited Dec 14 at 2:53
answered Dec 13 at 21:43
Jesse_b
11.7k23064
answered Dec 13 at 21:43
Jesse_b
11.7k23064
answered Dec 13 at 21:43
Jesse_b
11.7k23064
11.7k23064
thanks. I tried so many options, but not this one.
– Paul
Dec 13 at 21:47
3
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
Dec 13 at 21:56
add a comment |
thanks. I tried so many options, but not this one.
– Paul
Dec 13 at 21:47
3
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
Dec 13 at 21:56
thanks. I tried so many options, but not this one.
– Paul
Dec 13 at 21:47
thanks. I tried so many options, but not this one.
– Paul
Dec 13 at 21:47
3
3
You might want the line-start anchor (
^) as well. And + instead of * for one or more digits.– glenn jackman
Dec 13 at 21:56
You might want the line-start anchor (
^) as well. And + instead of * for one or more digits.– glenn jackman
Dec 13 at 21:56
add a comment |
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered Dec 14 at 0:58
Claes Wikner
13713
add a comment |
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered Dec 14 at 0:58
Claes Wikner
13713
add a comment |
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered Dec 14 at 0:58
Claes Wikner
13713
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered Dec 14 at 0:58
Claes Wikner
13713
answered Dec 14 at 0:58
Claes Wikner
13713
answered Dec 14 at 0:58
Claes Wikner
13713
answered Dec 14 at 0:58
Claes Wikner
13713
13713
add a comment |
add a comment |
command:sed 's/^>[0-9]{1,9}_/>/g' filename
output
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 15 hours ago
Praveen Kumar BS
1,176138
add a comment |
command:sed 's/^>[0-9]{1,9}_/>/g' filename
output
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 15 hours ago
Praveen Kumar BS
1,176138
add a comment |
command:sed 's/^>[0-9]{1,9}_/>/g' filename
output
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 15 hours ago
Praveen Kumar BS
1,176138
command:sed 's/^>[0-9]{1,9}_/>/g' filename
output
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 15 hours ago
Praveen Kumar BS
1,176138
answered 15 hours ago
Praveen Kumar BS
1,176138
answered 15 hours ago
Praveen Kumar BS
1,176138
answered 15 hours ago
Praveen Kumar BS
1,176138
1,176138
add a comment |
add a comment |
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