sed or awk: remove numbers after a symbol
up vote
2
down vote
favorite
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 5 hours ago
Paul
937
add a comment |
up vote
2
down vote
favorite
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 5 hours ago
Paul
937
add a comment |
up vote
2
down vote
favorite
up vote
2
down vote
favorite
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 5 hours ago
Paul
937
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 5 hours ago
Paul
937
asked 5 hours ago
Paul
937
asked 5 hours ago
Paul
937
asked 5 hours ago
Paul
937
asked 5 hours ago
Paul
937
937
add a comment |
add a comment |
2 Answers
2
active
oldest
votes
up vote
4
down vote
accepted
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 5 hours ago
Jesse_b
11.6k23063
thanks. I tried so many options, but not this one.
– Paul
4 hours ago
2
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
4 hours ago
add a comment |
up vote
0
down vote
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 1 hour ago
Claes Wikner
12713
add a comment |
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2 Answers
2
active
oldest
votes
2 Answers
2
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
4
down vote
accepted
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 5 hours ago
Jesse_b
11.6k23063
thanks. I tried so many options, but not this one.
– Paul
4 hours ago
2
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
4 hours ago
add a comment |
up vote
4
down vote
accepted
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 5 hours ago
Jesse_b
11.6k23063
thanks. I tried so many options, but not this one.
– Paul
4 hours ago
2
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
4 hours ago
add a comment |
up vote
4
down vote
accepted
up vote
4
down vote
accepted
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 5 hours ago
Jesse_b
11.6k23063
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 5 hours ago
Jesse_b
11.6k23063
edited 4 hours ago
answered 5 hours ago
Jesse_b
11.6k23063
answered 5 hours ago
Jesse_b
11.6k23063
answered 5 hours ago
Jesse_b
11.6k23063
11.6k23063
thanks. I tried so many options, but not this one.
– Paul
4 hours ago
2
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
4 hours ago
add a comment |
thanks. I tried so many options, but not this one.
– Paul
4 hours ago
2
You might want the line-start anchor (^) as well. And+instead of*for one or more digits.
– glenn jackman
4 hours ago
thanks. I tried so many options, but not this one.
– Paul
4 hours ago
thanks. I tried so many options, but not this one.
– Paul
4 hours ago
2
2
You might want the line-start anchor (
^) as well. And + instead of * for one or more digits.– glenn jackman
4 hours ago
You might want the line-start anchor (
^) as well. And + instead of * for one or more digits.– glenn jackman
4 hours ago
add a comment |
up vote
0
down vote
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 1 hour ago
Claes Wikner
12713
add a comment |
up vote
0
down vote
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 1 hour ago
Claes Wikner
12713
add a comment |
up vote
0
down vote
up vote
0
down vote
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 1 hour ago
Claes Wikner
12713
awk '{sub(/^>._|^>...._/,">")}1' file
>CR-B_CR56_t
MTKIIKFVYFMTIFISPNHHCPVYNCTHPKQPWCKLVRLQLLFHGSLIGLCDCI
>R-B_R46_t
MVEVTKLVNVMLIFLTLSPLVYDCQAYECELPFKPDCLMVEYSPQFVALRCGCV
>N-N274_M
MVEVTKLVNVMLIFLTLFVYTDSDCQAYACELPFKPDCLMVEYAPQFFRLACGCV
answered 1 hour ago
Claes Wikner
12713
answered 1 hour ago
Claes Wikner
12713
answered 1 hour ago
Claes Wikner
12713
answered 1 hour ago
Claes Wikner
12713
12713
add a comment |
add a comment |
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