copy the names of DNA sequences in a phylogenetic tree file and add the names of the species to it?
Multi tool use
Clash Royale CLAN TAG#URR8PPP
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From a file looking like this one :
(AJirio:0.00230,(AJama.1.1:0.00171,(AJkago.1:0.00057,AJtok:0.00033)1.00 :0.00080)0.94:0.00085,Atab.1.1.1:0.27697);
I need to obtain this file :
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
So basically extract the name of the DNA sequences in a phylogenetic tree and add the name of the species (AJirio, AJkama..) with quotation marks to it.
shell-script text-processing scripting
asked Mar 6 at 14:28
DavidB
114
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up vote
-1
down vote
favorite
From a file looking like this one :
(AJirio:0.00230,(AJama.1.1:0.00171,(AJkago.1:0.00057,AJtok:0.00033)1.00 :0.00080)0.94:0.00085,Atab.1.1.1:0.27697);
I need to obtain this file :
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
So basically extract the name of the DNA sequences in a phylogenetic tree and add the name of the species (AJirio, AJkama..) with quotation marks to it.
shell-script text-processing scripting
asked Mar 6 at 14:28
DavidB
114
add a comment |Â
up vote
-1
down vote
favorite
up vote
-1
down vote
favorite
From a file looking like this one :
(AJirio:0.00230,(AJama.1.1:0.00171,(AJkago.1:0.00057,AJtok:0.00033)1.00 :0.00080)0.94:0.00085,Atab.1.1.1:0.27697);
I need to obtain this file :
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
So basically extract the name of the DNA sequences in a phylogenetic tree and add the name of the species (AJirio, AJkama..) with quotation marks to it.
shell-script text-processing scripting
asked Mar 6 at 14:28
DavidB
114
From a file looking like this one :
(AJirio:0.00230,(AJama.1.1:0.00171,(AJkago.1:0.00057,AJtok:0.00033)1.00 :0.00080)0.94:0.00085,Atab.1.1.1:0.27697);
I need to obtain this file :
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
So basically extract the name of the DNA sequences in a phylogenetic tree and add the name of the species (AJirio, AJkama..) with quotation marks to it.
shell-script text-processing scripting
asked Mar 6 at 14:28
DavidB
114
asked Mar 6 at 14:28
DavidB
114
asked Mar 6 at 14:28
DavidB
114
asked Mar 6 at 14:28
DavidB
114
114
add a comment |Â
add a comment |Â
1 Answer
1
active
oldest
votes
up vote
1
down vote
accepted
Two approaches:
Awk approach:
awk -v RS=',' -F':' '
sub(/(*/, ""); dna = $1;
gsub(/[^a-zA-Z]/, "", $1);
printf "%s42%s42n", dna, $1
' file
sed approach:
sed -En 's/(*?(([a-zA-Z]+)[^:]*):[^,]+/1"2"/g; s/,/n/gp' file
The output:
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
answered Mar 6 at 14:44
RomanPerekhrest
22.4k12144
Thank you! It's working on this file but in most of my files I have more parenthesis. For example : ((((AJirio.1.1 will become (((AJirio.1.1"AJirio" And I would like to have AJirio.1.1"AJirio". Do you know how to modify your script to have this?
– DavidB
Mar 6 at 15:39
@DavidB, yes, use my update
– RomanPerekhrest
Mar 6 at 15:55
Great, thank you very much
– DavidB
Mar 6 at 16:00
@DavidB, you're welcome
– RomanPerekhrest
Mar 6 at 16:02
add a comment |Â
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
1
down vote
accepted
Two approaches:
Awk approach:
awk -v RS=',' -F':' '
sub(/(*/, ""); dna = $1;
gsub(/[^a-zA-Z]/, "", $1);
printf "%s42%s42n", dna, $1
' file
sed approach:
sed -En 's/(*?(([a-zA-Z]+)[^:]*):[^,]+/1"2"/g; s/,/n/gp' file
The output:
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
answered Mar 6 at 14:44
RomanPerekhrest
22.4k12144
Thank you! It's working on this file but in most of my files I have more parenthesis. For example : ((((AJirio.1.1 will become (((AJirio.1.1"AJirio" And I would like to have AJirio.1.1"AJirio". Do you know how to modify your script to have this?
– DavidB
Mar 6 at 15:39
@DavidB, yes, use my update
– RomanPerekhrest
Mar 6 at 15:55
Great, thank you very much
– DavidB
Mar 6 at 16:00
@DavidB, you're welcome
– RomanPerekhrest
Mar 6 at 16:02
add a comment |Â
up vote
1
down vote
accepted
Two approaches:
Awk approach:
awk -v RS=',' -F':' '
sub(/(*/, ""); dna = $1;
gsub(/[^a-zA-Z]/, "", $1);
printf "%s42%s42n", dna, $1
' file
sed approach:
sed -En 's/(*?(([a-zA-Z]+)[^:]*):[^,]+/1"2"/g; s/,/n/gp' file
The output:
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
answered Mar 6 at 14:44
RomanPerekhrest
22.4k12144
Thank you! It's working on this file but in most of my files I have more parenthesis. For example : ((((AJirio.1.1 will become (((AJirio.1.1"AJirio" And I would like to have AJirio.1.1"AJirio". Do you know how to modify your script to have this?
– DavidB
Mar 6 at 15:39
@DavidB, yes, use my update
– RomanPerekhrest
Mar 6 at 15:55
Great, thank you very much
– DavidB
Mar 6 at 16:00
@DavidB, you're welcome
– RomanPerekhrest
Mar 6 at 16:02
add a comment |Â
up vote
1
down vote
accepted
up vote
1
down vote
accepted
Two approaches:
Awk approach:
awk -v RS=',' -F':' '
sub(/(*/, ""); dna = $1;
gsub(/[^a-zA-Z]/, "", $1);
printf "%s42%s42n", dna, $1
' file
sed approach:
sed -En 's/(*?(([a-zA-Z]+)[^:]*):[^,]+/1"2"/g; s/,/n/gp' file
The output:
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
answered Mar 6 at 14:44
RomanPerekhrest
22.4k12144
Two approaches:
Awk approach:
awk -v RS=',' -F':' '
sub(/(*/, ""); dna = $1;
gsub(/[^a-zA-Z]/, "", $1);
printf "%s42%s42n", dna, $1
' file
sed approach:
sed -En 's/(*?(([a-zA-Z]+)[^:]*):[^,]+/1"2"/g; s/,/n/gp' file
The output:
AJirio"AJirio"
AJama.1.1"AJama"
AJkago.1"AJkago"
AJtok"AJtok"
Atab.1.1.1"Atab"
answered Mar 6 at 14:44
RomanPerekhrest
22.4k12144
edited Mar 6 at 15:55
answered Mar 6 at 14:44
RomanPerekhrest
22.4k12144
answered Mar 6 at 14:44
RomanPerekhrest
22.4k12144
answered Mar 6 at 14:44
RomanPerekhrest
22.4k12144
22.4k12144
Thank you! It's working on this file but in most of my files I have more parenthesis. For example : ((((AJirio.1.1 will become (((AJirio.1.1"AJirio" And I would like to have AJirio.1.1"AJirio". Do you know how to modify your script to have this?
– DavidB
Mar 6 at 15:39
@DavidB, yes, use my update
– RomanPerekhrest
Mar 6 at 15:55
Great, thank you very much
– DavidB
Mar 6 at 16:00
@DavidB, you're welcome
– RomanPerekhrest
Mar 6 at 16:02
add a comment |Â
Thank you! It's working on this file but in most of my files I have more parenthesis. For example : ((((AJirio.1.1 will become (((AJirio.1.1"AJirio" And I would like to have AJirio.1.1"AJirio". Do you know how to modify your script to have this?
– DavidB
Mar 6 at 15:39
@DavidB, yes, use my update
– RomanPerekhrest
Mar 6 at 15:55
Great, thank you very much
– DavidB
Mar 6 at 16:00
@DavidB, you're welcome
– RomanPerekhrest
Mar 6 at 16:02
Thank you! It's working on this file but in most of my files I have more parenthesis. For example : ((((AJirio.1.1 will become (((AJirio.1.1"AJirio" And I would like to have AJirio.1.1"AJirio". Do you know how to modify your script to have this?
– DavidB
Mar 6 at 15:39
Thank you! It's working on this file but in most of my files I have more parenthesis. For example : ((((AJirio.1.1 will become (((AJirio.1.1"AJirio" And I would like to have AJirio.1.1"AJirio". Do you know how to modify your script to have this?
– DavidB
Mar 6 at 15:39
@DavidB, yes, use my update
– RomanPerekhrest
Mar 6 at 15:55
@DavidB, yes, use my update
– RomanPerekhrest
Mar 6 at 15:55
Great, thank you very much
– DavidB
Mar 6 at 16:00
Great, thank you very much
– DavidB
Mar 6 at 16:00
@DavidB, you're welcome
– RomanPerekhrest
Mar 6 at 16:02
@DavidB, you're welcome
– RomanPerekhrest
Mar 6 at 16:02
add a comment |Â
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