collecting specific genome data from a file and collect it in the same title

Clash Royale CLAN TAG#URR8PPP

up vote
4
down vote

favorite

I have genomes data in a file genomes-seq.txt, the titles of the sequences begain with>then the genome name

>genome.1
atcg
atcg
atcggtc

>genome.2
atct
tgcgtgctt
attttt

>genome.
sdkf
sdf;ksdf
sdlfkjdslc
edsfsfv

>genome.3
as;ldkhaskjd
asdkljdsl
asdkljasdk;l

>genome.4
ekjfhdhsa
dsfkjskajd
asdknasd


>genome.1
iruuwi
sdkljbh
sdfljnsdl

>genome.234
efijhusidh
siduhygfhuji

>genome.1
ljhdcj
sdljhsdil
fweusfhygc

I want to collect the similar data for genome.1 in one file so it look like this

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

but every time I do it using sed I get

>genome.1
atcg
atcg
atcggtc

>genome.1
iruuwi
sdkljbh
sdfljnsdl

>genome.1
ljhdcj
sdljhsdil
fweusfhygc

multiple genome.1 how can I do it correctly so on large data set I don't need to remove all the repetitions.

bash

share|improve this question

edited 35 mins ago

Rui F Ribeiro

37k1273117

asked 1 hour ago

paul

233

New contributor

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

• 
  
  
  

  
  

  
  
  
  
  
  

  
  Hi @paul, what is your sed command that you used?
  – Goro
  58 mins ago
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  I tried but it didn't work
  – paul
  54 mins ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  Show what you tried and we can help fix your errors.
  – glenn jackman
  24 mins ago
  

  
  
  
  

add a comment | 

up vote
4
down vote

favorite

I have genomes data in a file genomes-seq.txt, the titles of the sequences begain with>then the genome name

>genome.1
atcg
atcg
atcggtc

>genome.2
atct
tgcgtgctt
attttt

>genome.
sdkf
sdf;ksdf
sdlfkjdslc
edsfsfv

>genome.3
as;ldkhaskjd
asdkljdsl
asdkljasdk;l

>genome.4
ekjfhdhsa
dsfkjskajd
asdknasd


>genome.1
iruuwi
sdkljbh
sdfljnsdl

>genome.234
efijhusidh
siduhygfhuji

>genome.1
ljhdcj
sdljhsdil
fweusfhygc

I want to collect the similar data for genome.1 in one file so it look like this

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

but every time I do it using sed I get

>genome.1
atcg
atcg
atcggtc

>genome.1
iruuwi
sdkljbh
sdfljnsdl

>genome.1
ljhdcj
sdljhsdil
fweusfhygc

multiple genome.1 how can I do it correctly so on large data set I don't need to remove all the repetitions.

bash

share|improve this question

edited 35 mins ago

Rui F Ribeiro

37k1273117

asked 1 hour ago

paul

233

New contributor

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

• 
  
  
  

  
  

  
  
  
  
  
  

  
  Hi @paul, what is your sed command that you used?
  – Goro
  58 mins ago
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  I tried but it didn't work
  – paul
  54 mins ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  Show what you tried and we can help fix your errors.
  – glenn jackman
  24 mins ago
  

  
  
  
  

add a comment | 

up vote
4
down vote

favorite

up vote
4
down vote

favorite

I have genomes data in a file genomes-seq.txt, the titles of the sequences begain with>then the genome name

>genome.1
atcg
atcg
atcggtc

>genome.2
atct
tgcgtgctt
attttt

>genome.
sdkf
sdf;ksdf
sdlfkjdslc
edsfsfv

>genome.3
as;ldkhaskjd
asdkljdsl
asdkljasdk;l

>genome.4
ekjfhdhsa
dsfkjskajd
asdknasd


>genome.1
iruuwi
sdkljbh
sdfljnsdl

>genome.234
efijhusidh
siduhygfhuji

>genome.1
ljhdcj
sdljhsdil
fweusfhygc

I want to collect the similar data for genome.1 in one file so it look like this

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

but every time I do it using sed I get

>genome.1
atcg
atcg
atcggtc

>genome.1
iruuwi
sdkljbh
sdfljnsdl

>genome.1
ljhdcj
sdljhsdil
fweusfhygc

multiple genome.1 how can I do it correctly so on large data set I don't need to remove all the repetitions.

bash

share|improve this question

edited 35 mins ago

Rui F Ribeiro

37k1273117

asked 1 hour ago

paul

233

New contributor

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

I have genomes data in a file genomes-seq.txt, the titles of the sequences begain with>then the genome name

>genome.1
atcg
atcg
atcggtc

>genome.2
atct
tgcgtgctt
attttt

>genome.
sdkf
sdf;ksdf
sdlfkjdslc
edsfsfv

>genome.3
as;ldkhaskjd
asdkljdsl
asdkljasdk;l

>genome.4
ekjfhdhsa
dsfkjskajd
asdknasd


>genome.1
iruuwi
sdkljbh
sdfljnsdl

>genome.234
efijhusidh
siduhygfhuji

>genome.1
ljhdcj
sdljhsdil
fweusfhygc

I want to collect the similar data for genome.1 in one file so it look like this

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

but every time I do it using sed I get

>genome.1
atcg
atcg
atcggtc

>genome.1
iruuwi
sdkljbh
sdfljnsdl

>genome.1
ljhdcj
sdljhsdil
fweusfhygc

multiple genome.1 how can I do it correctly so on large data set I don't need to remove all the repetitions.

bash

bash

share|improve this question

edited 35 mins ago

Rui F Ribeiro

37k1273117

asked 1 hour ago

paul

233

New contributor

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

share|improve this question

edited 35 mins ago

Rui F Ribeiro

37k1273117

asked 1 hour ago

paul

233

New contributor

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

share|improve this question

share|improve this question

edited 35 mins ago

Rui F Ribeiro

37k1273117

edited 35 mins ago

Rui F Ribeiro

37k1273117

edited 35 mins ago

Rui F Ribeiro

37k1273117

37k1273117

asked 1 hour ago

paul

233

New contributor

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

asked 1 hour ago

paul

233

asked 1 hour ago

paul

233

233

New contributor

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

New contributor

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

paul is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

• 
  
  
  

  
  

  
  
  
  
  
  

  
  Hi @paul, what is your sed command that you used?
  – Goro
  58 mins ago
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  I tried but it didn't work
  – paul
  54 mins ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  Show what you tried and we can help fix your errors.
  – glenn jackman
  24 mins ago
  

  
  
  
  

add a comment | 

• 
  
  
  

  
  

  
  
  
  
  
  

  
  Hi @paul, what is your sed command that you used?
  – Goro
  58 mins ago
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  I tried but it didn't work
  – paul
  54 mins ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  Show what you tried and we can help fix your errors.
  – glenn jackman
  24 mins ago
  

  
  
  
  

Hi @paul, what is your sed command that you used?
– Goro
58 mins ago

Hi @paul, what is your sed command that you used?
– Goro
58 mins ago

I tried but it didn't work
– paul
54 mins ago

I tried but it didn't work
– paul
54 mins ago

Show what you tried and we can help fix your errors.
– glenn jackman
24 mins ago

Show what you tried and we can help fix your errors.
– glenn jackman
24 mins ago

add a comment | 

2 Answers
2

active

oldest

votes

up vote
3
down vote



accepted

$sed -nr />genome.1/,/^$/p file | sed '2,$/^>genome.1$/d'

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

genome.1 is the key word, change depending on the list you would like to generate.

share|improve this answer

edited 17 mins ago

answered 52 mins ago

Goro

7,86653473

add a comment | 

up vote
1
down vote

With perl

perl -00 -ne 'if (/^>genome.1n/) s/// if $. > 1; print' file

share|improve this answer

answered 20 mins ago

glenn jackman

48.4k366105

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
3
down vote



accepted

$sed -nr />genome.1/,/^$/p file | sed '2,$/^>genome.1$/d'

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

genome.1 is the key word, change depending on the list you would like to generate.

share|improve this answer

edited 17 mins ago

answered 52 mins ago

Goro

7,86653473

add a comment | 

up vote
3
down vote



accepted

$sed -nr />genome.1/,/^$/p file | sed '2,$/^>genome.1$/d'

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

genome.1 is the key word, change depending on the list you would like to generate.

share|improve this answer

edited 17 mins ago

answered 52 mins ago

Goro

7,86653473

add a comment | 

up vote
3
down vote



accepted

up vote
3
down vote



accepted

$sed -nr />genome.1/,/^$/p file | sed '2,$/^>genome.1$/d'

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

genome.1 is the key word, change depending on the list you would like to generate.

share|improve this answer

edited 17 mins ago

answered 52 mins ago

Goro

7,86653473

$sed -nr />genome.1/,/^$/p file | sed '2,$/^>genome.1$/d'

>genome.1
atcg
atcggtc

iruuwi
sdkljbh
sdfljnsdl
ljhdcj
sdljhsdil
fweusfhygc

genome.1 is the key word, change depending on the list you would like to generate.

share|improve this answer

edited 17 mins ago

answered 52 mins ago

Goro

7,86653473

share|improve this answer

share|improve this answer

edited 17 mins ago

edited 17 mins ago

edited 17 mins ago

answered 52 mins ago

Goro

7,86653473

answered 52 mins ago

Goro

7,86653473

answered 52 mins ago

Goro

7,86653473

7,86653473

add a comment | 

add a comment | 

up vote
1
down vote

With perl

perl -00 -ne 'if (/^>genome.1n/) s/// if $. > 1; print' file

share|improve this answer

answered 20 mins ago

glenn jackman

48.4k366105

add a comment | 

up vote
1
down vote

With perl

perl -00 -ne 'if (/^>genome.1n/) s/// if $. > 1; print' file

share|improve this answer

answered 20 mins ago

glenn jackman

48.4k366105

add a comment | 

up vote
1
down vote

up vote
1
down vote

With perl

perl -00 -ne 'if (/^>genome.1n/) s/// if $. > 1; print' file

share|improve this answer

answered 20 mins ago

glenn jackman

48.4k366105

With perl

perl -00 -ne 'if (/^>genome.1n/) s/// if $. > 1; print' file

share|improve this answer

answered 20 mins ago

glenn jackman

48.4k366105

share|improve this answer

share|improve this answer

answered 20 mins ago

glenn jackman

48.4k366105

answered 20 mins ago

glenn jackman

48.4k366105

answered 20 mins ago

glenn jackman

48.4k366105

48.4k366105

add a comment | 

add a comment | 

paul is a new contributor. Be nice, and check out our Code of Conduct.

 

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