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Print multiple filenames to specific lines in txt file

.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ margin-bottom:0;
}

0

1

I am trying to print a list of filenames to a text file, with the requirement of printing certain filenames on the same line. For example, I have 4 files.

Paleo_R1.fastq

Paleo_R2.fastq

Vegan_R1.fastq

Vegan_R2.fastq

I want the output to be

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

I know I can use the ls function and direct output to a text file, using ls >> file.txt but there are no options to print specific input line items to specific output lines.

Additionally, I am aware of that I can use for loops like this >

for file in Vegan*R1*.fastq; 

do echo $file ${file%_R1.fastq}_R2.fastq >> file.txt;

done

But I do not want to have a separate command for each filename, ie. for vegan and paleo.

Is there a way to print certain lines to specific output lines (print input lines 1 and 2 to output line 1, and input lines 3 and 4 to output line 2, and so on...)

linux files ls bioinformatics

share|improve this question

asked 3 hours ago

Jamie AlfieriJamie Alfieri

1

New contributor

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

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Is the rule based on the file names (all files with the same first 5 characters), or every N=2 files regardless of name?
  
  – Jeff Schaller♦
  3 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  The rule is based on every N=2 files regardless of name.
  
  – Jamie Alfieri
  3 hours ago
  

  
  
  
  

add a comment | 

0

1

I am trying to print a list of filenames to a text file, with the requirement of printing certain filenames on the same line. For example, I have 4 files.

Paleo_R1.fastq

Paleo_R2.fastq

Vegan_R1.fastq

Vegan_R2.fastq

I want the output to be

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

I know I can use the ls function and direct output to a text file, using ls >> file.txt but there are no options to print specific input line items to specific output lines.

Additionally, I am aware of that I can use for loops like this >

for file in Vegan*R1*.fastq; 

do echo $file ${file%_R1.fastq}_R2.fastq >> file.txt;

done

But I do not want to have a separate command for each filename, ie. for vegan and paleo.

Is there a way to print certain lines to specific output lines (print input lines 1 and 2 to output line 1, and input lines 3 and 4 to output line 2, and so on...)

linux files ls bioinformatics

share|improve this question

asked 3 hours ago

Jamie AlfieriJamie Alfieri

1

New contributor

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

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Is the rule based on the file names (all files with the same first 5 characters), or every N=2 files regardless of name?
  
  – Jeff Schaller♦
  3 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  The rule is based on every N=2 files regardless of name.
  
  – Jamie Alfieri
  3 hours ago
  

  
  
  
  

add a comment | 

I am trying to print a list of filenames to a text file, with the requirement of printing certain filenames on the same line. For example, I have 4 files.

Paleo_R1.fastq

Paleo_R2.fastq

Vegan_R1.fastq

Vegan_R2.fastq

I want the output to be

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

I know I can use the ls function and direct output to a text file, using ls >> file.txt but there are no options to print specific input line items to specific output lines.

Additionally, I am aware of that I can use for loops like this >

for file in Vegan*R1*.fastq; 

do echo $file ${file%_R1.fastq}_R2.fastq >> file.txt;

done

But I do not want to have a separate command for each filename, ie. for vegan and paleo.

Is there a way to print certain lines to specific output lines (print input lines 1 and 2 to output line 1, and input lines 3 and 4 to output line 2, and so on...)

linux files ls bioinformatics

share|improve this question

asked 3 hours ago

Jamie AlfieriJamie Alfieri

1

New contributor

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

Paleo_R1.fastq

Paleo_R2.fastq

Vegan_R1.fastq

Vegan_R2.fastq

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

for file in Vegan*R1*.fastq; 

do echo $file ${file%_R1.fastq}_R2.fastq >> file.txt;

done

share|improve this question

asked 3 hours ago

Jamie AlfieriJamie Alfieri

1

New contributor

Jamie Alfieri 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

asked 3 hours ago

Jamie AlfieriJamie Alfieri

1

New contributor

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

asked 3 hours ago

Jamie AlfieriJamie Alfieri

1

New contributor

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

asked 3 hours ago

Jamie AlfieriJamie Alfieri

1

2 Answers
2

active

oldest

votes

2

Maybe

$ ls *.fastq | xargs -n2

Bar_R1.fastq Bar_R2.fastq

Bar_R3.fastq Foo_R1.fastq

Foo_R2.fastq Foo_R3.fastq

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

or for column output

$ ls *.fastq | xargs -n2 | column -t

Bar_R1.fastq    Bar_R2.fastq

Bar_R3.fastq    Foo_R1.fastq

Foo_R2.fastq    Foo_R3.fastq

Paleo_R1.fastq  Paleo_R2.fastq

Vegan_R1.fastq  Vegan_R2.fastq

(add >> file.txt to the command to append the output to the file)

Note that both examples only work with filenames without spaces.

For files with spaces:

$ for i in *.fastq; do echo -ne "$i"; done | xargs -0 -n2

share|improve this answer

edited 2 hours ago

answered 3 hours ago

FreddyFreddy

2,157210

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Note that redirecting this to a new file would include the name of that file in the output.
  
  – Kusalananda♦
  3 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thanks @Kusalananda, fixed by workaround. I guess it's time for bed.
  
  – Freddy
  2 hours ago
  

  
  
  
  

add a comment | 

0

Using the solution you already have, it's just a matter of not specifying the filename prefix Vegan:

for file in *_R1.fastq; do

    printf '%s %sn' "$file" "${file%_R1.fastq}_R2.fastq"

done >file.txt

Using printf and redirecting after the loop instead of for each output command is just my personal preference.

For the given filenames, this generates file.txt with

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

share|improve this answer

answered 3 hours ago

Kusalananda♦Kusalananda

143k18267445

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Yes this would work with the data I supplied. However, this would not work if the files were not named in a consistent manner.
  
  – Jamie Alfieri
  2 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  @JamieAlfieri Do give an example of that, because there is none in the question.
  
  – Kusalananda♦
  2 hours ago
  
  
  

  
  
  
  

add a comment | 

Your Answer

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2

Maybe

$ ls *.fastq | xargs -n2

Bar_R1.fastq Bar_R2.fastq

Bar_R3.fastq Foo_R1.fastq

Foo_R2.fastq Foo_R3.fastq

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

or for column output

$ ls *.fastq | xargs -n2 | column -t

Bar_R1.fastq    Bar_R2.fastq

Bar_R3.fastq    Foo_R1.fastq

Foo_R2.fastq    Foo_R3.fastq

Paleo_R1.fastq  Paleo_R2.fastq

Vegan_R1.fastq  Vegan_R2.fastq

(add >> file.txt to the command to append the output to the file)

Note that both examples only work with filenames without spaces.

For files with spaces:

$ for i in *.fastq; do echo -ne "$i"; done | xargs -0 -n2

share|improve this answer

edited 2 hours ago

answered 3 hours ago

FreddyFreddy

2,157210

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Note that redirecting this to a new file would include the name of that file in the output.
  
  – Kusalananda♦
  3 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thanks @Kusalananda, fixed by workaround. I guess it's time for bed.
  
  – Freddy
  2 hours ago
  

  
  
  
  

add a comment | 

2

Maybe

$ ls *.fastq | xargs -n2

Bar_R1.fastq Bar_R2.fastq

Bar_R3.fastq Foo_R1.fastq

Foo_R2.fastq Foo_R3.fastq

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

or for column output

$ ls *.fastq | xargs -n2 | column -t

Bar_R1.fastq    Bar_R2.fastq

Bar_R3.fastq    Foo_R1.fastq

Foo_R2.fastq    Foo_R3.fastq

Paleo_R1.fastq  Paleo_R2.fastq

Vegan_R1.fastq  Vegan_R2.fastq

(add >> file.txt to the command to append the output to the file)

Note that both examples only work with filenames without spaces.

For files with spaces:

$ for i in *.fastq; do echo -ne "$i"; done | xargs -0 -n2

share|improve this answer

edited 2 hours ago

answered 3 hours ago

FreddyFreddy

2,157210

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Note that redirecting this to a new file would include the name of that file in the output.
  
  – Kusalananda♦
  3 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thanks @Kusalananda, fixed by workaround. I guess it's time for bed.
  
  – Freddy
  2 hours ago
  

  
  
  
  

add a comment | 

Maybe

$ ls *.fastq | xargs -n2

Bar_R1.fastq Bar_R2.fastq

Bar_R3.fastq Foo_R1.fastq

Foo_R2.fastq Foo_R3.fastq

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

or for column output

$ ls *.fastq | xargs -n2 | column -t

Bar_R1.fastq    Bar_R2.fastq

Bar_R3.fastq    Foo_R1.fastq

Foo_R2.fastq    Foo_R3.fastq

Paleo_R1.fastq  Paleo_R2.fastq

Vegan_R1.fastq  Vegan_R2.fastq

(add >> file.txt to the command to append the output to the file)

Note that both examples only work with filenames without spaces.

For files with spaces:

$ for i in *.fastq; do echo -ne "$i"; done | xargs -0 -n2

share|improve this answer

edited 2 hours ago

answered 3 hours ago

FreddyFreddy

2,157210

$ ls *.fastq | xargs -n2

Bar_R1.fastq Bar_R2.fastq

Bar_R3.fastq Foo_R1.fastq

Foo_R2.fastq Foo_R3.fastq

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

$ ls *.fastq | xargs -n2 | column -t

Bar_R1.fastq    Bar_R2.fastq

Bar_R3.fastq    Foo_R1.fastq

Foo_R2.fastq    Foo_R3.fastq

Paleo_R1.fastq  Paleo_R2.fastq

Vegan_R1.fastq  Vegan_R2.fastq

$ for i in *.fastq; do echo -ne "$i"; done | xargs -0 -n2

share|improve this answer

edited 2 hours ago

answered 3 hours ago

FreddyFreddy

2,157210

answered 3 hours ago

FreddyFreddy

2,157210

answered 3 hours ago

FreddyFreddy

2,157210

0

Using the solution you already have, it's just a matter of not specifying the filename prefix Vegan:

for file in *_R1.fastq; do

    printf '%s %sn' "$file" "${file%_R1.fastq}_R2.fastq"

done >file.txt

Using printf and redirecting after the loop instead of for each output command is just my personal preference.

For the given filenames, this generates file.txt with

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

share|improve this answer

answered 3 hours ago

Kusalananda♦Kusalananda

143k18267445

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Yes this would work with the data I supplied. However, this would not work if the files were not named in a consistent manner.
  
  – Jamie Alfieri
  2 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  @JamieAlfieri Do give an example of that, because there is none in the question.
  
  – Kusalananda♦
  2 hours ago
  
  
  

  
  
  
  

add a comment | 

0

Using the solution you already have, it's just a matter of not specifying the filename prefix Vegan:

for file in *_R1.fastq; do

    printf '%s %sn' "$file" "${file%_R1.fastq}_R2.fastq"

done >file.txt

Using printf and redirecting after the loop instead of for each output command is just my personal preference.

For the given filenames, this generates file.txt with

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

share|improve this answer

answered 3 hours ago

Kusalananda♦Kusalananda

143k18267445

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Yes this would work with the data I supplied. However, this would not work if the files were not named in a consistent manner.
  
  – Jamie Alfieri
  2 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  @JamieAlfieri Do give an example of that, because there is none in the question.
  
  – Kusalananda♦
  2 hours ago
  
  
  

  
  
  
  

add a comment | 

Using the solution you already have, it's just a matter of not specifying the filename prefix Vegan:

for file in *_R1.fastq; do

    printf '%s %sn' "$file" "${file%_R1.fastq}_R2.fastq"

done >file.txt

Using printf and redirecting after the loop instead of for each output command is just my personal preference.

For the given filenames, this generates file.txt with

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

share|improve this answer

answered 3 hours ago

Kusalananda♦Kusalananda

143k18267445

for file in *_R1.fastq; do

    printf '%s %sn' "$file" "${file%_R1.fastq}_R2.fastq"

done >file.txt

Paleo_R1.fastq Paleo_R2.fastq

Vegan_R1.fastq Vegan_R2.fastq

share|improve this answer

answered 3 hours ago

Kusalananda♦Kusalananda

143k18267445

answered 3 hours ago

Kusalananda♦Kusalananda

143k18267445

answered 3 hours ago

Kusalananda♦Kusalananda

143k18267445