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extract specific cheracters from each line

Extract keyword from lineExtract specific columns from text fileSearch for a specific word in each line and print rest of the lineUse awk/sed to remove everything but matching pattern in a specific columnHow to extract one line followed by range of linesHow to extract a line based on the multiple fields in perlExtract specific thing from each row in columnExtract text from bracketsExtract specific fields from file

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

1

I have a text file and i want extract the a string from each line coming after "OS="

input file line
A0A0A9PBI3_ARUDO Uncharacterized protein OS=Arundo donax OX=35708 PE=4 SV=1
K3Y356_SETIT ATP-dependent DNA helicase OS=Setaria italica OX=4555 PE=3 SV=1

output desired

OS=Arundo donax
OS=Setaria italica

OR

Arundo donax
Setaria italica

awk perl cat

share|improve this question

edited 8 hours ago

Kevdog777

2,1321313 gold badges3636 silver badges6161 bronze badges

asked 8 hours ago

shahzadshahzad

611 bronze badge

New contributor

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

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Are there always 2 words to print after OS= or do you want all words between OS= and OX=?
  
  – oliv
  8 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  i need only two words
  
  – shahzad
  8 hours ago
  

  
  
  
  

add a comment | 

1

I have a text file and i want extract the a string from each line coming after "OS="

input file line
A0A0A9PBI3_ARUDO Uncharacterized protein OS=Arundo donax OX=35708 PE=4 SV=1
K3Y356_SETIT ATP-dependent DNA helicase OS=Setaria italica OX=4555 PE=3 SV=1

output desired

OS=Arundo donax
OS=Setaria italica

OR

Arundo donax
Setaria italica

awk perl cat

share|improve this question

edited 8 hours ago

Kevdog777

2,1321313 gold badges3636 silver badges6161 bronze badges

asked 8 hours ago

shahzadshahzad

611 bronze badge

New contributor

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

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Are there always 2 words to print after OS= or do you want all words between OS= and OX=?
  
  – oliv
  8 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  i need only two words
  
  – shahzad
  8 hours ago
  

  
  
  
  

add a comment | 

I have a text file and i want extract the a string from each line coming after "OS="

input file line
A0A0A9PBI3_ARUDO Uncharacterized protein OS=Arundo donax OX=35708 PE=4 SV=1
K3Y356_SETIT ATP-dependent DNA helicase OS=Setaria italica OX=4555 PE=3 SV=1

output desired

OS=Arundo donax
OS=Setaria italica

OR

Arundo donax
Setaria italica

awk perl cat

share|improve this question

edited 8 hours ago

Kevdog777

2,1321313 gold badges3636 silver badges6161 bronze badges

asked 8 hours ago

shahzadshahzad

611 bronze badge

New contributor

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

input file line
A0A0A9PBI3_ARUDO Uncharacterized protein OS=Arundo donax OX=35708 PE=4 SV=1
K3Y356_SETIT ATP-dependent DNA helicase OS=Setaria italica OX=4555 PE=3 SV=1

OS=Arundo donax
OS=Setaria italica

Arundo donax
Setaria italica

share|improve this question

edited 8 hours ago

Kevdog777

2,1321313 gold badges3636 silver badges6161 bronze badges

asked 8 hours ago

shahzadshahzad

611 bronze badge

New contributor

shahzad 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 8 hours ago

Kevdog777

2,1321313 gold badges3636 silver badges6161 bronze badges

asked 8 hours ago

shahzadshahzad

611 bronze badge

New contributor

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

edited 8 hours ago

Kevdog777

2,1321313 gold badges3636 silver badges6161 bronze badges

edited 8 hours ago

Kevdog777

2,1321313 gold badges3636 silver badges6161 bronze badges

asked 8 hours ago

shahzadshahzad

611 bronze badge

New contributor

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

asked 8 hours ago

shahzadshahzad

611 bronze badge

3 Answers
3

active

oldest

votes

2

Use GNU grep (or compatible) with extended regex:

grep -Eo "OS=w+ w+" file

or basic regex (does not know about + quantifier)

grep -o "OS=w* w*" file

Output:

OS=Arundo donax
OS=Setaria italica

share|improve this answer

edited 8 hours ago

Stéphane Chazelas

333k5858 gold badges650650 silver badges10201020 bronze badges

answered 8 hours ago

pLumopLumo

7,5631515 silver badges3434 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you. It worked great.
  
  – shahzad
  8 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  how can i use this if i want to extract the string stating from 2nd word till the OS= i.e from the mentioned above input THE desired output is "Uncharacterized protein" and "ATP-dependent DNA helicase" in each new line
  
  – shahzad
  6 hours ago
  

  
  
  
  

add a comment | 

1

In Perl, two non-whitespace "words":

$ perl -lne 'print $1 if /OS=(S+ S+)/' input

or everything up to OX=:

$ perl -lne 'print $1 if /OS=(.*?) OX=/' input 

or everything up to the next something=:

$ perl -lne 'print $1 if /OS=(.*?) (w+)=/' input

With your sample input, they all give the same output, but the output would be different with e.g. an input like this:

ABC=something here OS=foo bar doo PE=3 OX=1234

share|improve this answer

answered 8 hours ago

ilkkachuilkkachu

68.1k1010 gold badges113113 silver badges196196 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  thank you it worked
  
  – shahzad
  8 hours ago
  

  
  
  
  

add a comment | 

1

A more robust way is to use sed to parse the full value until the word containing the next = is found. That way it will work on any sized value (e.g. if you have a font with one word or three words).

sed 's/.*OS=([^=]*).*/1/;s/ [^ ]*$//'

The first block grabs everything up to OS=, the second block in the capture group (denoted by ()'s) matches upto the next = and can be referred to in the replacement as 1. The next substitution rids the last word which is a fragment from the next assignment.

Note: the ^ in []'s is to exclude match the character in this case everything that is not an = sign.

share|improve this answer

edited 7 hours ago

answered 8 hours ago

A.DanischewskiA.Danischewski

23422 silver badges77 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  how can i use this if i want to extract the string stating from 2nd word till the OS= i.e from the mentioned above input THE desired output is "Uncharacterized protein" and "ATP-dependent DNA helicase" in each new line
  
  – shahzad
  6 hours ago
  
  

  
  
  
  

add a comment | 

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2

Use GNU grep (or compatible) with extended regex:

grep -Eo "OS=w+ w+" file

or basic regex (does not know about + quantifier)

grep -o "OS=w* w*" file

Output:

OS=Arundo donax
OS=Setaria italica

share|improve this answer

edited 8 hours ago

Stéphane Chazelas

333k5858 gold badges650650 silver badges10201020 bronze badges

answered 8 hours ago

pLumopLumo

7,5631515 silver badges3434 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you. It worked great.
  
  – shahzad
  8 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  how can i use this if i want to extract the string stating from 2nd word till the OS= i.e from the mentioned above input THE desired output is "Uncharacterized protein" and "ATP-dependent DNA helicase" in each new line
  
  – shahzad
  6 hours ago
  

  
  
  
  

add a comment | 

2

Use GNU grep (or compatible) with extended regex:

grep -Eo "OS=w+ w+" file

or basic regex (does not know about + quantifier)

grep -o "OS=w* w*" file

Output:

OS=Arundo donax
OS=Setaria italica

share|improve this answer

edited 8 hours ago

Stéphane Chazelas

333k5858 gold badges650650 silver badges10201020 bronze badges

answered 8 hours ago

pLumopLumo

7,5631515 silver badges3434 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you. It worked great.
  
  – shahzad
  8 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  how can i use this if i want to extract the string stating from 2nd word till the OS= i.e from the mentioned above input THE desired output is "Uncharacterized protein" and "ATP-dependent DNA helicase" in each new line
  
  – shahzad
  6 hours ago
  

  
  
  
  

add a comment | 

Use GNU grep (or compatible) with extended regex:

grep -Eo "OS=w+ w+" file

or basic regex (does not know about + quantifier)

grep -o "OS=w* w*" file

Output:

OS=Arundo donax
OS=Setaria italica

share|improve this answer

edited 8 hours ago

Stéphane Chazelas

333k5858 gold badges650650 silver badges10201020 bronze badges

answered 8 hours ago

pLumopLumo

7,5631515 silver badges3434 bronze badges

grep -Eo "OS=w+ w+" file

grep -o "OS=w* w*" file

OS=Arundo donax
OS=Setaria italica

share|improve this answer

edited 8 hours ago

Stéphane Chazelas

333k5858 gold badges650650 silver badges10201020 bronze badges

answered 8 hours ago

pLumopLumo

7,5631515 silver badges3434 bronze badges

edited 8 hours ago

Stéphane Chazelas

333k5858 gold badges650650 silver badges10201020 bronze badges

edited 8 hours ago

Stéphane Chazelas

333k5858 gold badges650650 silver badges10201020 bronze badges

answered 8 hours ago

pLumopLumo

7,5631515 silver badges3434 bronze badges

answered 8 hours ago

pLumopLumo

7,5631515 silver badges3434 bronze badges

1

In Perl, two non-whitespace "words":

$ perl -lne 'print $1 if /OS=(S+ S+)/' input

or everything up to OX=:

$ perl -lne 'print $1 if /OS=(.*?) OX=/' input 

or everything up to the next something=:

$ perl -lne 'print $1 if /OS=(.*?) (w+)=/' input

With your sample input, they all give the same output, but the output would be different with e.g. an input like this:

ABC=something here OS=foo bar doo PE=3 OX=1234

share|improve this answer

answered 8 hours ago

ilkkachuilkkachu

68.1k1010 gold badges113113 silver badges196196 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  thank you it worked
  
  – shahzad
  8 hours ago
  

  
  
  
  

add a comment | 

1

In Perl, two non-whitespace "words":

$ perl -lne 'print $1 if /OS=(S+ S+)/' input

or everything up to OX=:

$ perl -lne 'print $1 if /OS=(.*?) OX=/' input 

or everything up to the next something=:

$ perl -lne 'print $1 if /OS=(.*?) (w+)=/' input

With your sample input, they all give the same output, but the output would be different with e.g. an input like this:

ABC=something here OS=foo bar doo PE=3 OX=1234

share|improve this answer

answered 8 hours ago

ilkkachuilkkachu

68.1k1010 gold badges113113 silver badges196196 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  thank you it worked
  
  – shahzad
  8 hours ago
  

  
  
  
  

add a comment | 

In Perl, two non-whitespace "words":

$ perl -lne 'print $1 if /OS=(S+ S+)/' input

or everything up to OX=:

$ perl -lne 'print $1 if /OS=(.*?) OX=/' input 

or everything up to the next something=:

$ perl -lne 'print $1 if /OS=(.*?) (w+)=/' input

With your sample input, they all give the same output, but the output would be different with e.g. an input like this:

ABC=something here OS=foo bar doo PE=3 OX=1234

share|improve this answer

answered 8 hours ago

ilkkachuilkkachu

68.1k1010 gold badges113113 silver badges196196 bronze badges

$ perl -lne 'print $1 if /OS=(S+ S+)/' input

$ perl -lne 'print $1 if /OS=(.*?) OX=/' input 

$ perl -lne 'print $1 if /OS=(.*?) (w+)=/' input

ABC=something here OS=foo bar doo PE=3 OX=1234

share|improve this answer

answered 8 hours ago

ilkkachuilkkachu

68.1k1010 gold badges113113 silver badges196196 bronze badges

answered 8 hours ago

ilkkachuilkkachu

68.1k1010 gold badges113113 silver badges196196 bronze badges

answered 8 hours ago

ilkkachuilkkachu

68.1k1010 gold badges113113 silver badges196196 bronze badges

1

A more robust way is to use sed to parse the full value until the word containing the next = is found. That way it will work on any sized value (e.g. if you have a font with one word or three words).

sed 's/.*OS=([^=]*).*/1/;s/ [^ ]*$//'

The first block grabs everything up to OS=, the second block in the capture group (denoted by ()'s) matches upto the next = and can be referred to in the replacement as 1. The next substitution rids the last word which is a fragment from the next assignment.

Note: the ^ in []'s is to exclude match the character in this case everything that is not an = sign.

share|improve this answer

edited 7 hours ago

answered 8 hours ago

A.DanischewskiA.Danischewski

23422 silver badges77 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  how can i use this if i want to extract the string stating from 2nd word till the OS= i.e from the mentioned above input THE desired output is "Uncharacterized protein" and "ATP-dependent DNA helicase" in each new line
  
  – shahzad
  6 hours ago
  
  

  
  
  
  

add a comment | 

1

A more robust way is to use sed to parse the full value until the word containing the next = is found. That way it will work on any sized value (e.g. if you have a font with one word or three words).

sed 's/.*OS=([^=]*).*/1/;s/ [^ ]*$//'

The first block grabs everything up to OS=, the second block in the capture group (denoted by ()'s) matches upto the next = and can be referred to in the replacement as 1. The next substitution rids the last word which is a fragment from the next assignment.

Note: the ^ in []'s is to exclude match the character in this case everything that is not an = sign.

share|improve this answer

edited 7 hours ago

answered 8 hours ago

A.DanischewskiA.Danischewski

23422 silver badges77 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  how can i use this if i want to extract the string stating from 2nd word till the OS= i.e from the mentioned above input THE desired output is "Uncharacterized protein" and "ATP-dependent DNA helicase" in each new line
  
  – shahzad
  6 hours ago
  
  

  
  
  
  

add a comment | 

A more robust way is to use sed to parse the full value until the word containing the next = is found. That way it will work on any sized value (e.g. if you have a font with one word or three words).

sed 's/.*OS=([^=]*).*/1/;s/ [^ ]*$//'

The first block grabs everything up to OS=, the second block in the capture group (denoted by ()'s) matches upto the next = and can be referred to in the replacement as 1. The next substitution rids the last word which is a fragment from the next assignment.

Note: the ^ in []'s is to exclude match the character in this case everything that is not an = sign.

share|improve this answer

edited 7 hours ago

answered 8 hours ago

A.DanischewskiA.Danischewski

23422 silver badges77 bronze badges

sed 's/.*OS=([^=]*).*/1/;s/ [^ ]*$//'

share|improve this answer

edited 7 hours ago

answered 8 hours ago

A.DanischewskiA.Danischewski

23422 silver badges77 bronze badges

answered 8 hours ago

A.DanischewskiA.Danischewski

23422 silver badges77 bronze badges

answered 8 hours ago

A.DanischewskiA.Danischewski

23422 silver badges77 bronze badges