How to substitute a specific string pattern in a multi-line FASTA file using bash?

Question

I have a large multi-line FASTA file that looks like the following:

>NWQ47741.1 CLTR1 protein, partial [Melospiza_melodia] Vertebrate
CLSQGTMTALSPNLSCHNPSIDDFRNSVYSTLYSMISIMGFVGNGVVLYVLIRTYRQKTA
FQIYMLNLALSDFLCVLTLPLRVIYYVHKGHWFFSDFLCRLSSYALYVNLYCSIFFMTAM
SFFRCIAIVFPVRNISLVSEKKAKFLCVGIWVFVTLTSAPFLRNGTYQHGNKTKCFEPPE
NSQKTNMVVILDFIALFVGFIFPFVIITICYTMIIRTLLRNSLRKNEANRRKAVWMIVIV
TATFLVSFTPYHVLRTVHLHALRLRGPGCADTVFLQKAVIVTLPLAAANCCFDPLLYFFS
GGNFRQRLTTLRKASSSSLSQAFRKKISVKEKEEEPFGE
>XP_002763076.2 cysteinyl leukotriene receptor 1 [Callithrix_jacchus] Vertebrate
MDGTGNLTVSSATCHDTIDEFRNQVYSTLYSMISVVGFFGNGFVLYVLIKTYHEKSAFQI
YMINLAIADLLCVCTLPLRVVYYVHKGIWFFGDFLCRLSTYALYVNLYCSIFFMTAMSFF
RCIAIVFPVQNINLVTQKKARFVCVGIWIFVILASSPFLITKSYKDEKNNTKCFEPPQDN
QTKNHVLILHYVSLFLGFIIPFVIIIVCYTMIILTLLKKSMKKNLSSHKKAIRMIMVVTA
AFLVSFMPYHIQRTIHLHFLHNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFFSGG
NFRRRLSTFRKHSLSSMTYVPRKKASLPEKGEEICKV
>XP_036988076.1 cysteinyl leukotriene receptor 1 [Artibeus_jamaicensis] Vertebrate
MDGTGNLTASSASNNMCNSSIDDFRNQVYSTMYSMISIVGFFGNGFVLYVLIRTYHEKSA
FQIYMINLAVSDLLCVCTLPLRVVYYVHKGMWFFGDILCRLSTYALYVNLYCSIFFMTAM
SFFRCIAIVFPVKNINLVTEKKARFVCASIWVFVILTSSPFLMSKSYKDEKNNTKCFEPP
QDNETKNHIFILHYVSLLVGFLIPFIIIIVCYTMIIFTLLKNSMQKNVPSRKKAVGMIII
VTAAFLISFMPYHIQRTIHLHFLYNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFF
SGGNFRRRLSTFRKHSLSSMTYVPKKKVSLPEKEDEVCK

I need to replace a specific substring within each sequence in the file. The substring to be replaced is the part after the accession ID and before the first '[' character. For example, in the first sequence, I want to replace "CLTR1 protein, partial" with "new_string", resulting in:

>NWQ47741.1 new_string [Melospiza_melodia] Vertebrate
CLSQGTMTALSPNLSCHNPSIDDFRNSVYSTLYSMISIMGFVGNGVVLYVLIRTYRQKTA
FQIYMLNLALSDFLCVLTLPLRVIYYVHKGHWFFSDFLCRLSSYALYVNLYCSIFFMTAM
SFFRCIAIVFPVRNISLVSEKKAKFLCVGIWVFVTLTSAPFLRNGTYQHGNKTKCFEPPE
NSQKTNMVVILDFIALFVGFIFPFVIITICYTMIIRTLLRNSLRKNEANRRKAVWMIVIV
TATFLVSFTPYHVLRTVHLHALRLRGPGCADTVFLQKAVIVTLPLAAANCCFDPLLYFFS
GGNFRQRLTTLRKASSSSLSQAFRKKISVKEKEEEPFGE

I'm looking for a way to achieve this using AWK or Sed, as the file is large, and I want an efficient solution. Can someone provide a sample script or command for this task?

I tried the following script:

awk '/^>/ {gsub(/\[[^[]*/, "new_string"); print; next} 1' your_file.fasta > modified_file.fasta

But got the following output:

>NWQ47741.1 CLTR1 protein, partial new_string
CLSQGTMTALSPNLSCHNPSIDDFRNSVYSTLYSMISIMGFVGNGVVLYVLIRTYRQKTA
FQIYMLNLALSDFLCVLTLPLRVIYYVHKGHWFFSDFLCRLSSYALYVNLYCSIFFMTAM
SFFRCIAIVFPVRNISLVSEKKAKFLCVGIWVFVTLTSAPFLRNGTYQHGNKTKCFEPPE
NSQKTNMVVILDFIALFVGFIFPFVIITICYTMIIRTLLRNSLRKNEANRRKAVWMIVIV
TATFLVSFTPYHVLRTVHLHALRLRGPGCADTVFLQKAVIVTLPLAAANCCFDPLLYFFS
GGNFRQRLTTLRKASSSSLSQAFRKKISVKEKEEEPFGE
>XP_002763076.2 cysteinyl leukotriene receptor 1 new_string
MDGTGNLTVSSATCHDTIDEFRNQVYSTLYSMISVVGFFGNGFVLYVLIKTYHEKSAFQI
YMINLAIADLLCVCTLPLRVVYYVHKGIWFFGDFLCRLSTYALYVNLYCSIFFMTAMSFF
RCIAIVFPVQNINLVTQKKARFVCVGIWIFVILASSPFLITKSYKDEKNNTKCFEPPQDN
QTKNHVLILHYVSLFLGFIIPFVIIIVCYTMIILTLLKKSMKKNLSSHKKAIRMIMVVTA
AFLVSFMPYHIQRTIHLHFLHNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFFSGG
NFRRRLSTFRKHSLSSMTYVPRKKASLPEKGEEICKV
>XP_036988076.1 cysteinyl leukotriene receptor 1 new_string
MDGTGNLTASSASNNMCNSSIDDFRNQVYSTMYSMISIVGFFGNGFVLYVLIRTYHEKSA
FQIYMINLAVSDLLCVCTLPLRVVYYVHKGMWFFGDILCRLSTYALYVNLYCSIFFMTAM
SFFRCIAIVFPVKNINLVTEKKARFVCASIWVFVILTSSPFLMSKSYKDEKNNTKCFEPP
QDNETKNHIFILHYVSLLVGFLIPFIIIIVCYTMIIFTLLKNSMQKNVPSRKKAVGMIII
VTAAFLISFMPYHIQRTIHLHFLYNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFF
SGGNFRRRLSTFRKHSLSSMTYVPKKKVSLPEKEDEVCK

Answer 1

I want an efficient solution

Observe that you do not need gsub (global sub) there as you will have at most 1 replacement in each line sub will suffice.

I would GNU AWK for this task following way, let file.txt content be

>NWQ47741.1 CLTR1 protein, partial [Melospiza_melodia] Vertebrate
CLSQGTMTALSPNLSCHNPSIDDFRNSVYSTLYSMISIMGFVGNGVVLYVLIRTYRQKTA
FQIYMLNLALSDFLCVLTLPLRVIYYVHKGHWFFSDFLCRLSSYALYVNLYCSIFFMTAM
SFFRCIAIVFPVRNISLVSEKKAKFLCVGIWVFVTLTSAPFLRNGTYQHGNKTKCFEPPE
NSQKTNMVVILDFIALFVGFIFPFVIITICYTMIIRTLLRNSLRKNEANRRKAVWMIVIV
TATFLVSFTPYHVLRTVHLHALRLRGPGCADTVFLQKAVIVTLPLAAANCCFDPLLYFFS
GGNFRQRLTTLRKASSSSLSQAFRKKISVKEKEEEPFGE
>XP_002763076.2 cysteinyl leukotriene receptor 1 [Callithrix_jacchus] Vertebrate
MDGTGNLTVSSATCHDTIDEFRNQVYSTLYSMISVVGFFGNGFVLYVLIKTYHEKSAFQI
YMINLAIADLLCVCTLPLRVVYYVHKGIWFFGDFLCRLSTYALYVNLYCSIFFMTAMSFF
RCIAIVFPVQNINLVTQKKARFVCVGIWIFVILASSPFLITKSYKDEKNNTKCFEPPQDN
QTKNHVLILHYVSLFLGFIIPFVIIIVCYTMIILTLLKKSMKKNLSSHKKAIRMIMVVTA
AFLVSFMPYHIQRTIHLHFLHNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFFSGG
NFRRRLSTFRKHSLSSMTYVPRKKASLPEKGEEICKV
>XP_036988076.1 cysteinyl leukotriene receptor 1 [Artibeus_jamaicensis] Vertebrate
MDGTGNLTASSASNNMCNSSIDDFRNQVYSTMYSMISIVGFFGNGFVLYVLIRTYHEKSA
FQIYMINLAVSDLLCVCTLPLRVVYYVHKGMWFFGDILCRLSTYALYVNLYCSIFFMTAM
SFFRCIAIVFPVKNINLVTEKKARFVCASIWVFVILTSSPFLMSKSYKDEKNNTKCFEPP
QDNETKNHIFILHYVSLLVGFLIPFIIIIVCYTMIIFTLLKNSMQKNVPSRKKAVGMIII
VTAAFLISFMPYHIQRTIHLHFLYNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFF
SGGNFRRRLSTFRKHSLSSMTYVPKKKVSLPEKEDEVCK

then

awk 'BEGIN{FS=OFS="["}/^>/{sub(/ .*/,"",$1);$1=$1 " new_string "}{print}' file.txt

gives output

>NWQ47741.1 new_string [Melospiza_melodia] Vertebrate
CLSQGTMTALSPNLSCHNPSIDDFRNSVYSTLYSMISIMGFVGNGVVLYVLIRTYRQKTA
FQIYMLNLALSDFLCVLTLPLRVIYYVHKGHWFFSDFLCRLSSYALYVNLYCSIFFMTAM
SFFRCIAIVFPVRNISLVSEKKAKFLCVGIWVFVTLTSAPFLRNGTYQHGNKTKCFEPPE
NSQKTNMVVILDFIALFVGFIFPFVIITICYTMIIRTLLRNSLRKNEANRRKAVWMIVIV
TATFLVSFTPYHVLRTVHLHALRLRGPGCADTVFLQKAVIVTLPLAAANCCFDPLLYFFS
GGNFRQRLTTLRKASSSSLSQAFRKKISVKEKEEEPFGE
>XP_002763076.2 new_string [Callithrix_jacchus] Vertebrate
MDGTGNLTVSSATCHDTIDEFRNQVYSTLYSMISVVGFFGNGFVLYVLIKTYHEKSAFQI
YMINLAIADLLCVCTLPLRVVYYVHKGIWFFGDFLCRLSTYALYVNLYCSIFFMTAMSFF
RCIAIVFPVQNINLVTQKKARFVCVGIWIFVILASSPFLITKSYKDEKNNTKCFEPPQDN
QTKNHVLILHYVSLFLGFIIPFVIIIVCYTMIILTLLKKSMKKNLSSHKKAIRMIMVVTA
AFLVSFMPYHIQRTIHLHFLHNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFFSGG
NFRRRLSTFRKHSLSSMTYVPRKKASLPEKGEEICKV
>XP_036988076.1 new_string [Artibeus_jamaicensis] Vertebrate
MDGTGNLTASSASNNMCNSSIDDFRNQVYSTMYSMISIVGFFGNGFVLYVLIRTYHEKSA
FQIYMINLAVSDLLCVCTLPLRVVYYVHKGMWFFGDILCRLSTYALYVNLYCSIFFMTAM
SFFRCIAIVFPVKNINLVTEKKARFVCASIWVFVILTSSPFLMSKSYKDEKNNTKCFEPP
QDNETKNHIFILHYVSLLVGFLIPFIIIIVCYTMIIFTLLKNSMQKNVPSRKKAVGMIII
VTAAFLISFMPYHIQRTIHLHFLYNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFF
SGGNFRRRLSTFRKHSLSSMTYVPKKKVSLPEKEDEVCK

Explanation: I inform GNU AWK that [ is both field separator (FS) and output field separator (OFS), for lines starting with > I use sub function to remove 1st space and everything after it up to end of 1st line (i.e. [) then I concatenate it with new_string (observe leading and trailing space). Every line is printed.

(tested in GNU Awk 5.1.0)

Answer 2

Using sed

$ sed -E '/^>/s/ [^[]*/ new_string /' input_file
>NWQ47741.1 new_string [Melospiza_melodia] Vertebrate
CLSQGTMTALSPNLSCHNPSIDDFRNSVYSTLYSMISIMGFVGNGVVLYVLIRTYRQKTA
FQIYMLNLALSDFLCVLTLPLRVIYYVHKGHWFFSDFLCRLSSYALYVNLYCSIFFMTAM
SFFRCIAIVFPVRNISLVSEKKAKFLCVGIWVFVTLTSAPFLRNGTYQHGNKTKCFEPPE
NSQKTNMVVILDFIALFVGFIFPFVIITICYTMIIRTLLRNSLRKNEANRRKAVWMIVIV
TATFLVSFTPYHVLRTVHLHALRLRGPGCADTVFLQKAVIVTLPLAAANCCFDPLLYFFS
GGNFRQRLTTLRKASSSSLSQAFRKKISVKEKEEEPFGE
>XP_002763076.2 new_string [Callithrix_jacchus] Vertebrate
MDGTGNLTVSSATCHDTIDEFRNQVYSTLYSMISVVGFFGNGFVLYVLIKTYHEKSAFQI
YMINLAIADLLCVCTLPLRVVYYVHKGIWFFGDFLCRLSTYALYVNLYCSIFFMTAMSFF
RCIAIVFPVQNINLVTQKKARFVCVGIWIFVILASSPFLITKSYKDEKNNTKCFEPPQDN
QTKNHVLILHYVSLFLGFIIPFVIIIVCYTMIILTLLKKSMKKNLSSHKKAIRMIMVVTA
AFLVSFMPYHIQRTIHLHFLHNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFFSGG
NFRRRLSTFRKHSLSSMTYVPRKKASLPEKGEEICKV
>XP_036988076.1 new_string [Artibeus_jamaicensis] Vertebrate
MDGTGNLTASSASNNMCNSSIDDFRNQVYSTMYSMISIVGFFGNGFVLYVLIRTYHEKSA
FQIYMINLAVSDLLCVCTLPLRVVYYVHKGMWFFGDILCRLSTYALYVNLYCSIFFMTAM
SFFRCIAIVFPVKNINLVTEKKARFVCASIWVFVILTSSPFLMSKSYKDEKNNTKCFEPP
QDNETKNHIFILHYVSLLVGFLIPFIIIIVCYTMIIFTLLKNSMQKNVPSRKKAVGMIII
VTAAFLISFMPYHIQRTIHLHFLYNETKPCDSVLRMQKSVVITLSLAASNCCFDPLLYFF
SGGNFRRRLSTFRKHSLSSMTYVPKKKVSLPEKEDEVCK