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  1. #!/bin/bash
  2.  
  3.  
  4. awk '/^>/ { wrap=1; print; next }
  5.    wrap && /^$/ { print wrapped; wrapped = ""; wrap = 0 }
  6.    wrap { wrapped = wrapped $0; next }
  7.    1
  8.     END { if (wrap) print wrapped }'
  9.  
Success #stdin #stdout 0.01s 5288KB
comments (?)
stdin 
Ipcress result
Experiment: Primer1
Primers: B A
Target: QLOD02000001.1:filter(unmasked), whole genome shotgun sequence
Matches: 20/20 20/20
Product: 2601 bp (range 100-5000)
Result type: revcomp
ipcress: QLOD02000001.1:filter(unmasked) Primer1 2601 B 91258 0 A 93839 0 revcomp
>F-RK1_product_1 seq QLOD02000001.1:filter(unmasked) start 91258 length 2601
AAGCGGATTGAGAAGTGGTGGTGGTAGTAGCAGTCATGTGGGTAACGAAGACTACAACAGCAGTATTATA
ATTAGGAAAAGGTTTGAAGAAAAGATGAGGCTTGAAAGGGACGACGACGACGACAAGATCTTCAATCCCA
CCAAGTACTTTGTCCAAGAAGTTGTTAATTGCTTTGATGAGTCTGACCTCTACAGAACT...

Ipcress result
Experiment: Primer2
Primers: B A
Target: QLOD02000001.1:filter(unmasked), whole genome shotgun sequence
Matches: 20/20 20/20
Product: 854 bp (range 100-5000)
Result type: revcomp
ipcress: QLOD02000001.1:filter(unmasked) Primer2 854 B 149835 0 A 150669 0 revcomp
>F-RK3_product_1 seq QLOD02000001.1:filter(unmasked) start 149835 length 854
AGGATGACATGGGAATCTGGGACCTCAACCATTTTGTCTAGCTCTCTCCCAAGAGAAAGCGACGAAAATG
ACATGGGTTTGGCTCTGTATTGTTTAACAAATTTAAGTGGCTTAAAAACTCTAC....
stdout 
Ipcress result
Experiment: Primer1
Primers: B A
Target: QLOD02000001.1:filter(unmasked), whole genome shotgun sequence
Matches: 20/20 20/20
Product: 2601 bp (range 100-5000)
Result type: revcomp
ipcress: QLOD02000001.1:filter(unmasked) Primer1 2601 B 91258 0 A 93839 0 revcomp
>F-RK1_product_1 seq QLOD02000001.1:filter(unmasked) start 91258 length 2601
AAGCGGATTGAGAAGTGGTGGTGGTAGTAGCAGTCATGTGGGTAACGAAGACTACAACAGCAGTATTATAATTAGGAAAAGGTTTGAAGAAAAGATGAGGCTTGAAAGGGACGACGACGACGACAAGATCTTCAATCCCACCAAGTACTTTGTCCAAGAAGTTGTTAATTGCTTTGATGAGTCTGACCTCTACAGAACT...

Ipcress result
Experiment: Primer2
Primers: B A
Target: QLOD02000001.1:filter(unmasked), whole genome shotgun sequence
Matches: 20/20 20/20
Product: 854 bp (range 100-5000)
Result type: revcomp
ipcress: QLOD02000001.1:filter(unmasked) Primer2 854 B 149835 0 A 150669 0 revcomp
>F-RK3_product_1 seq QLOD02000001.1:filter(unmasked) start 149835 length 854
AGGATGACATGGGAATCTGGGACCTCAACCATTTTGTCTAGCTCTCTCCCAAGAGAAAGCGACGAAAATGACATGGGTTTGGCTCTGTATTGTTTAACAAATTTAAGTGGCTTAAAAACTCTAC....
https://ideone.com/ZCkKss
https://stackoverflow.com/questions/77570201/how-to-linearize-fasta-sequences-within-a-not-only-fasta-file
language:
Bash (bash 5.0.3)
created:
172 days ago
visibility:
secret

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