Re^2: Finding pattern in a file

But IIUC, the pattern to be searched for may be broken across multiple lines. How would your code handle, e.g., the record:

>AAF88103.1 zinc finger protein 226 [Homo sapiens]
AAAAAAAAAAAAAACDECGKEFSQ
GAHLQTHQKVHZZZZZZZZZZZ
[download]

(assuming we're now dealing with kosher FASTA files)?.

Give a man a fish: <%-{-{-{-<

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Re^3: Finding pattern in a file by tybalt89 (Monsignor) on Apr 14, 2020 at 23:08 UTC
Here's one way (snicker). It shows the location of each occurrence, even if they are overlapping. #!/usr/bin/perl use strict; # https://perlmonks.org/?node_id=11115501 use warnings; $_ = do { local $/; <DATA> }; # or however you want to read the file my $pattern = 'CDECGKEFSQGAHLQTHQKVH' =~ s/\B/\n?/gr; print lc($`) . $1 . lc(substr $', length $1) . "\n" while /(?=($patter +n))/g; __DATA__ >AAF88103.1 zinc finger protein 226 [Homo sapiens] MNMFKEAVTFKDVAVAFTEEELGLLGPAXRKLYRDVMVENFRNLLSVGHPPFKQDVSPIERNEQLWIMTT ATRRQGNLGEKNQSKLITVQDRESEEELSCWQIWQQIANDLTRCQDSMINNSQCHKQGDFPYQVGTELSI QISEDENYIVNKADGPNNTGNPEFPILRTQDSWRKTFLTESQRLNRDQQISIKNKLCQCKKGVDPIGWIS HHDGHRVHKSEKSYRPNDYEKDNMKILTFDHNSMIHTGQKSYQCNECKKPFSDLSSFDLHQQLQSGEKSL TCVERGKGFCYSPVLPVHQKVHVGEKLKCDECGKEFSQGAHLQTHQKVHVIEKPYKCKQCGKGFSRRSAL NVHCKVHTAEKPYNCEECGRAFSQASHLQDHQRLHTGEKPFKCDACGKSFSRNSHLQSHQRVHTGEKPYK CEECGKGFICSSNLYIHQRVHTGEKPYKCEECGKGFSRPSSLQAHQGVHTGEKSYICTVCGKGFTLSSNL QAHQRVHTGEKPYKCNECGKSFRRNSHYQVHLVVHTGEKPYKCEICGKGFSQSSYLQIHQKAHSIEKPFK CEECGQGFNQSSRLQIHQLIHTGEKPYKCEECGKGFSRRADLKIHCRIHTGEKPYNCEECGKVFRQASNL LAHQRVHSGEKPFKCEECGKSFGRSAHLQAHQKVHTGDKPYKCDECGKGFKWSLNLDMHQRVHTGEKPYK CGECGKYFSQASSLQLHQSVHTGEKPYKCDVCGKVFSRSSQLQSHQRVHTGEKPYKCEICGKSFSWRSNL TVHHRIHVGDKSYKSNRGGKNIRESTQEKKSIK. AAAAAAAAAAAAAACDECGKEFSQ GAHLQTHQKVHZZZZZZZZZZZ [download]	[reply] [d/l]

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Re^3: Finding pattern in a file
by tybalt89 (Monsignor) on Apr 14, 2020 at 23:08 UTC

Here's one way (snicker).
It shows the location of each occurrence, even if they are overlapping.

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11115501
use warnings;

$_ = do { local $/; <DATA> }; # or however you want to read the file

my $pattern = 'CDECGKEFSQGAHLQTHQKVH' =~ s/\B/\n?/gr;

print lc($`) . $1 . lc(substr $', length $1) . "\n" while /(?=($patter
+n))/g;

__DATA__
>AAF88103.1 zinc finger protein 226 [Homo sapiens]
MNMFKEAVTFKDVAVAFTEEELGLLGPAXRKLYRDVMVENFRNLLSVGHPPFKQDVSPIERNEQLWIMTT
ATRRQGNLGEKNQSKLITVQDRESEEELSCWQIWQQIANDLTRCQDSMINNSQCHKQGDFPYQVGTELSI
QISEDENYIVNKADGPNNTGNPEFPILRTQDSWRKTFLTESQRLNRDQQISIKNKLCQCKKGVDPIGWIS
HHDGHRVHKSEKSYRPNDYEKDNMKILTFDHNSMIHTGQKSYQCNECKKPFSDLSSFDLHQQLQSGEKSL
TCVERGKGFCYSPVLPVHQKVHVGEKLKCDECGKEFSQGAHLQTHQKVHVIEKPYKCKQCGKGFSRRSAL
NVHCKVHTAEKPYNCEECGRAFSQASHLQDHQRLHTGEKPFKCDACGKSFSRNSHLQSHQRVHTGEKPYK
CEECGKGFICSSNLYIHQRVHTGEKPYKCEECGKGFSRPSSLQAHQGVHTGEKSYICTVCGKGFTLSSNL
QAHQRVHTGEKPYKCNECGKSFRRNSHYQVHLVVHTGEKPYKCEICGKGFSQSSYLQIHQKAHSIEKPFK
CEECGQGFNQSSRLQIHQLIHTGEKPYKCEECGKGFSRRADLKIHCRIHTGEKPYNCEECGKVFRQASNL
LAHQRVHSGEKPFKCEECGKSFGRSAHLQAHQKVHTGDKPYKCDECGKGFKWSLNLDMHQRVHTGEKPYK
CGECGKYFSQASSLQLHQSVHTGEKPYKCDVCGKVFSRSSQLQSHQRVHTGEKPYKCEICGKSFSWRSNL
TVHHRIHVGDKSYKSNRGGKNIRESTQEKKSIK.
AAAAAAAAAAAAAACDECGKEFSQ
GAHLQTHQKVHZZZZZZZZZZZ
[download]

[reply]
[d/l]