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Re: finding sequence

by tybalt89 (Monsignor)
on Jun 22, 2018 at 23:09 UTC ( [id://1217264]=note: print w/replies, xml ) Need Help??


in reply to finding sequence

#!/usr/bin/perl # https://perlmonks.org/?node_id=1217240 use strict; use warnings; open my $patterns, '<', \<<END; ATCCCACCGCTGCCACCA ACCCTGCTCGCTGCGCCA TCCCCGGCACCTCCACCA TCCCCGGCATCTCCACCA ATCCTGCCGACTACGCCA TCGATTCCCGGCCCATGCACCA TCGATTCCCGGCCAACGCACCA GTCCCACCAGAGTCGCCA ACCCCACTCCTGGTACCA GTCCCTTCGTGGTCGCCA END open my $fh, '<', \<<END; AACCCCATCCCACCGCTGCCACCA 1 AACCCCATCCTCGTCGCC 1 AACCCCATGAAATAAGAG 2 AACCCCATGATCAGGACAAG 1 AACCCCATTAAAAAATGG 1 AACTGGATTCTCTGAAATCCCACCGCTGCCACCA 1 AACTGGATTGTCTGTTTGT 1 AACTGGCAAGTTCAGGCATG 1 AACTGGCACACACAACC 1 AACTGGCACACACAACCT 1 END my $seqs = join '|', map tr/ACGT//cdr, <$patterns>; my $match = qr/^\w*($seqs)/; /$match/ and print "$1\t$_" while <$fh>;

Outputs:

ATCCCACCGCTGCCACCA AACCCCATCCCACCGCTGCCACCA 1 ATCCCACCGCTGCCACCA AACTGGATTCTCTGAAATCCCACCGCTGCCACCA 1

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