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Perl script to extract a sequence from multifasta with range !
By BioStar 2269 days ago
# filterfastarange.pl
#!/usr/bin/perl
use strict;
use warnings;
#perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta
my $minlen = shift or die "Error: `minlen` parameter not provided\n";
my $maxlen = shift or die "Error: `maxlen` parameter not provided\n";
{
local $/=">";
while(<>) {
chomp;
next unless /\w/;
s/>$//gs;
my @chunk = split /\n/;
my $header = shift @chunk;
my $seqlen = length join "", @chunk;
print ">$_" if($seqlen >= $minlen and $seqlen <= maxlen);
}
local $/="\n";
}
