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Perl script to split fasta sequence / overlaps
By BioStar 2251 days ago
#!/usr/bin/perl
use strict;
use warnings;
my $len = 5000;
my $over = 200;
my $seq_id=$ARGV[0];
my $seqFile = $ARGV[1];
my $seq;
open(my $fh, "<", "$seqFile") or die "Can't open < $seqFile: $!";
while (<$fh>) {
chomp;
if (m/^>/) { $seq_id = $_; } else { $seq .= $_; }
}
for (my $i = 1; $i <= length $seq; $i += ($len - $over)) {
my $s = substr ($seq, $i - 1, $len);
print "$seq_id.($i-", $i + (length $s) - 1, ")\n$s\n";
}
