#!/usr/bin/perl
use strict;
use warnings;
my $ifn = shift | die "USAGE: maskFasta.pl UNMASKED_IN.fasta MASKED_OUT.fasta";
my $ofn = shift | die "USAGE: maskFasta.pl UNMASKED_IN.fasta MASKED_OUT.fasta";
my $maxlen = 9;
sub mask {
my ($seq) = @_;
my $seqlen = length($seq);
for (my $i = 0; $i < int($seqlen / $maxlen / 5); $i++) {
my $masklen = int(rand() * ($maxlen + 1));
next unless $masklen;
my $idx = int(rand() * ($seqlen - $masklen - $maxlen * 2)) + $maxlen;
for (my $valid = 0; $valid == 0; $idx = int(rand() * ($seqlen - $masklen - $maxlen * 2)) + $maxlen) {
$valid = 1;
for (my $j = $idx - $maxlen; $j < $idx + $masklen + $maxlen; $j++) {
next if $j < 0;
last if $j >= $seqlen;
if (substr($seq, $j, 1) eq "_") {
$valid = 0;
last;
}
}
}
substr($seq, $idx, $masklen) = "_" x $masklen;
}
return $seq;
}
my ($header, $buffer) = (undef, "");
open(INPUT, $ifn);
open(OUTPUT, ">$ofn");
while (<INPUT>) {
if (/^>/) {
print(OUTPUT $header, mask($buffer), "\n") if $header;
($header, $buffer) = ($_, "");
} else {
chomp($buffer .= $_);
}
}
print(OUTPUT $header, mask($buffer), "\n") if $header;
close(OUTPUT);
close(INPUT);

这个 在命令行 我输入的文件名应该是什么呢

我应该在命令行这样输入吗
perl maskFasta.pl UNMASKED_IN.fasta MASKED_OUT.fasta