## removesmalls.pl
#!/usr/bin/perl
use strict;
use warnings;

my $minlen = shift or die "Error: `minlen` 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);
    }
    local $/="\n";
}

Exexecuting the script as follows:

perl removesmalls.pl 1000 contigs.fasta > contigs-1000.fasta

The above script works for me but there is a problem, i have 109 different fasta files with different file names. i can run the script for individual file but i want to run the script at once for all files and the result file should be individually different for each.

file names are like SRR8224532.fasta, SRR8224533.fasta, SRR8224534.fasta, and so on i want the result files after removing the contigs (i.e., for me less than 1000) something like SRR8224532-out.fasta, SRR8224533-out.fasta, and so on.

Any help or suggestion would be helpfull.