I am supposed to be writing a code to rearrange some data in some files I have. The rearranging code has been written for me (by a co-researcher). My problem now is I have to finish the file so that it'll loop through all 50 of my files. I'm in a slow process of learning, but I still am VERY new and have no idea what I am doing most of the time.

Below is the code as it is right now, to be used one file at a time. $InputFile2 will be the files that are changing name (testprefix# - where the number ranges from 162-217 - with 50 total files). Any help would be greatly appreciated.

#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;

my $InputFile1 = "edited_archaea_master_list.txt";
open FILE1, $InputFile1 or die "Can't read source file: $InputFile1\n"
+;

my $InputFile2 = "testprefix172_single_line_nostrains_aligned_gaps_tes
+t.meg";
open FILE2, $InputFile2 or die "Can't read second source file: $InputF
+ile2\n"; 

my $OutputFile3 = "rearrangement_out_test.txt";
open FILE3, ">$OutputFile3" or die "Can't open output file: $OutputFil
+e3\n";

print FILE3 "Input #1: $InputFile1\n";
print FILE3 "Input #2: $InputFile2\n\n";

my @species = <FILE1>; #take file 1 and make into an array
my @align = <FILE2>; #samsies
print "array @align\n";
my $limit = @align; #Number of lines read in the array

my $species; #used in the foreach loop through @species array ...
my $i;
my $j;
my $FoundFlag; #variable used to store names not found and print out a
+t the end
my @notFound; #used to remember species that are not found in order to
+ print at the end ...

#loop through master list ...
foreach $species(@species)
{
    chomp($species); #deletes the enter character at the end the speci
+es, so rather than looking for "species\n", it can just find "species
+"
    #print "$species\n";
    $FoundFlag = 0;

    #Scan second file for a match ...
    for ($i=0; $i<$limit; $i++) #$i is the line number, set to start a
+t zero, $limit is the total number of lines in file, $i++ continues t
+o every consecutive line
    {
        chomp($align[$i]);
        if ($align[$i] =~ /$species/) #if the line in align array matc
+hes the line in the species file, then print, and will print to outpu
+t file
            {
                #print "Found ....\n";
                print $align[$i];
                $j = $i; #$j equals to the species found in the mega f
+ile, do then prints the align of $j plus all the lines that follow, u
+ntil the next # sign.
                do
                {
                    print FILE3 "$align[$j]";
                    $j = $j + 1;
                    
                } while (($j < $limit) && !($align[$j] =~ /^#/)); #ali
+gn of j will continue to print until the $limit, which is the end of 
+the file, AND until the next pound sign.

                $FoundFlag = 1; #if the species is found, then foundfl
+ag equals one, meaning its true.
                last; #quit FOR loop ... and look for the next species
            }
    }
    if ($FoundFlag == 0)
    {
        print "I did not find $species\n";
        #print FILE3 "I did not find $species\n";
        push @notFound, $species;
    }
    #print "Next one ...\n";
}

#Write not found species ...
foreach my $item(@notFound)
{
    print FILE3 "I did not find $item\n";
}

close FILE3;

print "Done!\n";

exit;

[download]

I apologize for all of the comments, it is the only way I know what the code is doing at this point in my learning. Again, I would greatly appreciate any help.

In reply to I'm new and unwise and need help by ishazyi

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