I think this is a unique situation. I tried it with hash but I think because the keys of hash are unique I cannot implement if with hash. Then I switched to array of array which I think it will work. Obviously my code does not work but want to show one way that it can be implemented.

here is the problem and examples.

1- Read column one of File1

2- Split the string in that column to its components (gene name-startbase_endbase)

3- We will have genename, startbase, end base.

4- Put it into an array of array

5- Read column one of File2 6- Do the same thing as 2-4

7- Query through array of array of file1 and find common elements in file2 that:

a. First match genename if they matched then check if

b. Start position of the matched genename in file1 falls between start and end position of the same genename in file2

File1:


CLS_S3_Contig2721-139_168
CLS_S3_Contig2722-375_390
CLS_S3_Contig2725-323_362
CLS_S3_Contig2725-455_480
CLS_S3_Contig2728-117_144
CLS_S3_Contig2728-437_472
CLS_S3_Contig2729-119_130
CLS_S3_Contig2729-163_220
CLS_S3_Contig2730-181_202
CLS_S3_Contig2730-361_384
CLS_S3_Contig2731-824_843
CLS_S3_Contig2731-1150_1201
CLS_S3_Contig2735-571_636
CLS_S3_Contig2735-677_710
CLS_S3_Contig2735-775_810
.
.
.
[download]

File2

CLS_S3_Contig2721-142_169
CLS_S3_Contig6525-509_514
CLS_S3_Contig6525-493_502
CLS_S3_Contig6525-503_508
CLS_S3_Contig2977-365_376
CLS_S3_Contig2977-77_82
CLS_S3_Contig2977-83_90
CLS_S3_Contig4978-271_274
CLS_S3_Contig4978-385_388
CLS_S3_Contig2730-365_389
.
.
.
[download]

Output:
Genename(file1) start  end ** Genename(file2)     start    end

CLS_S3_Contig2721 139 168 ** CLS_S3_Contig2721 142   169
CLS_S3_Contig2730 361 384 ** CLS_S3_Contig2730 365   389    
.
.
[download]

while(<INPUT1>){
         chomp;
         my @id = split /\t/;
            if ($id[0] =~ /(.+?)\-(\d+?)_(\d+)/) {
            my @line_map = ("$1",  $2, $3);
            push @file_map, [@line_map];
     }
}

close(INPUT1);


while(<INPUT2>){
         chomp;
         my @map_id = split /\t/;
            if ($tg_id[0] =~ /(.+?)\-(\d+?)_(\d+)/) {
            my @tg_id = ("$1",  $2, $3);
            push @file_tg, [@tg_id];
    }
}  

     
   
          if (($from_tg == $from_map) && ($to_tg == $to_map)){

                print  join("\t",$two_geno_id, $from_map,$to_map,"<-Ma
+pside**TGside->",$two_geno_id, $from_tg, $to_tg, $from_map_tg_range, 
+$to_map_tg_range),"\n";
            $lines_1++;
            }
            elsif (($from_tg < $to_map) && ($from_tg > $from_map)){

                print  join("\t",$two_geno_id, $from_map,$to_map,"<-Ma
+pside**TGside->",$two_geno_id, $from_tg, $to_tg, $from_map_tg_range, 
+$to_map_tg_range),"\n";
             $lines_9++;

    }
[download]