Takes hamming distance output from Mascher et al., 2013a, and a genetic map. Places each imputed marker in the most likely position in the map.

add.imputedmks.2.map.pl

#!/usr/bin/perl
# BY:           Juan Gutierrez-Gonzalez
# USED FOR:     Takes hamming distance output from Mascher et al., 2013a, and a genetic map. Places each imputed marker in the most likely position in the map.
# USAGE          perl add.imputedmks.2.map.pl -m linkage.map.file -i hamming.file 
#   format of the linkage map file               format of the hamming file (That is, output from Mascher et al., 2013a, with the genotype calls removed)
#   1A	0   chr1A_1145442                       chr1A_1158042	16	0	0	2	chr1A_1145442,chr1A_1238074
#   1A	6.734047969 chr1A_3793383               chr1A_1159442	16	0	0	2	chr1A_1145442,chr1A_1238074
#   1A	7.872710958 chr1A_4804732               chr1A_1159478	16	0	0	2	chr1A_1145442,chr1A_1238074
#   1A	8.904535851 chr1A_4812400	            chr1A_3838416	16	0	0	1	chr1A_3793383
#   1A	8.904535851 chr1A_6027915	            chr1A_9567537	38	0	3	5	chr1A_10132856,chr1A_12502888,chr1A_12822017,chr1A_12822041,chr1A_12822066
#
#  ---------------------------------------------------------------
#  *** TERMS ***
#  ...............................................................
#
#    User acknowledges that the program is a research tool still
#    under the development and that it is being supplied "as is".
#    User is responsible for throughly testing program and ensure
#    results are functionally corrected.
#
#    Developer(s) shall not be held liable for any liability nor for
#    any direct, indirect or consequential damages with respect
#    to any claim by RECIPIENT or any third party on account of
#    or arising from in use of the programs
#
#  .......................................................................

use File::Basename;
use Getopt::Long;
my $PROGRAM = basename($0);
use strict;
use warnings;
sub usage { print "\nUsage: $PROGRAM -m linkage map -i hammingfile [-o output]\n"; }

if ($#ARGV < 2) { warn "number of commandline args: $#ARGV\n"; &usage; exit 1; }
my @Options =
(
    "m=s"   => \(my $mapfile),       
    "i=s"   => \(my $hammingfile),      
    "o=s"   => \(my $output),
);
if (!&GetOptions(@Options) ){ &usage; exit 1;                                       }
if (!$mapfile      ){ warn "\nMust specify a file containing a linkage map\n"; &usage; exit 1;   }
if (!$hammingfile      ){ warn "\nMust specify a file containing hamming distantces as Mascher et al,2013 \n"; &usage; exit 1;   }
if (!$output    ){ $output   = &defaultName( $mapfile ); $output .= ".withimputedmks";             }
print "\n==========================================================================\n";
print " *** $PROGRAM running ***";
print "\n==========================================================================\n\n";
my @chrorder = qw(1A 2A 3A 4A 5A 6A 7A 1B 2B 3B 4B 5B 6B 7B 1D 2D 3D 4D 5D 6D 7D);

open (OUT, "> $output"  ) or print "\nFail open $output \n" and die;
open (MAPFILE, "< $mapfile"   ) or print "\nFail open $mapfile \n" and die;
open (HAMMINGFILE, "< $hammingfile"   ) or print "\nFail open $hammingfile \n" and die;
my %hashLG;
while (<MAPFILE>){
    chomp; my @mapfileline = split( /\t/, $_);
    my $chr = $mapfileline[0]; $chr =~ s/\s+//g;
    my $pos = $mapfileline[1]; $pos =~ s/\s+//g;
    my $mk  = $mapfileline[2]; $mk =~ s/\s+//g;
    if (!exists $hashLG{$chr}{$pos}){
       @{$hashLG{$chr}{$pos}} = ();
       push @{$hashLG{$chr}{$pos}}, $mk;
    }else{
       push @{$hashLG{$chr}{$pos}}, $mk;
    }
} 
close (MAPFILE);
my %hashsimilarmks;
while (<HAMMINGFILE>){
    chomp; my @hammingfileline = split( /\t/, $_);
    my $mkid = $hammingfileline[0];
    my @similarmks = split (/\,/, $hammingfileline[5]);    
    foreach my $i (@similarmks){
       push @{$hashsimilarmks{$mkid}}, $i;
    }
    foreach my $n (@chrorder) {
       foreach my $key1 (sort hashValueAscending (keys %{$hashLG{$n}}) ){
         if(isSubset(\@{$hashsimilarmks{$mkid}},\@{$hashLG{$n}{$key1}})){
            push @{$hashLG{$n}{$key1}}, $mkid;
         }
       }
    }
}          
close (HAMMINGFILE);

foreach my $nn (@chrorder) {
   foreach my $k1 (sort {$a <=> $b} (keys %{$hashLG{$nn}}) ){
      foreach my $k2 (@{$hashLG{$nn}{$k1}}) {
         print OUT "$nn\t$k1\t$k2\n";
     }
   }
}close (OUT);
print " *** $PROGRAM ended ***\n";

sub hashValueAscending {$a cmp $b};
sub defaultName {
    my ($sub_input) = @_;
    my @sub_inline = split ( /\//, $sub_input );
    my $sub_filename = $sub_inline[scalar(@sub_inline)-1];
    return $sub_filename;
}
sub isSubset {
    my ($littleSet, $bigSet) = @_;
    my %hash;
    undef @hash{@$littleSet}; 
    delete @hash{@$bigSet};    
    return !%hash;            
}

Reference

Dense genotyping-by-sequencing linkage maps of two Synthetic W7984×Opata reference populations provide insights into wheat structural diversity

https://www.nature.com/articles/s41598-018-38111-3#MOESM15