drlecb has asked for the wisdom of the Perl Monks concerning the following question:

Dear Monks, I really need some help please! I'm trying to merge 3 genetic data (.var) files containing 2 parent and offpring samples in a way that I can obtain whether they are heterozygous/homozygous for a particular allele. Dummy data for the three samples are supplied below.

I'm nearly there, but I believe my issue is when I am returning values in my hash %zygos which I want to give me either a "HET" or "HOM". When I put in the key "$variant" I return an array coordinate, not the HET/HOM value I'm looking for. However when I use Data Dumper I get out the value I want. I think if I can fix this, the script will work.... but I'm just not that clever. I've tried all day to get my script to work and now I'm in need of some kind help please... I am not an efficient coder, as you will see.

Please be gentle. Best wishes LECB

#!/usr/bin/perl;
use strict; use v5.8.8;
use Data::Dumper;

##List all .var files in directory

my $path = '.'; #Reads same directory as running .pl file
opendir(DIR, $path);
my @files = grep { /\.var$/ } readdir(DIR); #Reads names of .var files
+ into @files
@files = sort @files;
my @samples;
foreach (@files) {
    if ($_ =~ /\_/) {
        $_ =~ /(^.+?)\_/;
        push @samples, $1; 
    } else {
        $_ =~ /(^.+)\.var/;
        push @samples, $1;
    }
}
closedir(DIR);
@files = sort @files; 
my $file_count = @files;
print "\nRunning on $file_count files:\n";
print "@files ";

#Make unique list of variants observed in all opened .var files

my @variants; ##Create concatenated list of all variant locations and 
+alleles
my @zygosity;
my $zyg;
my %zygos;
foreach my $file (@files) {
    open VAR, $file;
    chomp (my @var = <VAR>);
    ##sub in $file for ID (3rd column)
    while ($var[0] =~ s/ID/$file/) {
        shift @var;
    }
    foreach (@var) {
        my @fields = split /\t/, $_;
        $fields[2] = $file;
        my $locus = join "\t", @fields[0,1,2,3,4,5];
        push @variants, $locus;
        #pull out genotype
        $fields[9] =~ /(^\d\/\d\:)/;
            if ($1 =~ /0\/1\:/) {
            $zyg = "HET"; } else { $zyg = "HOM"; }        
            $fields[9] = $zyg;
            # push @zygosity, $zyg;
            push @{$zygos{$locus}}, $zyg;
            }
    }
    close VAR;


my %variants_hash = map { $_, 1 } @variants; ##Generates the unique li
+st
my @variants_list = keys %variants_hash;
%variants_hash = undef;
@variants_list = sort @variants_list; #List of just loci
my %variants_geno; #List of loci to which genotypes will be appended
my %variants_info; # List of variant information to append after genot
+ypes for printing.

my $sum_variants = @variants_list;
print "\nRunning on $sum_variants non-redundant variants.\n";

# Pull out genotypes for all of the non-redundant variants for each in
+dividual

my @variant_geno; #Pointless array for anonymous assignation of arrays
+ in hash

foreach my $file (@files) {
    open VAR, $file;
    my @var = <VAR>;    
    foreach my $variant (@variants_list) {
        my $found = 0;
        my $genotype = 'REF?';
        foreach my $line (@var) {    
            my @fields2 = split /\t/, $line;
                $fields2[2] = $file;
                $fields2[9] = $zygos{$variant};
                my $newline = join "\t", @fields2[0..123];
                $line = $newline;                
                    if ($line =~ /$variant/) {
                        if ($found == 0) {
                    $variants_info{$variant} = (join "\t", @fields2[10
+..123]);
                    $found ++;
                }
                        if ($fields2[9] eq 'HET') {
                    $genotype = 'HET';
                }
                        if ($fields2[9] eq 'HOM') {
                    $genotype = 'HOM';
                }
                last;    
                }}
            
        if ($variants_geno{$variant} =~ /./) {
            push @{$variants_geno{$variant}}, $genotype;
        } else {
            @{$variants_geno{$variant}} = [@variant_geno];
            push @{$variants_geno{$variant}}, $genotype;
        
    }}
    close VAR;
}

open OUT, ">$ARGV[0]" . 'merged.vars';

my $samples_list = join "\t", @samples;
print OUT "CHROM    POS    ID    REF    ALT    QUAL    $samples_list  
+  Chr    Start    End    Ref    Alt    Func.refGene    Gene.refGene  
+  GeneDetail.refGene    ExonicFunc.refGene    AAChange.refGene    Fun
+c.knownGene    Gene.knownGene    GeneDetail.knownGene    ExonicFunc.k
+nownGene    AAChange.knownGene    avsnp144    1000g2015aug_all    100
+0g2015aug_afr    1000g2015aug_amr    1000g2015aug_sas    1000g2015aug
+_eur    1000g2015aug_eas    esp6500siv2_all    esp6500siv2_ea    esp6
+500siv2_aa    ExAC_ALL    ExAC_AFR    ExAC_AMR    ExAC_EAS    ExAC_FI
+N    ExAC_NFE    ExAC_OTH    ExAC_SAS    cosmic70    SIFT_score    SI
+FT_pred    Polyphen2_HDIV_score    Polyphen2_HDIV_pred    Polyphen2_H
+VAR_score    Polyphen2_HVAR_pred    LRT_score    LRT_pred    Mutation
+Taster_score    MutationTaster_pred    MutationAssessor_score    Muta
+tionAssessor_pred    FATHMM_score    FATHMM_pred    PROVEAN_score    
+PROVEAN_pred    VEST3_score    CADD_raw    CADD_phred    DANN_score  
+  fathmm-MKL_coding_score    fathmm-MKL_coding_pred    MetaSVM_score 
+   MetaSVM_pred    MetaLR_score    MetaLR_pred    integrated_fitCons_
+score    integrated_confidence_value    GERP++_RS    phyloP7way_verte
+brate    phyloP20way_mammalian    phastCons7way_vertebrate    phastCo
+ns20way_mammalian    SiPhy_29way_logOdds    Interpro_domain    dbscSN
+V_ADA_SCORE    dbscSNV_RF_SCORE    CLINSIG    CLNDBN    CLNACC    CLN
+DSDB    CLNDSDBID    HRC_AF    HRC_AC    HRC_AN    HRC_non1000G_AF   
+ HRC_non1000G_AC    HRC_non1000G_AN    Kaviar_AF    Kaviar_AC    Kavi
+ar_AN    nci60    KEY3    INFO_AC    INFO_AF    INFO_BaseQRankSum    
+INFO_ClippingRankSum    INFO_DP    INFO_DS    INFO_END    INFO_Excess
+Het    INFO_FS    INFO_HaplotypeScore    INFO_InbreedingCoeff    INFO
+_MLEAC    INFO_MLEAF    INFO_MQ    INFO_MQRankSum    INFO_QD    INFO_
+RAW_MQ    INFO_ReadPosRankSum    INFO_SOR    seq    seq_flag    AAcha
+nge    Grantham    Mutability    FuentesFalsePositive    ACMG";


foreach my $variant_ident (@variants_list) {
    shift @{$variants_geno{$variant_ident}};
    my $genotypes = join "\t", @{$variants_geno{$variant_ident}};
    my $joined = join "\t", $variant_ident, $genotypes, $variants_info
+{$variant_ident};
    $joined =~ s/^\s+//;
    chop $joined;
    print OUT "$joined";
}

close OUT;

[download]
--Dummydata1.var--
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT 
+   IFS003-W    Chr    Start    End    Ref    Alt    Func.refGene    G
+ene.refGene    GeneDetail.refGene    ExonicFunc.refGene    AAChange.r
+efGene    Func.knownGene    Gene.knownGene    GeneDetail.knownGene   
+ ExonicFunc.knownGene    AAChange.knownGene    avsnp144    1000g2015a
+ug_all    1000g2015aug_afr    1000g2015aug_amr    1000g2015aug_sas   
+ 1000g2015aug_eur    1000g2015aug_eas    esp6500siv2_all    esp6500si
+v2_ea    esp6500siv2_aa    ExAC_ALL    ExAC_AFR    ExAC_AMR    ExAC_E
+AS    ExAC_FIN    ExAC_NFE    ExAC_OTH    ExAC_SAS    cosmic70    SIF
+T_score    SIFT_pred    Polyphen2_HDIV_score    Polyphen2_HDIV_pred  
+  Polyphen2_HVAR_score    Polyphen2_HVAR_pred    LRT_score    LRT_pre
+d    MutationTaster_score    MutationTaster_pred    MutationAssessor_
+score    MutationAssessor_pred    FATHMM_score    FATHMM_pred    PROV
+EAN_score    PROVEAN_pred    VEST3_score    CADD_raw    CADD_phred   
+ DANN_score    fathmm-MKL_coding_score    fathmm-MKL_coding_pred    M
+etaSVM_score    MetaSVM_pred    MetaLR_score    MetaLR_pred    integr
+ated_fitCons_score    integrated_confidence_value    GERP++_RS    phy
+loP7way_vertebrate    phyloP20way_mammalian    phastCons7way_vertebra
+te    phastCons20way_mammalian    SiPhy_29way_logOdds    Interpro_dom
+ain    dbscSNV_ADA_SCORE    dbscSNV_RF_SCORE    CLINSIG    CLNDBN    
+CLNACC    CLNDSDB    CLNDSDBID    HRC_AF    HRC_AC    HRC_AN    HRC_n
+on1000G_AF    HRC_non1000G_AC    HRC_non1000G_AN    Kaviar_AF    Kavi
+ar_AC    Kaviar_AN    nci60    KEY3    INFO_AC    INFO_AF    INFO_Bas
+eQRankSum    INFO_ClippingRankSum    INFO_DP    INFO_DS    INFO_END  
+  INFO_ExcessHet    INFO_FS    INFO_HaplotypeScore    INFO_Inbreeding
+Coeff    INFO_MLEAC    INFO_MLEAF    INFO_MQ    INFO_MQRankSum    INF
+O_QD    INFO_RAW_MQ    INFO_ReadPosRankSum    INFO_SOR    seq    seq_
+flag    AAchange    Grantham    Mutability    FuentesFalsePositive   
+ ACMG
chr1    14653    .    C    T    191.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=1.23;ClippingRankSum=0.00;DP=26;ExcessHet=3.0103;FS=6.641;ML
+EAC=1;MLEAF=0.500;MQ=32.19;MQRankSum=0.580;QD=7.38;ReadPosRankSum=-1.
+830e-01;SOR=2.280    GT:AD:DP:GQ:PL    0/1:15,11:26:99:220,0,292    c
+hr1    14653    14653    C    T    ncRNA_exonic    WASH7P            
+    intergenic    NONE,MIR6859-3    dist=NONE;dist=2716            rs
+62635297                                                             
+                                                                     
+                                                                     
+                                                                     
+0.0011526    30    26028        chr1:14653:14653:C:T    1    0.5    1
+.23    0    26    no_DS    no_END    3.0103    6.641    no_HaplotypeS
+core    no_InbreedingCoeff    1    0.5    32.19    0.58    7.38    no
+_RAW_MQ    -1.83E-01    2.28    AAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTC
+CATGTCAGAGCAA[C]GGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATT   
+ pass    XX    .    0    1    0
chr1    16949    .    A    C    240.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=1.57;ClippingRankSum=0.00;DP=39;ExcessHet=3.0103;FS=1.264;ML
+EAC=1;MLEAF=0.500;MQ=21.03;MQRankSum=-7.380e-01;QD=6.17;ReadPosRankSu
+m=1.62;SOR=0.693    GT:AD:DP:GQ:PL    0/1:24,15:39:99:269,0,502    ch
+r1    16949    16949    A    C    ncRNA_exonic    WASH7P             
+   downstream    MIR6859-3                rs199745162    0.0139776   
+ 0.0227    0.0144    0.0143    0.0159                                
+                                                                     
+                                                                     
+                                                                     
+         0.0159444    415    26028        chr1:16949:16949:A:C    1  
+  0.5    1.57    0    39    no_DS    no_END    3.0103    1.264    no_
+HaplotypeScore    no_InbreedingCoeff    1    0.5    21.03    -7.38E-0
+1    6.17    no_RAW_MQ    1.62    0.693    CTGGAATGGTGCCAGGGGCAGAGGGG
+GCAATGCCGGGGCCCAGGTCGGCA[A]TGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGT
+AGGATGGA    pass    XX    .    0    1    0
chr1    17020    .    G    A    58.77    .    AC=1;AF=0.500;AN=2;BaseQ
+RankSum=-4.670e-01;ClippingRankSum=0.00;DP=43;ExcessHet=3.0103;FS=23.
+602;MLEAC=1;MLEAF=0.500;MQ=21.00;MQRankSum=0.00;QD=1.37;ReadPosRankSu
+m=-1.126e+00;SOR=1.132    GT:AD:DP:GQ:PL    0/1:34,9:43:87:87,0,789  
+  chr1    17020    17020    G    A    ncRNA_exonic    WASH7P         
+       downstream    MIR6859-3                rs199740902            
+                                                                     
+                                                                     
+                                                                     
+                                                 0.0141002    367    
+26028        chr1:17020:17020:G:A    1    0.5    -4.67E-01    0    43
+    no_DS    no_END    3.0103    23.602    no_HaplotypeScore    no_In
+breedingCoeff    1    0.5    21    0    1.37    no_RAW_MQ    -1.13E+0
+0    1.132    ATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG[G]CC
+CAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCA    pass    XX    .  
+  0    1    0
chr1    17385    .    G    A    81.77    .    AC=1;AF=0.500;AN=2;BaseQ
+RankSum=0.653;ClippingRankSum=0.00;DP=71;ExcessHet=3.0103;FS=3.091;ML
+EAC=1;MLEAF=0.500;MQ=48.65;MQRankSum=0.417;QD=1.15;ReadPosRankSum=1.0
+2;SOR=0.311    GT:AD:DP:GQ:PL    0/1:60,11:71:99:110,0,1715    chr1  
+  17385    17385    G    A    ncRNA_exonic;splicing    MIR6859-1,MIR6
+859-2,MIR6859-3,MIR6859-4;WASH7P    NR_024540:exon6:c.588-17C>T      
+      ncRNA_exonic    MIR6859-3                rs201535981           
+                             0.2454    0.2331    0.2857    0.0423    
+0.2817    0.2743    0.2321    0.2092                                 
+                                                                     
+                                                                     
+                             0.0015912    246    154602        chr1:1
+7385:17385:G:A    1    0.5    0.653    0    71    no_DS    no_END    
+3.0103    3.091    no_HaplotypeScore    no_InbreedingCoeff    1    0.
+5    48.65    0.417    1.15    no_RAW_MQ    1.02    0.311    AGCCAGGG
+GGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCGACATG[G]GGGTCAGGCAAGCTGACACCCGCT
+GTCCTGAGCCCATGTTCCTCTCCCAC    pass    XX    .    0    0    0
chr1    17408    .    C    G    134.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=-9.480e-01;ClippingRankSum=0.00;DP=94;ExcessHet=3.0103;FS=0.
+000;MLEAC=1;MLEAF=0.500;MQ=52.27;MQRankSum=-8.570e-01;QD=1.45;ReadPos
+RankSum=0.359;SOR=0.527    GT:AD:DP:GQ:PL    0/1:79,14:93:99:163,0,23
+39    chr1    17408    17408    C    G    ncRNA_exonic    MIR6859-1,M
+IR6859-2,MIR6859-3,MIR6859-4                ncRNA_exonic    MIR6859-3
+                rs747093451                                        0.
+0352    0.0339    0.049    0    0.0273    0.0438    0    0.0074      
+                                                                     
+                                                                     
+                                                        0.0013842    
+214    154602        chr1:17408:17408:C:G    1    0.5    -9.48E-01   
+ 0    94    no_DS    no_END    3.0103    0    no_HaplotypeScore    no
+_InbreedingCoeff    1    0.5    52.27    -8.57E-01    1.45    no_RAW_
+MQ    0.359    0.527    ACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGAC
+ACCCG[C]TGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCAC    pass   
+ XX    .    0    0    0
chr1    17697    .    G    C    125.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=-2.529e+00;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=0.
+000;MLEAC=1;MLEAF=0.500;MQ=39.25;MQRankSum=-8.310e-01;QD=4.49;ReadPos
+RankSum=1.07;SOR=0.124    GT:AD:DP:GQ:PL    0/1:21,7:28:99:154,0,714 
+   chr1    17697    17697    G    C    ncRNA_exonic    WASH7P        
+        upstream    MIR6859-3                rs374995955             
+                                                                     
+                                                                     
+                                                                     
+                                                0.0155602    405    2
+6028        chr1:17697:17697:G:C    1    0.5    -2.53E+00    0    28 
+   no_DS    no_END    3.0103    0    no_HaplotypeScore    no_Inbreedi
+ngCoeff    1    0.5    39.25    -8.31E-01    4.49    no_RAW_MQ    1.0
+7    0.124    GCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGG[G]CT
+CCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAG    pass    XX    .  
+  0    1    0

[download]
--Dummydata2.var--
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT 
+   IFS001_W1515808    Chr    Start    End    Ref    Alt    Func.refGe
+ne    Gene.refGene    GeneDetail.refGene    ExonicFunc.refGene    AAC
+hange.refGene    Func.knownGene    Gene.knownGene    GeneDetail.known
+Gene    ExonicFunc.knownGene    AAChange.knownGene    avsnp144    100
+0g2015aug_all    1000g2015aug_afr    1000g2015aug_amr    1000g2015aug
+_sas    1000g2015aug_eur    1000g2015aug_eas    esp6500siv2_all    es
+p6500siv2_ea    esp6500siv2_aa    ExAC_ALL    ExAC_AFR    ExAC_AMR   
+ ExAC_EAS    ExAC_FIN    ExAC_NFE    ExAC_OTH    ExAC_SAS    cosmic70
+    SIFT_score    SIFT_pred    Polyphen2_HDIV_score    Polyphen2_HDIV
+_pred    Polyphen2_HVAR_score    Polyphen2_HVAR_pred    LRT_score    
+LRT_pred    MutationTaster_score    MutationTaster_pred    MutationAs
+sessor_score    MutationAssessor_pred    FATHMM_score    FATHMM_pred 
+   PROVEAN_score    PROVEAN_pred    VEST3_score    CADD_raw    CADD_p
+hred    DANN_score    fathmm-MKL_coding_score    fathmm-MKL_coding_pr
+ed    MetaSVM_score    MetaSVM_pred    MetaLR_score    MetaLR_pred   
+ integrated_fitCons_score    integrated_confidence_value    GERP++_RS
+    phyloP7way_vertebrate    phyloP20way_mammalian    phastCons7way_v
+ertebrate    phastCons20way_mammalian    SiPhy_29way_logOdds    Inter
+pro_domain    dbscSNV_ADA_SCORE    dbscSNV_RF_SCORE    CLINSIG    CLN
+DBN    CLNACC    CLNDSDB    CLNDSDBID    HRC_AF    HRC_AC    HRC_AN  
+  HRC_non1000G_AF    HRC_non1000G_AC    HRC_non1000G_AN    Kaviar_AF 
+   Kaviar_AC    Kaviar_AN    nci60    KEY3    INFO_AC    INFO_AF    I
+NFO_BaseQRankSum    INFO_ClippingRankSum    INFO_DP    INFO_DS    INF
+O_END    INFO_ExcessHet    INFO_FS    INFO_HaplotypeScore    INFO_Inb
+reedingCoeff    INFO_MLEAC    INFO_MLEAF    INFO_MQ    INFO_MQRankSum
+    INFO_QD    INFO_RAW_MQ    INFO_ReadPosRankSum    INFO_SOR    seq 
+   seq_flag    AAchange    Grantham    Mutability    FuentesFalsePosi
+tive    ACMG
chr1    14464    .    A    T    39.77    .    AC=1;AF=0.500;AN=2;BaseQ
+RankSum=1.38;ClippingRankSum=0.00;DP=4;ExcessHet=3.0103;FS=0.000;MLEA
+C=1;MLEAF=0.500;MQ=40.51;MQRankSum=-6.740e-01;QD=9.94;ReadPosRankSum=
+0.674;SOR=2.303    GT:AD:DP:GQ:PL    0/1:2,2:4:64:68,0,64    chr1    
+14464    14464    A    T    ncRNA_exonic    WASH7P                int
+ergenic    NONE,MIR6859-3    dist=NONE;dist=2905            rs5461694
+44    0.0958466    0.0144    0.1138    0.1943    0.1859    0.005     
+                                                                     
+                                                                     
+                                                                     
+                                0.0346166    901    26028        chr1
+:14464:14464:A:T    1    0.5    1.38    0    4    no_DS    no_END    
+3.0103    0    no_HaplotypeScore    no_InbreedingCoeff    1    0.5   
+ 40.51    -6.74E-01    9.94    no_RAW_MQ    0.674    2.303    GTTCTTT
+ATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACAC[A]GTGGCGCAGGCTGGGTGGAGCCG
+TCCCCCCATGGAGCACAGGCAGACAGA    pass    XX    .    0    1    0
chr1    17407    .    G    A    140.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=2.44;ClippingRankSum=0.00;DP=60;ExcessHet=3.0103;FS=0.000;ML
+EAC=1;MLEAF=0.500;MQ=49.25;MQRankSum=1.74;QD=2.39;ReadPosRankSum=-1.5
+00e-02;SOR=0.608    GT:AD:DP:GQ:PL    0/1:49,10:59:99:169,0,1261    c
+hr1    17407    17407    G    A    ncRNA_exonic    MIR6859-1,MIR6859-
+2,MIR6859-3,MIR6859-4                ncRNA_exonic    MIR6859-3       
+         rs372841554                                        0.0765   
+ 0.0303    0.054    0.0672    0.0273    0.0894    0.0714    0.1352   
+                                                                     
+                                                                     
+                                                           0.0030013 
+   464    154602        chr1:17407:17407:G:A    1    0.5    2.44    0
+    60    no_DS    no_END    3.0103    0    no_HaplotypeScore    no_I
+nbreedingCoeff    1    0.5    49.25    1.74    2.39    no_RAW_MQ    -
+1.50E-02    0.608    TACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACAC
+CC[G]CTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCA    pass    XX
+    .    0    0    0
chr1    17758    .    T    A    75.77    .    AC=1;AF=0.500;AN=2;BaseQ
+RankSum=0.674;ClippingRankSum=0.00;DP=5;ExcessHet=3.0103;FS=0.000;MLE
+AC=1;MLEAF=0.500;MQ=38.87;MQRankSum=-5.240e-01;QD=15.15;ReadPosRankSu
+m=-5.240e-01;SOR=1.022    GT:AD:DP:GQ:PL    0/1:2,3:5:63:104,0,63    
+chr1    17758    17758    T    A    ncRNA_splicing    WASH7P    NR_02
+4540:exon5:c.451-16A>T            upstream    MIR6859-3              
+                                                                     
+                                                                     
+                                                                     
+                                                                     
+          chr1:17758:17758:T:A    1    0.5    0.674    0    5    no_D
+S    no_END    3.0103    0    no_HaplotypeScore    no_InbreedingCoeff
+    1    0.5    38.87    -5.24E-01    15.15    no_RAW_MQ    -5.24E-01
+    1.022    GTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAGAGGGCCAGGA[T]GGC
+CAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGCTGCCATCCC    pass    XX    .   
+ 0    1    0
chr1    69511    .    A    G    2186.77    .    AC=2;AF=1.00;AN=2;DP=7
+8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.68;QD=28.04;SOR=
+0.744    GT:AD:DP:GQ:PL    1/1:0,78:78:99:2215,234,0    chr1    69511
+    69511    A    G    exonic    OR4F5        nonsynonymous SNV    OR
+4F5:NM_001005484:exon1:c.A421G:p.T141A    exonic    OR4F5        nons
+ynonymous SNV    OR4F5:uc001aal.1:exon1:c.A421G:p.T141A    rs2691305 
+                           0.7598    0.8874    0.5441    0.9394    0.
+5942    0.9507    0.9994    0.9907    0.9716    0.9597    0.9832     
+   0.652    T    0    B    0    B    0    N    1    P    -1.295    N 
+   1.26    T    1.54    N    0.012    -0.784    0.047    0.454    0.0
+03    N    -0.997    T    0    T    0.487    0    1.15    -0.016    -
+0.132    0.055    0.765    4.198    GPCR, rhodopsin-like, 7TM        
+                                                0.54161    83734    1
+54602    0.51    chr1:69511:69511:A:G    2    1    no_BaseQRankSum   
+ no_ClippingRankSum    78    no_DS    no_END    3.0103    0    no_Hap
+lotypeScore    no_InbreedingCoeff    2    1    43.68    no_MQRankSum 
+   28.04    no_RAW_MQ    no_ReadPosRankSum    0.744    ACTACACTACAATT
+ATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTC[A]CATGGGGAATTGGCTTTCTCCATTCGGTGA
+GCCAGTTGGCGTTTGCCGTG    pass    TA    .    0    1    0
chr1    138041    .    G    A    119.77    .    AC=1;AF=0.500;AN=2;Bas
+eQRankSum=1.97;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=8.903;M
+LEAC=1;MLEAF=0.500;MQ=30.73;MQRankSum=-1.007e+00;QD=6.30;ReadPosRankS
+um=1.18;SOR=0.493    GT:AD:DP:GQ:PL    0/1:12,7:19:99:148,0,289    ch
+r1    138041    138041    G    A    ncRNA_exonic    LOC729737        
+        intergenic    RP11-34P13.7,RP11-34P13.14    dist=4318;dist=17
+49            rs560358882    0.00239617        0.0029    0.0051    0.
+005                                                                  
+                                                                     
+                                                                     
+                                            0.0015368    40    26028 
+       chr1:138041:138041:G:A    1    0.5    1.97    0    19    no_DS
+    no_END    3.0103    8.903    no_HaplotypeScore    no_InbreedingCo
+eff    1    0.5    30.73    -1.01E+00    6.3    no_RAW_MQ    1.18    
+0.493    GAAGGGAAAAACTGGGCCTGGAAAGGCCGTTGTCAGGAATGAGCCCCATG[G]GCCTGAA
+GAGGCCACTGGCAGGCGGGAGCTGGGCCTGCCGAAGCGGCCGA    pass    XX    .    0  
+  0    0
chr1    138156    .    G    T    120.84    .    AC=2;AF=1.00;AN=2;DP=6
+;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.17;QD=20.14;SOR=0
+.693    GT:AD:DP:GQ:PL    1/1:0,6:6:18:149,18,0    chr1    138156    
+138156    G    T    ncRNA_exonic    LOC729737                intergen
+ic    RP11-34P13.7,RP11-34P13.14    dist=4433;dist=1634            rs
+370691115                                                            
+                                                                     
+                                                                     
+                                                                     
+ 0.0967804    2519    26028        chr1:138156:138156:G:T    2    1  
+  no_BaseQRankSum    no_ClippingRankSum    6    no_DS    no_END    3.
+0103    0    no_HaplotypeScore    no_InbreedingCoeff    2    1    20.
+17    no_MQRankSum    20.14    no_RAW_MQ    no_ReadPosRankSum    0.69
+3    GGACTCGGGAGGCCGCAGTGAAGCAACAGCTAGCTGGGCGTGGAGAGTCC[G]CTGTGAGGCAG
+AGGCTGGGCCTGTGCAGGCCTTCGGGAGGCAGGAGGCTG    pass    XX    .    0    0 
+   0
chr1    139213    .    A    G    1774.77    .    AC=1;AF=0.500;AN=2;Ba
+seQRankSum=-4.140e+00;ClippingRankSum=0.00;DP=97;ExcessHet=3.0103;FS=
+3.809;MLEAC=1;MLEAF=0.500;MQ=39.41;MQRankSum=-1.653e+00;QD=18.30;Read
+PosRankSum=-7.760e-01;SOR=1.060    GT:AD:DP:GQ:PGT:PID:PL    0/1:51,4
+6:97:99:0|1:139213_A_G:1803,0,3192    chr1    139213    139213    A  
+  G    ncRNA_exonic    LOC729737                downstream    RP11-34
+P13.14                rs370723703                                    
+    0.2506    0.3787    0.2879    0.3404    0.25    0.2597    0.3083 
+   0.2352                                                            
+                                                                     
+                                                                     
+  0.0259699    4015    154602        chr1:139213:139213:A:G    1    0
+.5    -4.14E+00    0    97    no_DS    no_END    3.0103    3.809    n
+o_HaplotypeScore    no_InbreedingCoeff    1    0.5    39.41    -1.65E
++00    18.3    no_RAW_MQ    -7.76E-01    1.06    GGAAGGTTGCCATGAGACAA
+AAGTTGGGCCTGGAAAGGCCCTTGTGAAGC[A]TGAGCTTGGCCTAAAGAGGCCACTGGGTGGCAGGAG
+CTGGGTGTGTAGAA    pass    XX    .    0    0    0
chr1    139233    .    C    A    1883.77    .    AC=1;AF=0.500;AN=2;Ba
+seQRankSum=-9.990e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS
+=2.463;MLEAC=1;MLEAF=0.500;MQ=39.80;MQRankSum=0.636;QD=17.13;ReadPosR
+ankSum=-1.834e+00;SOR=0.595    GT:AD:DP:GQ:PGT:PID:PL    0/1:56,54:11
+0:99:0|1:139213_A_G:1912,0,3261    chr1    139233    139233    C    A
+    ncRNA_exonic    LOC729737                downstream    RP11-34P13
+.14                rs373847457                                       
+ 0.2478    0.3763    0.2985    0.3548    .    0.2577    0.3103    0.2
+308                                                                  
+                                                                     
+                                                                 0.02
+54654    3937    154602        chr1:139233:139233:C:A    1    0.5    
+-9.99E-01    0    110    no_DS    no_END    3.0103    2.463    no_Hap
+lotypeScore    no_InbreedingCoeff    1    0.5    39.8    0.636    17.
+13    no_RAW_MQ    -1.83E+00    0.595    AAGTTGGGCCTGGAAAGGCCCTTGTGAA
+GCATGAGCTTGGCCTAAAGAGG[C]CACTGGGTGGCAGGAGCTGGGTGTGTAGAAGCTGCTGAAAGGTT
+GGGAGC    pass    XX    .    0    0    0

[download]
--Dummydata3.var--
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT 
+   IFS002_W1600378    Chr    Start    End    Ref    Alt    Func.refGe
+ne    Gene.refGene    GeneDetail.refGene    ExonicFunc.refGene    AAC
+hange.refGene    Func.knownGene    Gene.knownGene    GeneDetail.known
+Gene    ExonicFunc.knownGene    AAChange.knownGene    avsnp144    100
+0g2015aug_all    1000g2015aug_afr    1000g2015aug_amr    1000g2015aug
+_sas    1000g2015aug_eur    1000g2015aug_eas    esp6500siv2_all    es
+p6500siv2_ea    esp6500siv2_aa    ExAC_ALL    ExAC_AFR    ExAC_AMR   
+ ExAC_EAS    ExAC_FIN    ExAC_NFE    ExAC_OTH    ExAC_SAS    cosmic70
+    SIFT_score    SIFT_pred    Polyphen2_HDIV_score    Polyphen2_HDIV
+_pred    Polyphen2_HVAR_score    Polyphen2_HVAR_pred    LRT_score    
+LRT_pred    MutationTaster_score    MutationTaster_pred    MutationAs
+sessor_score    MutationAssessor_pred    FATHMM_score    FATHMM_pred 
+   PROVEAN_score    PROVEAN_pred    VEST3_score    CADD_raw    CADD_p
+hred    DANN_score    fathmm-MKL_coding_score    fathmm-MKL_coding_pr
+ed    MetaSVM_score    MetaSVM_pred    MetaLR_score    MetaLR_pred   
+ integrated_fitCons_score    integrated_confidence_value    GERP++_RS
+    phyloP7way_vertebrate    phyloP20way_mammalian    phastCons7way_v
+ertebrate    phastCons20way_mammalian    SiPhy_29way_logOdds    Inter
+pro_domain    dbscSNV_ADA_SCORE    dbscSNV_RF_SCORE    CLINSIG    CLN
+DBN    CLNACC    CLNDSDB    CLNDSDBID    HRC_AF    HRC_AC    HRC_AN  
+  HRC_non1000G_AF    HRC_non1000G_AC    HRC_non1000G_AN    Kaviar_AF 
+   Kaviar_AC    Kaviar_AN    nci60    KEY3    INFO_AC    INFO_AF    I
+NFO_BaseQRankSum    INFO_ClippingRankSum    INFO_DP    INFO_DS    INF
+O_END    INFO_ExcessHet    INFO_FS    INFO_HaplotypeScore    INFO_Inb
+reedingCoeff    INFO_MLEAC    INFO_MLEAF    INFO_MQ    INFO_MQRankSum
+    INFO_QD    INFO_RAW_MQ    INFO_ReadPosRankSum    INFO_SOR    seq 
+   seq_flag    AAchange    Grantham    Mutability    FuentesFalsePosi
+tive    ACMG
chr1    14590    .    G    A    118.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=2.43;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=3.090;ML
+EAC=1;MLEAF=0.500;MQ=28.67;MQRankSum=-1.513e+00;QD=10.80;ReadPosRankS
+um=0.357;SOR=1.981    GT:AD:DP:GQ:PGT:PID:PL    0/1:7,4:11:99:0|1:145
+90_G_A:147,0,307    chr1    14590    14590    G    A    ncRNA_exonic 
+   WASH7P                intergenic    NONE,MIR6859-3    dist=NONE;di
+st=2779                                                              
+                                                                     
+                                                                     
+                                                                     
+                           chr1:14590:14590:G:A    1    0.5    2.43  
+  0    11    no_DS    no_END    3.0103    3.09    no_HaplotypeScore  
+  no_InbreedingCoeff    1    0.5    28.67    -1.51E+00    10.8    no_
+RAW_MQ    0.357    1.981    CAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGT
+GCTGGTTCC[G]TCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCC    pas
+s    XX    .    0    1    0
chr1    14599    .    T    A    115.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=0.253;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=2.881;M
+LEAC=1;MLEAF=0.500;MQ=30.13;MQRankSum=-1.712e+00;QD=9.65;ReadPosRankS
+um=1.16;SOR=1.721    GT:AD:DP:GQ:PGT:PID:PL    0/1:8,4:12:99:0|1:1459
+0_G_A:144,0,349    chr1    14599    14599    T    A    ncRNA_exonic  
+  WASH7P                intergenic    NONE,MIR6859-3    dist=NONE;dis
+t=2770            rs531646671    0.147564    0.121    0.1758    0.209
+6    0.161    0.0893                                                 
+                                                                     
+                                                                     
+                                                         0.0283925   
+ 739    26028        chr1:14599:14599:T:A    1    0.5    0.253    0  
+  12    no_DS    no_END    3.0103    2.881    no_HaplotypeScore    no
+_InbreedingCoeff    1    0.5    30.13    -1.71E+00    9.65    no_RAW_
+MQ    1.16    1.721    CTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCAC
+CCCC[T]CCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAG    homopoly
+mer    XX    .    0    1    0
chr1    14604    .    A    G    151.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=1.02;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=2.881;ML
+EAC=1;MLEAF=0.500;MQ=30.13;MQRankSum=-1.712e+00;QD=12.65;ReadPosRankS
+um=1.34;SOR=1.721    GT:AD:DP:GQ:PGT:PID:PL    0/1:8,4:12:99:0|1:1459
+0_G_A:180,0,346    chr1    14604    14604    A    G    ncRNA_exonic  
+  WASH7P                intergenic    NONE,MIR6859-3    dist=NONE;dis
+t=2765            rs541940975    0.147564    0.121    0.1758    0.209
+6    0.161    0.0893                                                 
+                                                                     
+                                                                     
+                                                         0.0285846   
+ 744    26028        chr1:14604:14604:A:G    1    0.5    1.02    0   
+ 12    no_DS    no_END    3.0103    2.881    no_HaplotypeScore    no_
+InbreedingCoeff    1    0.5    30.13    -1.71E+00    12.65    no_RAW_
+MQ    1.34    1.721    GCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCT
+CCCA[A]GGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACG    pass    
+XX    .    0    1    0
chr1    14610    .    T    C    151.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=3.16;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=3.123;ML
+EAC=1;MLEAF=0.500;MQ=31.00;MQRankSum=-1.442e+00;QD=11.67;ReadPosRankS
+um=0.860;SOR=2.030    GT:AD:DP:GQ:PGT:PID:PL    0/1:8,5:13:99:0|1:145
+90_G_A:180,0,346    chr1    14610    14610    T    C    ncRNA_exonic 
+   WASH7P                intergenic    NONE,MIR6859-3    dist=NONE;di
+st=2759                                                              
+                                                                     
+                                                                     
+                                                                     
+           0.0001921    5    26028        chr1:14610:14610:T:C    1  
+  0.5    3.16    0    13    no_DS    no_END    3.0103    3.123    no_
+HaplotypeScore    no_InbreedingCoeff    1    0.5    31    -1.44E+00  
+  11.67    no_RAW_MQ    0.86    2.03    TGAAGCTGGTCTCCACACAGTGCTGGTTC
+CGTCACCCCCTCCCAAGGAAG[T]AGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGG
+CCCAA    pass    XX    .    0    1    0
chr1    14653    .    C    T    254.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=1.91;ClippingRankSum=0.00;DP=25;ExcessHet=3.0103;FS=7.952;ML
+EAC=1;MLEAF=0.500;MQ=30.99;MQRankSum=-1.236e+00;QD=10.19;ReadPosRankS
+um=0.792;SOR=2.642    GT:AD:DP:GQ:PL    0/1:12,13:25:99:283,0,238    
+chr1    14653    14653    C    T    ncRNA_exonic    WASH7P           
+     intergenic    NONE,MIR6859-3    dist=NONE;dist=2716            r
+s62635297                                                            
+                                                                     
+                                                                     
+                                                                     
+ 0.0011526    30    26028        chr1:14653:14653:C:T    1    0.5    
+1.91    0    25    no_DS    no_END    3.0103    7.952    no_Haplotype
+Score    no_InbreedingCoeff    1    0.5    30.99    -1.24E+00    10.1
+9    no_RAW_MQ    0.792    2.642    AAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTG
+TGTCCATGTCAGAGCAA[C]GGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGAT
+T    pass    XX    .    0    1    0
chr1    16949    .    A    C    183.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=-7.580e-01;ClippingRankSum=0.00;DP=31;ExcessHet=3.0103;FS=0.
+000;MLEAC=1;MLEAF=0.500;MQ=21.07;MQRankSum=-1.095e+00;QD=5.93;ReadPos
+RankSum=-3.240e-01;SOR=0.515    GT:AD:DP:GQ:PL    0/1:19,12:31:99:212
+,0,396    chr1    16949    16949    A    C    ncRNA_exonic    WASH7P 
+               downstream    MIR6859-3                rs199745162    
+0.0139776    0.0227    0.0144    0.0143    0.0159                    
+                                                                     
+                                                                     
+                                                                     
+                     0.0159444    415    26028        chr1:16949:1694
+9:A:C    1    0.5    -7.58E-01    0    31    no_DS    no_END    3.010
+3    0    no_HaplotypeScore    no_InbreedingCoeff    1    0.5    21.0
+7    -1.10E+00    5.93    no_RAW_MQ    -3.24E-01    0.515    CTGGAATG
+GTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCA[A]TGTACATGAGGTCGTTGGCAATGC
+CGGGCAGGTCAGGCAGGTAGGATGGA    pass    XX    .    0    1    0
chr1    17020    .    G    A    99.77    .    AC=1;AF=0.500;AN=2;BaseQ
+RankSum=-1.024e+00;ClippingRankSum=0.00;DP=26;ExcessHet=3.0103;FS=14.
+474;MLEAC=1;MLEAF=0.500;MQ=21.00;MQRankSum=0.00;QD=3.84;ReadPosRankSu
+m=-2.034e+00;SOR=2.800    GT:AD:DP:GQ:PL    0/1:18,8:26:99:128,0,424 
+   chr1    17020    17020    G    A    ncRNA_exonic    WASH7P        
+        downstream    MIR6859-3                rs199740902           
+                                                                     
+                                                                     
+                                                                     
+                                                  0.0141002    367   
+ 26028        chr1:17020:17020:G:A    1    0.5    -1.02E+00    0    2
+6    no_DS    no_END    3.0103    14.474    no_HaplotypeScore    no_I
+nbreedingCoeff    1    0.5    21    0    3.84    no_RAW_MQ    -2.03E+
+00    2.8    ATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG[G]CCC
+AGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCA    pass    XX    .   
+ 0    1    0
chr1    17365    .    C    G    154.77    .    AC=1;AF=0.500;AN=2;Base
+QRankSum=0.621;ClippingRankSum=0.00;DP=43;ExcessHet=3.0103;FS=0.000;M
+LEAC=1;MLEAF=0.500;MQ=43.91;MQRankSum=-1.245e+00;QD=3.60;ReadPosRankS
+um=-1.701e+00;SOR=0.485    GT:AD:DP:GQ:PGT:PID:PL    0/1:36,7:43:99:0
+|1:17365_C_G:183,0,2051    chr1    17365    17365    C    G    ncRNA_
+exonic    WASH7P                downstream    MIR6859-3              
+  rs369606208                                        0.2553    0.1603
+    0.221    0.3841    0.2245    0.2715    0.2581    0.2883          
+                                                                     
+                                                                     
+                                                    7.76E-05    12   
+ 154602        chr1:17365:17365:C:G    1    0.5    0.621    0    43  
+  no_DS    no_END    3.0103    0    no_HaplotypeScore    no_Inbreedin
+gCoeff    1    0.5    43.91    -1.25E+00    3.6    no_RAW_MQ    -1.70
+E+00    0.485    TGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTT[C
+]TACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTG    pass    XX    
+.    0    1    0

[download]

Replies are listed 'Best First'.
Re: error returning hash value?
by choroba (Cardinal) on Jan 08, 2017 at 23:56 UTC
    Your code and samples are too complicated. Try to simplify it: show only the relevant data (for example, 2 or 3 columns in the files should be enough). Also, remove any logic that's not relevant to your question.

    To be able to run your code, I first had to remove the filenames from the downloaded files, I then got a lot of warnings (why didn't you turn them on?) like: 

    Odd number of elements in hash assignment at ./1.pl line 61.
Use of uninitialized value in list assignment at ./1.pl line 61.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value in join or string at ./1.pl line 83, <VAR> 
+line 7.
Use of uninitialized value within %variants_geno in pattern match (m//
+) at ./1.pl line 100, <VAR> line 7.

    [download]

    The first two lines can be fixed by replacing the line with 

    undef %variants_hash;

    [download]

    as the original was equivalent to 

    %variants_hash = ( undef => );

    [download]

    ($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

    [download]
[reply]
[d/l]
[select]

      Thank you for your time in replying. I'm sorry that I am not very good at asking questions; it isn't easy to know how much detail to include/not include. I always get it wrong :-(. I'll be honest in that I didn't understand what you meant by "To be able to run your code, I first had to remove the filenames from the downloaded files". I put the file names in because the code works on the principle that it reads in all .var files from the directory, so it made sense to me to put a header to say that they were named .var. Sorry if that was wrong.

      I have managed to get a bit further with it. I realised that i should have defined my hash as $zygos{$uniqlocus} = $zyg. I also noticed that $locus needed to be non-unique.

      I'll figure it out I'm sure. Thank you for your valiant efforts anyway!

[reply]
        > I put the file names in

        Have you ever noticed the "download" link at the bottom of each code section? I clicked it to download the data including tabs, but they included the filenames. Don't make them part of the code section.

        ($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

        [download]
[reply]
[d/l]

        I'm struggling to understand why if you want to 'merge' records from 3 files you are creating hash keys containing the filename ? 

        $fields[2] = $file;
my $locus = join "\t", @fields[0,1,2,3,4,5];

        [download]

        From this output code, it looks like you want to create a 'cross tab' with HET/HOM derived from each file in a different column. Is that correct ?

        my $samples_list = join "\t", @samples;
print OUT "CHROM    POS    ID    REF    ALT    QUAL    $samples_list

        [download]

        update : my best guess at what you are trying to do.
        Read more... (2 kB)
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        it isn't easy to know how much detail to include/not include

        Think about: what is the minimum amount of code and sample data needed so that others can reproduce the problem? For each line of code, try removing it - does the problem still exist? If yes, it was ok to remove that line, if the problem goes away, put the line back in. And if removing the line causes a compilation failure, fix that first. See also Short, Self-Contained, Correct Example.

[reply]

        Hi drlecb. There are a few ways to include sample files with your program on Perlmonks. To include it like you did and have the Perl program still be runnable you can add __DATA__ or __END__ after your Perl program and anything after it will be treated as data or comments. Another way is to start a new code section for your sample file with  <c> ... </c> so that the monks can click download for the sample file.

        Here is an example of using __DATA__

        use warnings;
use strict;

while(<DATA>){
    my $line = $_;
    print $line;
}
__DATA__
Line 1
Line 2
Line 3

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