UNIX for Dummies Questions & Answers

print "$i\t$h{$i}\n";

print (sort ("$i\t$h{$i}")"\n");

SK1.scplasm1    1
SK1.chr06    1
SK1.chrm    2
SK1.chr08    2
SK1.chr07    2

SK1.chr06    1
SK1.chr07    2
SK1.chr08    2
SK1.chrm    2
SK1.scplasm1    1

@sorted=sort {$a cmp $b} keys %h;
for $i (@sorted){
  print "$i\t$h{$i}\n";
}

#!/usr/bin/perl 
print "Enter minimum coverage: ";
chomp($min_cov=<STDIN>);
print "Enter minimum novel_Allele_Starts: ";
chomp($min_nas=<STDIN>);
open I, "$ARGV[0]";
while (<I>){
         @F=split;     
  $F[8]=~/coverage=([^;]+)/;
  if ($1>=$min_cov){
  $cov{$F[0]}{$F[3]}+=$1;
  $F[8]=~/novelAlleleStarts=([^;]+)/;
  if ($1>=$min_nas){
  $nas{$F[0]}{$F[3]}+=$1;
  }
  $n{$F[0]}{$F[3]}++;
  $h{$F[0]}++;
  }
}
END{
    for $i (keys %cov){
    for $j (keys %{$cov{$i}}){
      print "$i\t$j\t";
      printf "%.1f\t", ($cov{$i}{$j}/$n{$i}{$j});
      printf "%.1f\n", ($nas{$i}{$j}/$n{$i}{$j});   
    }
  }
  for $i (keys %h){
      @sorted=sort {$a cmp $b} keys %h;
  }
for $i (@sorted){
  print "$i\t$h{$i}\n";
        $t+=$h{$i};
 }
}

SK1.chr10    SOLiD_diBayes    SNP    3120    3120    1.000000    .    .    genotype=A;reference=G;coverage=179;refAlleleCounts=32;refAlleleStarts=21;refAlleleMeanQV=15;novelAlleleCounts=117;novelAlleleStarts=27;novelAlleleMeanQV=17;diColor1=23;diColor2=23;het=0;flag=h8, 
SK1.chr01    SOLiD_diBayes    SNP    8621    8621    0.000000    .    .    genotype=C;reference=T;coverage=198;refAlleleCounts=5;refAlleleStarts=5;refAlleleMeanQV=18;novelAlleleCounts=150;novelAlleleStarts=49;novelAlleleMeanQV=18;diColor1=21;diColor2=21;het=0;flag=h4,h10,h9, 
SK1.chrm    SOLiD_diBayes    SNP    8844    8844    1.000000    .    .    genotype=C;reference=A;coverage=205;refAlleleCounts=38;refAlleleStarts=21;refAlleleMeanQV=24;novelAlleleCounts=164;novelAlleleStarts=51;novelAlleleMeanQV=27;diColor1=01;diColor2=01;het=0;flag=h8, 
SK1.chr07    SOLiD_diBayes    SNP    8852    8852    1.000000    .    .    genotype=T;reference=C;coverage=161;refAlleleCounts=31;refAlleleStarts=16;refAlleleMeanQV=24;novelAlleleCounts=127;novelAlleleStarts=47;novelAlleleMeanQV=23;diColor1=11;diColor2=11;het=0;flag=h8, 
SK1.chr07    SOLiD_diBayes    SNP    8865    8865    0.999102    .    .    genotype=G;reference=A;coverage=74;refAlleleCounts=11;refAlleleStarts=7;refAlleleMeanQV=26;novelAlleleCounts=59;novelAlleleStarts=29;novelAlleleMeanQV=24;diColor1=12;diColor2=12;het=0;flag=h8,