UNIX for Dummies Questions & Answers

#!/usr/bin/perl
open I, "$ARGV[0]";                                                    # open file with filename passed to script as first argument ($ARGV[0])
while (<I>){                                                           # sequentially read lines of that file and put them into $_ variable
  $pos=((split "[\t ]+",$_)[4]);                                       # extract position number from current line stored in $_ variable
  $cov=((split "=",(split ";",(split "[\t ]+",$_)[8])[2])[1]);         # extract coverage value in the same way
  $s{$pos}+=$cov;                                                      # add coverage value for particular position
  $n{$pos}++;                                                          # count number of occurrences for particular position
  $s_tot+=$cov;                                                        # add coverage value for total sum
  $n_tot++;                                                            # count number of coverage occurrences in total
}
END{
  for $i (keys %s){print "Mean_Coverage_for_position _$i = " . ($s{$i}/$n{$i}) . "\n"};   # calculate and print average coverage for each position
  print "Mean_Coverage = " . ($s_tot/$n_tot) . "\n"                    # calculate and print global average
}

chr01   levure5 SNP     12745   12745   0.000000        .       .       genotype=S;reference=C;coverage=91;refAlleleCounts=44;refAlleleStarts=28;refAlleleMeanQV=19;novelAlleleCounts=40;novelAlleleStarts=25;novelAlleleMeanQV=18;diColor1=22;diColor2=11;het=1;flag=
chr01   levure6 SNP     12745   12745   0.000000        .       .       genotype=S;reference=C;coverage=62;refAlleleCounts=29;refAlleleStarts=19;refAlleleMeanQV=19;novelAlleleCounts=32;novelAlleleStarts=20;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01   levure7 SNP     12745   12745   0.000000        .       .       genotype=S;reference=C;coverage=24;refAlleleCounts=9;refAlleleStarts=8;refAlleleMeanQV=23;novelAlleleCounts=13;novelAlleleStarts=12;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chrm    levure7 SNP     86086   86086   0.000000        .       .       genotype=A;reference=G;coverage=18;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=18;novelAlleleStarts=4;novelAlleleMeanQV=13;diColor1=21;diColor2=21;het=0;flag=h4,h10,;gene;ID=Q0
182;Name=Q0182;Alias=ORF11
chrm    levure8 SNP     86086   86086   0.000000        .       .       genotype=A;reference=G;coverage=20;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=19;novelAlleleStarts=4;novelAlleleMeanQV=14;diColor1=21;diColor2=21;het=0;flag=h4,h10,h9,;gene;ID
=Q0182;Name=Q0182;Alias=ORF11
chrm    levure5 SNP     98064   98064   0.000000        .       .       genotype=A;reference=G;coverage=61;refAlleleCounts=8;refAlleleStarts=4;refAlleleMeanQV=11;novelAlleleCounts=52;novelAlleleStarts=6;novelAlleleMeanQV=16;diColor1=20;diColor2=20;het=0;flag=h4,h10,
scplasm1        levure5 SNP     6153    6153    0.000000        .       .       genotype=C;reference=T;coverage=5752;refAlleleCounts=7;refAlleleStarts=7;refAlleleMeanQV=3;novelAlleleCounts=5588;novelAlleleStarts=58;novelAlleleMeanQV=20;diColor1=22;diColor2=22;het=0;flag=h4,h1
0,h9,;region;ID=scplasm1;dbxref=NCBI:NC_001398

chr01[TAB]1
chrm[TAB]2
scplasm[TAB]1

#!/bin/bash
for i in $*; do
echo "$i:"
perl -ane '$h{$F[0]}{$F[3]}++;END{for $i (keys %h){@x=keys %{$h{$i}};print "$i\t" . ($#x+1) . "\n"}}' $i
done

 %h = {
          'scplasm1' => {
                          '6153' => 1
                        },
          'chr01' => {
                       '12745' => 3
                     },
          'chrm' => {
                      '86086' => 2,
                      '98064' => 1
                    }
        };

%h = {
          'scplasm1' => {
                          '6153' => 1
                        },
          'chr01' => {
                       '12745' => 1
                     },
          'chrm' => {
                      '86086' => 1,
                      '98064' => 1
                    }
        };

$i = scplasm1
@x = [
          '6153'
        ];

$i = chr01
@x = [
          '12745'
        ];

$i = chrm
@x = [
          '86086',
          '98064'
        ];

. ($#x+1) .