Hello all, I'm struggling to get Perl to work in skipping lines containing certain features which means I don't need to use them, basically I'm just unsure of the syntax, though it appears to work in some places and not in others

Looking at this following table; 

 chrM    2928    A    G    17    0    0%    A    46    105    69.54%  
+  R    Somatic    1    1.23052720566294E-008    17    29    50    55 
+   4    13    0    0 
 chr1    108310    T    C    9    0    0%    T    3    5    62.5%    Y
+    Somatic    1    0.0090497738    2    1    2    3    7    2    0  
+  0 
 chr1    726958    T    A    11    0    0%    T    9    4    30.77%   
+ W    Somatic    1    0.0672877847    6    3    1    3    5    6    0
+    0 
 chr1    1412720    C    A    33    0    0%    C    22    6    21.43% 
+   M    Somatic    1    0.0067850063    10    12    3    3    14    1
+9    0    0 
chr1    1822396    C    G    6    0    0%    C    4    4    50%    S  
+  Somatic    1    0.0699300699    3    1    2    2    4    2    0    
+0 
 chr1    1822457    C    T    10    0    0%    C    4    4    50%    Y
+    Somatic    1    0.022875817    3    1    2    2    6    4    0   
+ 0

[download]

I'm trying to skip the lines which are chrM rather than chr1, the following code is what I came up with (I'm also extracting different columns) 

 while (my $line = <FILE>) {
    next if ($. == 1);
    chomp $line;
    my @sepline = split ("\t", $line);
    my $chromosome = $sepline[0];
    my $chrpos = $sepline[1];
    my $nmreads = $sepline[8];
    my $mutants = $sepline[9];
    my $totalreads = $nmreads + $mutants;
    next if ($chromosome = /^chrM/);
    print ("$nmreads $mutants $totalreads\n");
    

}

[download]

So the script works fine if I # out the lower next if function towards the bottom of the script, I've also tried "next if ($chromosome = "chrM");" and "if ($chromosome = "chrM") { next;} but neither will work. Is there something incorrect about my syntax or am I simply going about it completely the wrong way? Appreciate any help, cheers

In reply to Trouble skipping lines using Perl by LeBran

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