Re: Issues regarding for loops and recursion

Hi Nickmofoe, and welcome to Perl!

if ($_=~m/^ATOM\s+\d+\s+\w+\s+\w+\s+\w+\d+\s+(\S+)\s+(\S+)\s+(\S+)/){
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Here you match against $_, but it was never set. Did you want to match against $seq? I'm not sure.

Some general stylistic things:

open (IN, '6U9D.pdb.txt');
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You should check whether opening the file actually succeeded:

my $filename = '6U9D.pdb.txt';
open (IN, $filename)
    or die "Couldn't open '$filename': $!";
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You should use the strict pragma. This requires you to declare all variables but on the upside, it allows Perl to tell you about typos in your variable names.

When assigning the %amino_acid_conversion, you could use newlines to make the code a bit more readable:

%amino_acid_conversion = (
    ALA=>'A',
    TYR=>'Y',
    MET=>'M',
    LEU=>'L',
    CYS=>'C',
    GLY=>'G',
    ARG=>'R',
    ASN=>'N',
    ASP=>'D',
    GLN=>'Q',
    GLU=>'E',
    HIS=>'H',
    TRP=>'W',
    LYS=>'K',
    PHE=>'F',
    PRO=>'P',
    SER=>'S',
    THR=>'T',
    ILE=>'I',
    VAL=>'V'
);
[download]

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Re^2: Issues regarding for loops and recursion by hippo (Bishop) on Jan 09, 2023 at 13:32 UTC
When assigning the `%amino_acid_conversion`, you could use newlines to make the code a bit more readable Completely agree. I'd go even further and put whitespace around the fat commas and with so many entries I would sort by either key or value to make it easier to spot misses/dupes/typos. `%amino_acid_conversion = ( ALA => 'A', ARG => 'R', ASN => 'N', ASP => 'D', CYS => 'C', GLN => 'Q', GLU => 'E', GLY => 'G', HIS => 'H', ILE => 'I', LEU => 'L', LYS => 'K', MET => 'M', PHE => 'F', PRO => 'P', SER => 'S', THR => 'T', TRP => 'W', TYR => 'Y', VAL => 'V' );` [download] 🦛	[reply] [d/l] [select]
Re^2: Issues regarding for loops and recursion by Fletch (Bishop) on Jan 09, 2023 at 17:53 UTC
Another initialization readability trick is to use YAML in a HEREDOC which gets you (IMHO) less "noise" to initializing data: `use YAML::XS qw( Load ); my %conversions = %{Load(<<'EOT')}; --- ALA: A TYR: Y MET: M ... EOT` [download] The cake is a lie. The cake is a lie. The cake is a lie.	[reply] [d/l]


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