Re^4: Listing occurence of all residues

Here is a sample file. I have used shebang line and declarations of varibles.But since I am posing the question to experts I just avoided them. Thank you for considering my question.

>sp|P05100|3MG1_ECOLI DNA-3-methyladenine glycosylase 1

MERCGWVSQDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACF

HQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFVDFVWSUV

>sp|P30871|3PASE_ECOLI Inorganic triphosphatase

MAQEIELKFIVNHSAVEALRDHLNTLGGEHHDPVQLLNIYYETPDNWLRGHDMGLRI

RGE NGRYEMTMKVAGRVTGGLHQRPEYNVALSEPTLDLAQLPTEVWPNGELPADLASRVQPLF

Comment on Re^4: Listing occurence of all residues

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Re^5: Listing occurence of all residues by pme (Monsignor) on Mar 01, 2015 at 18:57 UTC
I hope this little piece of code help. I supposed that the residues are marked with letters A-Z. #!/usr/bin/perl -w use strict; open FILE1, "<e.txt" or die "can't open file for reading: $!\n"; my %Fasta_split; my $id; while (<FILE1>) { chomp; next if(/^\s*$/); my $FastaLine = $_; if ( $FastaLine =~ /^>sp\\|(\w+\S+)\\|/ ) { $id = $1; } else { $Fasta_split{$id} .= $FastaLine; } } # print header my @header = qw/A B C D E F G H I J K L M N O P Q R S T U V W X Y Z/; print "ID " . join(' ', @header) . "\n"; # print data foreach my $id (sort keys %Fasta_split) { my %words; # count letters $words{$_}++ for split('', $Fasta_split{$id}); printf "%8s ", $id; # print counts foreach my $w (@header) { if (defined $words{$w}) { printf "%2d ", $words{$w}; } else { print ' - '; } } print "\n"; } [download]	[reply] [d/l]

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Re^5: Listing occurence of all residues
by pme (Monsignor) on Mar 01, 2015 at 18:57 UTC

#!/usr/bin/perl -w

use strict;

open FILE1, "<e.txt" or die "can't open file for reading: $!\n";

my %Fasta_split;

my $id;
while (<FILE1>) {
  chomp;
  next if(/^\s*$/);

  my $FastaLine = $_;

  if ( $FastaLine =~ /^>sp\|(\w+\S+)\|/ ) {
    $id = $1;
  } else {
    $Fasta_split{$id} .= $FastaLine;
  }
}

# print header
my @header = qw/A B C D E F G H I J K L M N O P Q R S T U V W X Y Z/;
print "ID        " . join('  ', @header) . "\n";
# print data
foreach my $id (sort keys %Fasta_split) {
    my %words;
    # count letters
    $words{$_}++ for split('', $Fasta_split{$id});

    printf "%8s ",  $id;
    # print counts
    foreach my $w (@header) {
      if (defined $words{$w}) {
        printf "%2d ", $words{$w};
      } else {
        print ' - ';
      }
    }
    print "\n";
}
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