Re^2: how to sum over rows based on column headings in perl

I am trying to understand your code by modifying it myself and trying to read the data through a file

#!/usr/bin/perl -w

use strict;
use warnings;
use autodie;

if (@ARGV != 1){
    print "USAGE: ./parse-counts.pl file\n";
    exit(-1);
}

my $mutfile = $ARGV[0];

my (%counts, %unique, %masks);
my ($headname, @unique) = grep !$unique{$_}++, my @headers = split ' '
+, <DATA>;

for my $label ( @unique )
{
    $masks{$label} = join ' ',
    map { $_ eq $label ? 'M' : '_' } @headers[1..$#headers];
}

my $line;

open(INPUTR,"<$mutfile") || die "Can't open \$mutfile for reading. \n"
+;
while($line=<INPUTR>){
#while(<DATA>)
{
    chomp $line;
    s/\s+/ /g; # for uniform spacing
    my ($name, $letters) = split ' ', $line, 2;
    $counts{$name}{$line} += ($masks{$line} | $letters) =~ /M/ for @un
+ique;
}

print "$headname @unique\n";
print "$line @{ $counts{$_} }{@unique}\n" for sort keys %counts;
[download]

I am sorry i don't understand what I did wrong as now I get error as:

./parse-counts.pl junk.txt
Missing right curly or square bracket at ./parse-counts.pl line 36, at
+ end of line
syntax error at ./parse-counts.pl line 36, at EOF
Execution of ./parse-counts.pl aborted due to compilation errors.
[download]

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Re^3: how to sum over rows based on column headings in perl by 1nickt (Canon) on Jul 31, 2015 at 17:03 UTC
That error is pretty clear! You are missing the right curly bracket closing the `while` loop you opened on line 26. The end of line 36 is given as the location of the error because that's where Perl runs out of code in which to find the closing bracket. You have a stray opening bracket under the line you commented out at line 27. This is a good example of why you should have consistent syntax: your commented-out `while` statement has the bracket on the next line, while the new `while` statement has the bracket on the same line. Pick one and stick with it. In my view, putting the brackets on the same line reduces the chances of them going astray. Update: explain cause of error The way forward always starts with a minimal test.	[reply] [d/l] [select]
Re^4: how to sum over rows based on column headings in perl by angerusso (Novice) on Jul 31, 2015 at 19:07 UTC
Actually, I think I did reply too fast! Obviously i don't understand map function the way you used it. Could you explain your usage of map? E.g. I changed "M" to "MUTS" and the results are screwed up. Wherever you used "M", I changed it to "MUTS" and changed "M" in datafile to "MUTS" and I don't get the expected result. `map { $_ eq $label ? 'MUTS' : '_' } @headers[1..$#headers];` [download] My modified code gives wrong results #!/usr/bin/perl use strict; use warnings; use autodie; if (@ARGV != 1){ print "USAGE: ./parse-counts.pl file\n"; exit(1); } my $mutfile = $ARGV[0]; open(INPUTR,"<$mutfile") or die "Can't open \$mutfile for reading. \n" +; my (%counts, %unique, %masks); my ($headname, @unique) = grep !$unique{$_}++, my @headers = split /\t +/, <INPUTR>; # the basic syntax is @out = map { CODE } @in; for my $label ( @unique ) { $masks{$label} = join "\t", map { $_ eq $label ? 'MUTS' : '_' } @headers[1..$#headers]; } my $line; while($line=<INPUTR>) #while(<DATA>) { chomp $line; $line =~ s/\t/\t/g; # for uniform spacing my ($name, $letters) = split /\t/, $line, 2; $counts{$name}{$_} += ($masks{$_} \| $letters) =~ /MUTS/ for @uniqu +e; print $name."\n"; print $letters."\n"; } print "$headname @unique\n"; print "$_ @{ $counts{$_} }{@unique}\n" for sort keys %counts; The output produced is: Gname G1 G2 G3 A 3 2 0 B 2 1 1 C 2 0 0 The modified datafiles is Gname G1 G1 G1 G1 G2 G2 G3 A W W MUTS W W W MUTS A W W W W W W W A W W W W W W W B W W W W W MUTS MUTS B MUTS W W W W MUTS MUTS C MUTS MUTS MUTS W W W W C MUTS W W MUTS MUTS W W [download]	[reply] [d/l] [select]
Re^5: how to sum over rows based on column headings in perl by Anonymous Monk on Jul 31, 2015 at 19:29 UTC
No, the heart of the algorithm is the or operator, and changing M to MUTS breaks alignment that allows the or operator to work properly. Print out both sides of the or operator to see the misalignment.	[reply]
Re^6: how to sum over rows based on column headings in perl by angerusso (Novice) on Jul 31, 2015 at 19:58 UTC
Re^7: how to sum over rows based on column headings in perl by Anonymous Monk on Jul 31, 2015 at 20:09 UTC
Re^3: how to sum over rows based on column headings in perl by Anonymous Monk on Jul 31, 2015 at 17:12 UTC
#!/usr/bin/perl use strict; use warnings; use autodie; if (@ARGV != 1){ print "USAGE: ./parse-counts.pl file\n"; exit(1); } my $mutfile = $ARGV[0]; open(INPUTR,"<$mutfile") or die "Can't open \$mutfile for reading. \n" +; my (%counts, %unique, %masks); my ($headname, @unique) = grep !$unique{$_}++, my @headers = split ' ' +, <INPUTR>; for my $label ( @unique ) { $masks{$label} = join ' ', map { $_ eq $label ? 'M' : '_' } @headers[1..$#headers]; } my $line; while($line=<INPUTR>) #while(<DATA>) { chomp $line; $line =~ s/\s+/ /g; # for uniform spacing my ($name, $letters) = split ' ', $line, 2; $counts{$name}{$_} += ($masks{$_} \| $letters) =~ /M/ for @unique; } print "$headname @unique\n"; print "$_ @{ $counts{$_} }{@unique}\n" for sort keys %counts; [download]	[reply] [d/l]
Re^4: how to sum over rows based on column headings in perl by angerusso (Novice) on Jul 31, 2015 at 18:48 UTC
Thanks so much! It works beautifully and I understand it much better now. am also glad I learnt "map" function today. Also learnt how to use a 3rd parameter in the split function. Hoping to use them again for a new codes I plan to write in future. Will practice!	[reply]