I'm trying to write a program that can read from a file then put into a heap sort then output in a tree along with the sorted list. But I got stuck, instead of having the put be the numbers used in the heap sort, it just post 1-10 on one line then 1-9 on the next line. I'm really confused and I barely understand this language as it is. I put a example of the out below alone with the output I am hoping to have it draw.
#!/usr/bin/perl
use 5.006;
use strict;
use warnings;
use Tree::DAG_Node;
process_data(read_file('testing.txt'));
process_data((3,1,4,1,5,9,2,6,5,3,6));
sub read_file{
my($filename)=#_;
my #data=();
my #words;
open(my $fh, "<", $filename)
or die "Could not open file: $!\n";
while(<$fh>){
chomp;
#words = split(' ');
foreach my $word(#words){
push #data, $word;
}
}
close $fh;
return #data;
}
sub heap_sort {
my ($a) = #_;
my $n = #$a;
for (my $i = ($n - 2) / 2; $i >= 0; $i--) {
down_heap($a, $n, $i);
}
for (my $i = 0; $i < $n; $i++) {
my $t = $a->[$n - $i - 1];
$a->[$n - $i - 1] = $a->[0];
$a->[0] = $t;
down_heap($a, $n - $i - 1, 0);
}
}
sub down_heap {
my ($a, $n, $i) = #_;
while (1) {
my $j = max($a, $n, $i, 2 * $i + 1, 2 * $i + 2);
last if $j == $i;
my $t = $a->[$i];
$a->[$i] = $a->[$j];
$a->[$j] = $t;
$i = $j;
}
sub max {
my ($a, $n, $i, $j, $k) = #_;
my $m = $i;
$m = $j if $j < $n && $a->[$j] > $a->[$m];
$m = $k if $k < $n && $a->[$k] > $a->[$m];
return $m;
}
}
sub draw_tree{
my(#data)=#_;
my $root = Tree::DAG_Node->new;
$root->name($_[0]);
$root->new_daughter->name($_) for (1..10);
my #names = #data;
my $count = 50;
for my $n ($root->daughters) {
for (split //, $names[$count++]) {
$n->new_daughter->name($_)
}
}
print map "$_\n", #{$root->draw_ascii_tree};
}
sub process_data{
my(#data)=#_;
my #a = #data;
print "#a\n";
print "\n";
heap_sort(\#a);
draw_tree(#a);
print "\n";
print "#a\n";
print "\n";
}
here is the output I get
CMD output of my code
Output I am expecting:
(using example data)
1 1 9 4 5
1
|
1 ----- 9
|
/\
4 5
1 1 4 5 9
Related
This is supposed to put the contents of nums into decreasing order, however sort does not change the contents of nums. Many sites I read have said to pass by reference, but I don't think I'm dereferencing the argument correctly. Bear with me, this is my first Perl program :)
#! /usr/bin/env perl
sub sort {
my #arr = #_;
my $len = scalar #arr;
for (my $i = 1; $i < $len-1; $i = $i + 1) {
my $max = $i;
for (my $j = $i + 1; $j < $len; $j = $j + 1) {
if ($arr[$j] > $arr[$max]) {
$max = $j
}
}
$temp = $arr[$max];
$arr[$max] = $arr[$i];
$arr[$i] = $temp;
}
}
print "Enter 10 numbers: ";
my $numbers = <STDIN>;
my #nums = split ' ', $numbers;
print "Unsorted: #nums\n";
sort \#nums;
print "Sorted: #nums\n";
#Matt Jacob helped me out with this one. This is what I was looking for.
#! /usr/bin/env perl
sub selection_sort {
my $arr = shift;
my $len = scalar #$arr;
for (my $i = 0; $i < $len-1; $i++) {
my $max = $i;
for (my $j = $i + 1; $j < $len; $j++) {
if (#$arr[$j] > #$arr[$max]) {
$max = $j
}
}
my $temp = #$arr[$max];
#$arr[$max] = #$arr[$i];
#$arr[$i] = $temp;
}
}
print "Enter 10 numbers: ";
my $input = <STDIN>;
my #integers = split ' ', $input;
print "Unsorted: #integers\n";
selection_sort \#integers;
print "Sorted: #integers\n";
This code works but it prints in ascending order. Do I need to change my whole formula?
print "Enter an integer \n";
my $root = <STDIN>;
my #nums = (100..200);
my $i = 0;
# code in while loop executes as long as condition is true
while ( $i < $#nums )
{
print "$nums[$i]\n",if($nums[$i] % $root == 0); $i++;
}
Just set $i to $#nums instead of 0 and decrement it -- instead of incrementing. You'll need to change the loop condition to $i >= 0 (it should be $i <= $#nums in your code, otherwise it skips 200 when 10 was entered).
#!/usr/bin/perl
use warnings;
use strict;
print "Enter an integer \n";
my $root = <>;
my #nums = (100 .. 200);
my $i = $#nums;
while ( $i >= 0 ) {
print "$nums[$i]\n" if $nums[$i] % $root == 0;
--$i;
}
There are more than a few ways to do it ... not all equally good:
#!/usr/bin/env perl
use strict;
use warnings;
run(#ARGV);
sub run {
my $root = $_[0] // get_root();
my #nums = (100 .. 200);
my #functions = (
sub {
my ($root, $nums) = #_;
my $i = #$nums;
while ($i--) {
print "$nums->[$i]\n" unless $nums->[$i] % $root;
}
return;
},
sub {
my ($root, $nums) = #_;
for my $n ( reverse #$nums ) {
print "$n\n" unless $n % $root;
}
return;
},
sub {
my ($root, $nums) = #_;
my $i;
while ($i++ < #$nums) {
print "$nums->[#$nums - $i]\n" unless $nums->[#$nums - $i] % $root;
}
return;
},
sub {
my ($root, $nums) = #_;
my #multiples = reverse grep !($_ % $root), #$nums;
print "$_\n" for #multiples;
return;
},
);
for my $i ( 0 ... $#functions ) {
print "=== Function $i ===\n";
$functions[$i]->($root, \#nums);
}
}
sub get_root {
return scalar <STDIN>;
}
print "Enter an integer \n";
my $root = <STDIN>;
my #nums = (100..200);
#nums = reverse #nums; #Just reverse the arrays
my $i = 0;
# code in while loop executes as long as condition is true
while ( $i < $#nums )
{
print "$nums[$i]\n",if($nums[$i] % $root == 0); $i++;
}
May be it will helps you.
for (my $i = $#nums; $i >= 0; --$i) { ... }
for (my $i = #nums; $i--; ) { ... }
for my $i (reverse 0 .. $#nums) { ... }
for (1 .. #nums) { my $i = -$_; ... } # Or: my $i = #nums-$_;
for my $num (reverse #nums) { ... }
When ever I run this bit of code. it doesn't display any output. Anyone see anything wrong?
I am trying to display this in the out put:
A
AA
AAA
AAAB
AAABA
AAABAA
AAABAAA
AAABAAAB
etc.
#!/usr/local/bin/perl
$A = 3;
$B = 1;
$i = 1;
$output = "";
$j = 1;
while ($i <= $ARGV[0]) {
while ($j <= $i) {
if ($A == 0 && $B == 0) {
$A = 3;
$B = 1;
}
if ($A > 0) {
$output.= "A";
$A--;
}
else {
$output.= "B";
$B--;
}
$j++;
}
print($output . "\n");
$i++;
}
It works for me when I run it with a numeric argument (number of lines).
An idea how to simplify the code:
#!/usr/bin/perl
use warnings;
use strict;
my $count = shift;
my $A = 3;
my $B = 1;
my $string = q();
$string .= ('A' x $A) . ('B' x $B) while $count > length $string;
print substr($string, 0, $_), "\n" for 1 .. $count;
It uses a different algorithm - it creates the longest possible string, and then outputs parts of it.
if there is no #ARGV, while ($i <= $ARGV[0]) never runs.
#ARGV is an array of the command line arguments provided when the script is executed. you did not provide any command line arguments. if you had use warnings in effect, you would be warned that $ARGV[0] is uninitialized.
As from ikegami comment. You cann't pass the input at when the program is compile. For example, consider your file name is algo.pl. Can you run your program with
perl algo.pl 10
Here 10 is the input value of the program. In program value is retrieve by the $ARGV[0]
so in your program looks like while ($i <= $ARGV[0]).
If you want pass the several values like perl filename.pl 12 data1 data2In your data retrieve by $ARGV[0] $ARGV[1] $ARGV[2] for more information see here.
If you want pass the input at the time of execution used STDIN
use warnings;
use strict;
my $A = 3;
my $B = 1;
my $i = 1;
my $output = "";
my $j = 1;
print "Enter the value: ";
chomp(my $value = <STDIN>);
while ($i <= $value) {
while ($j <= $i) {
if ($A == 0 && $B == 0) {
$A = 3;
$B = 1;
}
if ($A > 0) {
$output.= "A";
$A--;
}
else {
$output.= "B";
$B--;
}
$j++;
}
print($output . "\n");
$i++;
}
I'm trying to use a foreach loop to loop through an array and then use a nested while loop to loop through each line of a text file to see if the array element matches a line of text; if so then I push data from that line into a new array to perform calculations.
The outer foreach loop appears to be working correctly (based on printed results with each array element) but the inner while loop is not looping (same data pushed into array each time).
Any advice?
The code is below
#! /usr/bin/perl -T
use CGI qw(:cgi-lib :standard);
print "Content-type: text/html\n\n";
my $input = param('sequence');
my $meanexpfile = "final_expression_complete.txt";
open(FILE, $meanexpfile) or print "unable to open file";
my #meanmatches;
#regex = (split /\s/, $input);
foreach $regex (#regex) {
while (my $line = <FILE>) {
if ( $line =~ m/$regex\s(.+\n)/i ) {
push(#meanmatches, $1);
}
}
my $average = average(#meanmatches);
my $std_dev = std_dev($average, #meanmatches);
my $average_round = sprintf("%0.4f", $average);
my $stdev_round = sprintf("%0.4f", $std_dev);
my $coefficient_of_variation = $stdev_round / $average_round;
my $cv_round = sprintf("%0.4f", $coefficient_of_variation);
print font(
{ color => "blue" }, "<br><B>$regex average: $average_round
 Standard deviation: $stdev_round Coefficient of
variation(Cv): $cv_round</B>"
);
}
sub average {
my (#values) = #_;
my $count = scalar #values;
my $total = 0;
$total += $_ for #values;
return $count ? $total / $count : 0;
}
sub std_dev {
my ($average, #values) = #_;
my $count = scalar #values;
my $std_dev_sum = 0;
$std_dev_sum += ($_ - $average)**2 for #values;
return $count ? sqrt($std_dev_sum / $count) : 0;
}
Yes, my advice would be:
Turn on strict and warnings.
perltidy your code,
use 3 argument open: open ( my $inputfile, "<", 'final_expression.txt' );
die if it doesn't open - the rest of your program is irrelevant.
chomp $line
you are iterating your filehandle, but once you've done this you're at the end of file for the next iteration of the foreach loop so your while loops becomes a null operation. Simplistically, reading the file into an array my #lines = <FILE>; would fix this.
So with that in mind:
#!/usr/bin/perl -T
use strict;
use warnings;
use CGI qw(:cgi-lib :standard);
print "Content-type: text/html\n\n";
my $input = param('sequence');
my $meanexpfile = "final_expression_complete.txt";
open( my $input_file, "<", $meanexpfile ) or die "unable to open file";
my #meanmatches;
my #regex = ( split /\s/, $input );
my #lines = <$input_file>;
chomp (#lines);
close($input_file) or warn $!;
foreach my $regex (#regex) {
foreach my $line (#lines) {
if ( $line =~ m/$regex\s(.+\n)/i ) {
push( #meanmatches, $1 );
}
}
my $average = average(#meanmatches);
my $std_dev = std_dev( $average, #meanmatches );
my $average_round = sprintf( "%0.4f", $average );
my $stdev_round = sprintf( "%0.4f", $std_dev );
my $coefficient_of_variation = $stdev_round / $average_round;
my $cv_round = sprintf( "%0.4f", $coefficient_of_variation );
print font(
{ color => "blue" }, "<br><B>$regex average: $average_round
 Standard deviation: $stdev_round Coefficient of
variation(Cv): $cv_round</B>"
);
}
sub average {
my (#values) = #_;
my $count = scalar #values;
my $total = 0;
$total += $_ for #values;
return $count ? $total / $count : 0;
}
sub std_dev {
my ( $average, #values ) = #_;
my $count = scalar #values;
my $std_dev_sum = 0;
$std_dev_sum += ( $_ - $average )**2 for #values;
return $count ? sqrt( $std_dev_sum / $count ) : 0;
}
The problem here is that starting from the second iteration of foreach you are trying to read from already read file handle. You need to rewind to the beginning to read it again:
foreach $regex (#regex) {
seek FILE, 0, 0;
while ( my $line = <FILE> ) {
However that does not look very performant. Why read file several times at all, when you can read it once before the foreach starts, and then iterate through the list:
my #lines;
while (<FILE>) {
push (#lines, $_);
}
foreach $regex (#regex) {
foreach $line (#lines) {
Having the latter, you might also what to consider using grep instead of the while loop.
This is the program as it stands right now, it takes in a .fasta file (a file containing genetic code), creates a hash table with the data and prints it, however, it is quite slow. It splits a string an compares it against all other letters in the file.
use strict;
use warnings;
use Data::Dumper;
my $total = $#ARGV + 1;
my $row;
my $compare;
my %hash;
my $unique = 0;
open( my $f1, '<:encoding(UTF-8)', $ARGV[0] ) or die "Could not open file '$ARGV[0]' $!\n";
my $discard = <$f1>;
while ( $row = <$f1> ) {
chomp $row;
$compare .= $row;
}
my $size = length($compare);
close $f1;
for ( my $i = 0; $i < $size - 6; $i++ ) {
my $vs = ( substr( $compare, $i, 5 ) );
for ( my $j = 0; $j < $size - 6; $j++ ) {
foreach my $value ( substr( $compare, $j, 5 ) ) {
if ( $value eq $vs ) {
if ( exists $hash{$value} ) {
$hash{$value} += 1;
} else {
$hash{$value} = 1;
}
}
}
}
}
foreach my $val ( values %hash ) {
if ( $val == 1 ) {
$unique++;
}
}
my $OUTFILE;
open $OUTFILE, ">output.txt" or die "Error opening output.txt: $!\n";
print {$OUTFILE} "Number of unique keys: " . $unique . "\n";
print {$OUTFILE} Dumper( \%hash );
close $OUTFILE;
Thanks in advance for any help!
It is not clear from the description what is wanted from this script, but if you're looking for matching sets of 5 characters, you don't actually need to do any string matching: you can just run through the whole sequence and keep a tally of how many times each 5-letter sequence occurs.
use strict;
use warnings;
use Data::Dumper;
my $str; # store the sequence here
my %hash;
# slurp in the whole file
open(IN, '<:encoding(UTF-8)', $ARGV[0]) or die "Could not open file '$ARGV[0]' $!\n";
while (<IN>) {
chomp;
$str .= $_;
}
close(IN);
# not sure if you were deliberately omitting the last two letters of sequence
# this looks at all the sequence
my $l_size = length($str) - 4;
for (my $i = 0; $i < $l_size; $i++) {
$hash{ substr($str, $i, 5) }++;
}
# grep in a scalar context will count the values.
my $unique = grep { $_ == 1 } values %hash;
open OUT, ">output.txt" or die "Error opening output.txt: $!\n";
print OUT "Number of unique keys: ". $unique."\n";
print OUT Dumper(\%hash);
close OUT;
It might help to remove searching for information that you already have.
I don't see that $j depends upon $i so you're actually matching values to themselves.
So you're getting bad counts as well. It works for 1, because 1 is the square of 1.
But if for each five-character string you're counting strings that match, you're going
to get the square of the actual number.
You would actually get better results if you did it this way:
# compute it once.
my $lim = length( $compare ) - 6;
for ( my $i = 0; $i < $lim; $i++ ){
my $vs = substr( $compare, $i, 5 );
# count each unique identity *once*
# if it's in the table, we've already counted it.
next if $hash{ $vs };
$hash{ $vs }++; # we've found it, record it.
for ( my $j = $i + 1; $j < $lim; $j++ ) {
my $value = substr( $compare, $j, 5 );
$hash{ $value }++ if $value eq $vs;
}
}
However, it could be an improvement on this to do an index for your second loop
and let the c-level of perl do your matching for you.
my $pos = $i;
while ( $pos > -1 ) {
$pos = index( $compare, $vs, ++$pos );
$hash{ $vs }++ if $pos > -1;
}
Also, if you used index, and wanted to omit the last two characters--as you do, it might make sense to remove those from the characters you have to search:
substr( $compare, -2 ) = ''
But you could do all of this in one pass, as you loop through file. I believe the code
below is almost an equivalent.
my $last_4 = '';
my $last_row = '';
my $discard = <$f1>;
# each row in the file after the first...
while ( $row = <$f1> ) {
chomp $row;
$last_row = $row;
$row = $last_4 . $row;
my $lim = length( $row ) - 5;
for ( my $i = 0; $i < $lim; $i++ ) {
$hash{ substr( $row, $i, 5 ) }++;
}
# four is the maximum we can copy over to the new row and not
# double count a strand of characters at the end.
$last_4 = substr( $row, -4 );
}
# I'm not sure what you're getting by omitting the last two characters of
# the last row, but this would replicate it
foreach my $bad_key ( map { substr( $last_row, $_ ) } ( -5, -6 )) {
--$hash{ $bad_key };
delete $hash{ $bad_key } if $hash{ $bad_key } < 1;
}
# grep in a scalar context will count the values.
$unique = grep { $_ == 1 } values %hash;
You may be interested in this more concise version of your code that uses a global regex match to find all the subsequences of five characters. It also reads the entire input file in one go, and removes the newlines afterwards.
The path to the input file is expected as a parameter on the command line, and the output is sent to STDIN, and can be redirected to a file on the command line, like this
perl subseq5.pl input.txt > output.txt
I've also used Data::Dump instead of Data::Dumper because I believe it to be vastly superior. However it is not a core module, and so you will probably need to install it.
use strict;
use warnings;
use open qw/ :std :encoding(utf-8) /;
use Data::Dump;
my $str = do { local $/; <>; };
$str =~ tr|$/||d;
my %dups;
++$dups{$1} while $str =~ /(?=(.{5}))/g;
my $unique = grep $_ == 1, values %dups;
print "Number of unique keys: $unique\n";
dd \%dups;