I am having an error saying that prototype not terminated at filename.txt line number 113 where as line number 113 belongs to a different program which is running successfully.
sub howmany(
my #H = #_;
my $m = 0;
foreach $x (#H) {
if ( $x > 5 ) {
$m +=1;
}
else {
$m +=0;
}
}
print "Number of elements greater than 5 is equal to: $m \n";
}
howmany(1,6,9);
The sub keyword should be followed by { } not ( ) (if you define a simple function), that's why the error
prototype not terminated
After this, always start with : use strict; use warnings;
Put this and debug your script, there's more errors.
Last but not least, indent your code properly, using an editor with syntax highlighting, you will save many time debugging
The error is due to parenthesis.
Never do $m += 0; As you actually load processor for nothing. Of course it's not gonna be visible on such a small function, but...
sub howmany {
my $m = 0;
foreach (#_) {
$m++ if ($_ > 5);
}
print "Number of elements greater than 5 is equal to: $m \n";
}
howmany(1,6,9);
Related
I am trying to find two character strings in a text file and print them and their frequencies out.
#!/usr/bin/perl
#digram finder
use strict; use warnings;
#finds digrams in a file and prints them and their frequencies out
die "Must input file\n" if (#ARGV != 1);
my ($file) = #ARGV;
my %wordcount;
open (my $in, "<$file") or die "Can't open $file\n";
while (my $words = <$in>){
chomp $words;
my $length = length($words);
for (my $i = 0; $i<$length; $i++){
my $duo = substr($words, $i; 2);
if (not exists $wordcount{$duo}){
$wordcount{$duo} = 1;
}
else {
$wordcount{$duo}++;
}
}
}
foreach my $word (sort {$wordcount{$b} cmp $wordcount{$a}} keys %wordcount){
print "$word\t$wordcount{$duo}\n";
}
close($in);
First I set the text file to a string $words.
Then, I run a for loop and create a substring $duo at each position along $words
If $duo doesn't exist within the hash %wordcount, then the program creates the key $duo
If $duo does exist, then the count for that key goes up by 1
Then the program prints out the digrams and their frequencies, in order of decreasing frequency
When I try to run the code, I get the error message that I forgot to declare $word on line 17 but I do not even have the string $word. I am not sure where this error message is coming from. Can someone help me find where the error is coming from?
Thank you
My best guess is that you actually have $word instead of $words; a typo. If the compilation found the symbol $word in the text then it's probably there.
However, I'd also like to comment on the code. A cleaned up version
while (my $words = <$in>) {
chomp $words;
my $last_duo_idx = length($words) - 2;
for my $i (0 .. $last_duo_idx) {
my $duo = substr($words, $i, 2);
++$wordcount{$duo};
}
}
my #skeys = sort { $wordcount{$b} <=> $wordcount{$a} } keys %wordcount;
foreach my $word (#skeys) {
print "$word\t$wordcount{$word}\n";
}
This runs correctly on a made-up file. (I sort separately only so to not run off of the page.)
Comments
Need to stop one before last in the line, and substr starts from 0; thus -2
One almost never needs a C-style loop
There is no need here to test for existence of a key. If it doesn't exist it is autovivified (created), then incremented to 1 with ++; otherwise the count is incremented.
To sort numerically use <=>, not cmp
Typos:
substr($words, $i; 2) needs a , not ;, so substr($words, $i, 2)
$wordcount{$duo} in print should be $wordcount{$word}.
I am not sure about naming: why is a line of text called $words?
I'm making a simple fortune teller program for a class. I wanted to start by having the user choose between four numbers, like on a paper fortune teller (cootie catcher, as it were).
I created an array, #number_choices = ( 1, 2, 3, 4 ); and I wanted to make sure the user input was equal to one of the numbers in the array. Here is what I have so far, which is not working at all (when I run the program, it prints the error message no matter what number I enter, except for sometimes 2 or 1):
my $number_chosen = <STDIN>;
chomp ($number_chosen);
my $num;
my $found = 0;
while ( $found == 0 )
{
foreach $num (#number_choices)
{
if ($number_chosen == $num)
{
$found = 1;
last;
}
else
{
print "I'm sorry, that number is not valid. Please pick a number: " . join(', ', #number_choices) . "\n";
$number_chosen = <STDIN>;
chomp ($number_chosen);
}
}
}
You have a logic error. You choose a number but for every loop through the array it makes you choose another one, so if in the second loop you enter number 2 it will be right regardless of your first input, and same number 3 for third loop.
You should put the error message out of the foreach loop and ask for a number inside the while. Besides that, the last only goes out of the nearest loop, so you need to use a label to go out of the while. Something similar to following dirty solution:
my #number_choices = (1, 2, 3, 4);
my $num;
my $found = 0;
LOOP:
while ( $found == 0 )
{
$number_chosen = <STDIN>;
chomp ($number_chosen);
foreach $num (#number_choices)
{
if ($number_chosen == $num)
{
$found = 1;
last LOOP;
}
}
print "I'm sorry, that number is not valid. Please pick a number: " . join(', ', #number_choices) . "\n";
}
I need to test a file with each line having the same number of columns and each entry is some value and I want to only select those lines with every values greater than, say 0.5.
I know I can loop through the array in each line by doing something like this:
open (IN, shift #ARGV);
while (<IN>){
chomp;
my $count = 0;
my #array = split/\t/;
foreach (#array){
if ($_ > 0.5) {
$count ++;
}
}
if ($count == scalar #array){
print $_,"\n";
}
}
close IN;
This is kinda long and I'm wondering if there is a better way to do it?
Thanks.
Use all from List::Util - it checks if passed code block (often with condition) returns true for all elements of list.
use List::Util qw(all);
if (all { $_ > 0.5 } #array) {
print "Pass!"
}
It will even short-circuit for you, terminating as soon as it finds first false value, producing most speed-effective result.
my #array = 10 .. 20;
# compare size of array with list size of grep
if (#array == grep { $_ > 0.5 } #array) {
print "All are greater than 0.5\n";
}
I have a Perl-Script, which executes a recursive function. Within it compares two elements of a 2dimensional Array:
I call the routine with a 2D-Array "#data" and "0" as a starting value. First I load the parameters into a separate 2D-Array "#test"
Then I want to see, if the array contains only one Element --> Compare if the last Element == the first. And this is where the Error occurs: Modification of non creatable array value attempted, subscript -1.
You tried to make an array value spring into existence, and the subscript was probably negative, even counting from end of the array backwards.
This didn't help me much...I'm pretty sure it has to do with the if-clause "$counter-1". But I don't know what, hope you guys can help me!
routine(#data,0);
sub routine {
my #test #(2d-Array)
my $counter = $_[-1]
for(my $c=0; $_[$c] ne $_[-1]; $c++){
for (my $j=0; $j<13;$j++){ #Each element has 13 other elements
$test[$c][$j] = $_[$c][$j];
}
}
if ($test[$counter-1][1] eq $test[-1][1]{
$puffertime = $test[$counter][4];
}
else{
for (my $l=0; $l<=$counter;$l++){
$puffertime+= $test[$l][4]
}
}
}
#
#
#
if ($puffertime <90){
if($test[$counter][8]==0){
$counter++;
routine(#test,$counter);
}
else{ return (print"false");}
}
else{return (print "true");}
Weird thing is that I tried it out this morning, and it worked. After a short time of running he again came up with this error message. Might be that I didn't catch up a error constellation, which could happen by the dynamic database-entries.
Your routine() function would be easier to read if it starts off like this:
sub routine {
my #data = #_;
my $counter = pop(#data);
my #test;
for(my $c=0; $c <= $#data; $c++){
for (my $j=0; $j<13;$j++){ #Each element has 13 other elements
$test[$c][$j] = $data[$c][$j];
}
}
You can check to see if #data only has one element by doing scalar(#data) == 1 or $#data == 0. From your code snippet, I do not see why you need to copy the data to passed to routine() to #test. Seems superfluous. You can just as well skip all this copying if you are not going to modify any of the data passed to your routine.
Your next code might look like this:
if ($#test == 0) {
$puffertime = $test[0][4];
} else {
for (my $l=0; $l <= $counter; $l++) {
$puffertime += $test[$l][4];
}
}
But if your global variable $puffertime was initialized to zero then you can replace this code with:
for (my $l=0; $l <= $counter; $l++) {
$puffertime += $test[$l][4];
}
I have a program that creates an array of hashes while parsing a FASTA file. Here is my code
use strict;
use warnings;
my $docName = "A_gen.txt";
my $alleleCount = 0;
my $flag = 1;
my $tempSequence;
my #tempHeader;
my #arrayOfHashes = ();
my $fastaDoc = open(my $FH, '<', $docName);
my #fileArray = <$FH>;
for (my $i = 0; $i <= $#fileArray; $i++) {
if ($fileArray[$i] =~ m/>/) { # creates a header for the hashes
$flag = 0;
$fileArray[$i] =~ s/>//;
$alleleCount++;
#tempHeader = split / /, $fileArray[$i];
pop(#tempHeader); # removes the pointless bp
for (my $j = 0; $j <= scalar(#tempHeader)-1; $j++) {
print $tempHeader[$j];
if ($j < scalar(#tempHeader)-1) {
print " : "};
if ($j == scalar(#tempHeader) - 1) {
print "\n";
};
}
}
# push(#arrayOfHashes, "$i");
if ($fileArray[$i++] =~ m/>/) { # goes to next line
push(#arrayOfHashes, {
id => $tempHeader[0],
hla => $tempHeader[1],
bpCount => $tempHeader[2],
sequence => $tempSequence
});
print $arrayOfHashes[0]{id};
#tempHeader = ();
$tempSequence = "";
}
$i--; # puts i back to the current line
if ($flag == 1) {
$tempSequence = $tempSequence.$fileArray[$i];
}
}
print $arrayOfHashes[0]{id};
print "\n";
print $alleleCount."\n";
print $#fileArray +1;
My problem is when the line
print $arrayOfHashes[0]{id};
is called, I get an error that says
Use of uninitialized value in print at fasta_tie.pl line 47, line 6670.
You will see in the above code I commented out a line that says
push(#arrayOfHashes, "$i");
because I wanted to make sure that the hash works. Also the data prints correctly in the
desired formatting. Which looks like this
HLA:HLA00127 : A*74:01 : 2918
try to add
print "Array length:" . scalar(#arrayOfHashes) . "\n";
before
print $arrayOfHashes[0]{id};
So you can see, if you got some content in your variable. You can also use the module Data::Dumper to see the content.
use Data::Dumper;
print Dumper(\#arrayOfHashes);
Note the '\' before the array!
Output would be something like:
$VAR1 = [
{
'sequence' => 'tempSequence',
'hla' => 'hla',
'bpCount' => 'bpCount',
'id' => 'id'
}
];
But if there's a Module for Fasta, try to use this. You don't have to reinvent the wheel each time ;)
First you do this:
$fileArray[$i] =~ s/>//;
Then later you try to match like this:
$fileArray[$i++] =~ m/>/
You step through the file array, removing the first "greater than" sign in the line on each line. And then you want to match the current line by that same character. That would be okay if you only want to push the line if it has a second "greater than", but you will never push anything into the array if you only expect 1, or there turns out to be only one.
Your comment "puts i back to the current line" shows what you were trying to do, but if you only use it once, why not use the expression $i + 1?
Also, because you're incrementing it post-fix and not using it for anything, your increment has no effect. If $i==0 before, then $fileArray[$i++] still accesses $fileArray[0], only $i==1 after the expression has been evaluated--and to no effect--until being later decremented.
If you want to peek ahead, then it is better to use the pre-fix increment:
if ($fileArray[++$i] =~ m/>/) ...