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?
Related
I'm new to Stack Overflow and I would like to ask for some advice with regard to a minor problem I have with my Perl code.
In short, I have written a small programme that opens text files from a pre-defined array, then searches for certain strings in them and finally prints out the line containing the string.
my #S1A_SING_Files = (
'S1A-001_SING_annotated.txt',
'S1A-002_SING_annotated.txt',
'S1A-003_SING_annotated.txt',
'S1A-004_SING_annotated.txt',
'S1A-005_SING_annotated.txt'
);
foreach (#S1A_SING_Files) {
print ("\n");
print ("Search results for $_:\n\n");
open (F, $_) or die("Can't open file!\n");
while ($line = <F>) {
if ($line =~ /\$(voc)?[R|L]D|\$Rep|\/\//) {
print ($line);
}
}
}
close (F);
I was wondering whether it is possible to create an exception to the foreach loop, so that the line containing
print ("\n");
not be executed if the file is $S1A_SING_Files[0]. It should then be normally executed if the file is any of the following ones. Do you think this could be accomplished?
Thank you very much in advance!
Yes. Just add a check for the first file. Change:
print ("\n");
to:
print ("\n") if $_ ne $S1A_SING_Files[0];
If the array contains unique strings, you can use the following:
print("\n") if $_ ne $S1A_SING_Files[0]; # Different stringification than 1st element?
The following will work even if the array contains non-strings or duplicate values (and it's faster too):
print("\n") if \$_ != \$S1A_SING_Files[0]; # Different scalar than 1st element?
Both of the above could fail for magical arrays. The most reliable solution is to iterate over the indexes.
for my $i (0..$#S1A_SING_Files) {
my $file = $S1A_SING_Files[$i];
print("\n") if $i; # Different index than 1st element?
...
}
Your code can be written in following form
use strict;
use warnings;
my #S1A_SING_Files = (
'S1A-001_SING_annotated.txt',
'S1A-002_SING_annotated.txt',
'S1A-003_SING_annotated.txt',
'S1A-004_SING_annotated.txt',
'S1A-005_SING_annotated.txt'
);
foreach (#S1A_SING_Files) {
print "\n" unless $_ ne $S1A_SING_Files[0];
print "Search results for $_:\n\n";
open my $fh, '<', $_ or die("Can't open file!\n");
m!\$(voc)?[R|L]D|\$Rep|//! && print while <$fh>;
close $fh;
}
Hello I am in the process of making a program that matches a given set of keywords to a file.
I want to output the matched data to a text file and include the regex keyword that triggered the match.
Below is my code related to my issue:
my $counter = 0;
foreach($words)
{
while($line = <FILE>)
{
if($line =~ /$words/)
{
print "#array[$counter] $line\n";
print OUTPUT $line;
}
}
$counter ++;
}
This does not produce the expected outcome. It works perfectly for the first element in the array but for the rest it just simply prints the first one again. I believe the counter is not being incremented.
Is there a better / easier way to get the current element being used in the loop? or even get the current regex match?
The problem is that <FILE> exhausts the file for the first word. For the next word, <FILE> tries to read at the end of the file, which means the whole loop is skipped.
You can iterate over the words inside the loop over the file, or you can seek
back to the beginning of the file at the end of the loop.
Here is what you should do:
use strict;
use warnings;
use 5.016;
my $fname = 'data.txt';
my #patterns = (
'do.',
'.at',
'.ir.',
);
open my $INFILE, '<', $fname
or die "Couldn't read from $fname: $!";
while (my $line = <$INFILE>) {
for my $pattern (#patterns) {
if ($line =~ /($pattern)/) {
print "$pattern --> $1";
}
}
}
close $INFILE:
Putting parentheses around parts of the regex causes perl to set the match variables $1, $2, $3, etc., which contain the match for each parenthesized group.
$line will have a newline at the end of the line, so if you write print "$line\n", you will add another newline, so your output file will have blank lines between every line you print.
I am trying to print the first 250 entries in an array to a .txt file, but I am having some trouble. When I run the script as is, I get nothing in my output.txt file.
#! /usr/bin/perl
use strict;
use warnings;
my $line;
my #array;
my $file = "moloch_chunker_output.txt";
open (OUT , ">","moloch_chunker_output.txt")or die "cant open: $!";
while ($line = <>){
chomp($line);
push(#array, $line);
if(#array == 250){
print OUT #array;
}
}
I know that I'm missing quite a bit here, but I have tried a couple of other methods after the if statement.
if(array == 250){
print "[", join(",",#array),"]","\n";
works exactly how I want. I just want it to be written to a .txt file instead of simply being printed to the screen. How can I print the array to a .txt file?
Instead of stuffing everything into an array and then printing the array contents when its size gets to 250, perhaps you could simply start a counter and print each line as you see it (and then quit once you reach 250). Kinda like:
$cnt = 0;
while (<>) {
chomp;
print;
last if ++$cnt >= 250;
}
Or... you could just run head -250 moloch_chunker_output.txt from the command line (and skip Perl altogether).
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/>/) ...
The purpose of the script is to process all words from a file and output ALL words that occur the most. So if there are 3 words that each occur 10 times, the program should output all the words.
The script now runs, thanks to some tips I have gotten here. However, it does not handle large text files (i.e. the New Testament). I'm not sure if that is a fault of mine or just a limitation of the code. I am sure there are several other problems with the program, so any help would be greatly appreciated.
#!/usr/bin/perl -w
require 5.10.0;
print "Your file: " . $ARGV[0] . "\n";
#Make sure there is only one argument
if ($#ARGV == 0){
#Make sure the argument is actually a file
if (-f $ARGV[0]){
%wordHash = (); #New hash to match words with word counts
$file=$ARGV[0]; #Stores value of argument
open(FILE, $file) or die "File not opened correctly.";
#Process through each line of the file
while (<FILE>){
chomp;
#Delimits on any non-alphanumeric
#words=split(/[^a-zA-Z0-9]/,$_);
$wordSize = #words;
#Put all words to lowercase, removes case sensitivty
for($x=0; $x<$wordSize; $x++){
$words[$x]=lc($words[$x]);
}
#Puts each occurence of word into hash
foreach $word(#words){
$wordHash{$word}++;
}
}
close FILE;
#$wordHash{$b} <=> $wordHash{$a};
$wordList="";
$max=0;
while (($key, $value) = each(%wordHash)){
if($value>$max){
$max=$value;
}
}
while (($key, $value) = each(%wordHash)){
if($value==$max && $key ne "s"){
$wordList.=" " . $key;
}
}
#Print solution
print "The following words occur the most (" . $max . " times): " . $wordList . "\n";
}
else {
print "Error. Your argument is not a file.\n";
}
}
else {
print "Error. Use exactly one argument.\n";
}
Your problem lies in the two missing lines at the top of your script:
use strict;
use warnings;
If they had been there, they would have reported lots of lines like this:
Argument "make" isn't numeric in array element at ...
Which comes from this line:
$list[$_] = $wordHash{$_} for keys %wordHash;
Array elements can only be numbers, and since your keys are words, that won't work. What happens here is that any random string is coerced into a number, and for any string that does not begin with a number, that will be 0.
Your code works fine reading the data in, although I would write it differently. It is only after that that your code becomes unwieldy.
As near as I can tell, you are trying to print out the most occurring words, in which case you should consider the following code:
use strict;
use warnings;
my %wordHash;
#Make sure there is only one argument
die "Only one argument allowed." unless #ARGV == 1;
while (<>) { # Use the diamond operator to implicitly open ARGV files
chomp;
my #words = grep $_, # disallow empty strings
map lc, # make everything lower case
split /[^a-zA-Z0-9]/; # your original split
foreach my $word (#words) {
$wordHash{$word}++;
}
}
for my $word (sort { $wordHash{$b} <=> $wordHash{$a} } keys %wordHash) {
printf "%-6s %s\n", $wordHash{$word}, $word;
}
As you'll note, you can sort based on hash values.
Here is an entirely different way of writing it (I could have also said "Perl is not C"):
#!/usr/bin/env perl
use 5.010;
use strict; use warnings;
use autodie;
use List::Util qw(max);
my ($input_file) = #ARGV;
die "Need an input file\n" unless defined $input_file;
say "Input file = '$input_file'";
open my $input, '<', $input_file;
my %words;
while (my $line = <$input>) {
chomp $line;
my #tokens = map lc, grep length, split /[^A-Za-z0-9]+/, $line;
$words{ $_ } += 1 for #tokens;
}
close $input;
my $max = max values %words;
my #argmax = sort grep { $words{$_} == $max } keys %words;
for my $word (#argmax) {
printf "%s: %d\n", $word, $max;
}
why not just get the keys from the hash sorted by their value and extract the first X?
this should provide an example: http://www.devdaily.com/perl/edu/qanda/plqa00016