Related
$text = "I like apples more than oranges\n";
#words = split /” “/, $text;
foreach (#words) [1..] {
if $words "AEIOUaeiou";
$words =~ tr/A E I O U a e i o u//d;
}
print "$words\n";
"I like apples more than oranges" will become "I lk appls mr thn orngs". "I" in "I", "a" in "appls" and "o" in "orngs" will stay because they are the first letter in the word.
This is my research assignment as a first year student. I am allowed to ask questions and later cite them. Please don't be mean.
I know you say you are not allowed to use a regex, but for everyone else that shows up here I'll show the use of proper tools. But, then I'll do something just as useful with tr///.
One of the tricks of programming (and mathematics) decomposing what look like hard problems into easier problems, especially if you already have solutions for the easy problems. (Read about Parnas decomposition, for example).
So, the question is "How can I remove all the vowels unless they are in word beginnings?" (after I made your title a bit shorter). This led the answers to think about words, so they split up the input, did some work to ensure they weren't working on the first character, and then reassembled the result.
But, another way to frame the problem is "How do I remove all the vowels that come after another letter?". The only letter that doesn't come after another letter is the first letter of a word.
The regex for a vowel that comes after another letter is simple (but I'll stick to ASCII here, although it is just as simple for any Unicode letter):
[a-z][aeiou]
That only matches when there is a vowel after the first letter. Now you want to replace all of those with nothing. Use the substitution operator, s///. The /g flag makes all global substitutions and the /i makes it case insensitive:
s/[a-z][aeiou]//gi;
But, there's a problem. It also replaces that leading letter. That's easy enough to fix. The \K in a substitution says to ignore the part of the pattern before it in the replacement. Anything before the \K is not replaced. So, this only replaces the vowels:
s/[a-z]\K[aeiou]//gi;
But, maybe there are vowels next to each other, so throw in the + quantifier for "one or more" of the preceding item:
s/[a-z]\K[aeiou]+//gi;
You don't need to care about words at all.
Some other ways
Saying that a letter must follow another letter has a special zero-width assertion: the non-word boundary, \B (although that also counts digits and underscore as "letters"):
s/\B[aeiou]+//gi;
The \K was introduced v5.10 and was really a nifty trick to have a variable-width lookbehind. But, the lookbehind here is fixed width: it's one character:
s/(?<=[a-z])[aeiou]+//gi;
But, caring about words
Suppose you need to handle each word separately, for some other requirement. It looks like you've mixed a little Python-ish sort of code, and it would be nice if Perl could do that :). The problem doesn't change that much because you can do the same thing for each individual word.
foreach my $word ( split /\s+/, $x ) {
.... # same thing for each word
}
But, here's an interesting twist? How do you put it all back together? The other solutions just use a single space assuming that's the separator. Maybe there should be two spaces, or tabs, or whatever. The split has a special "separator retention mode" that can keep whatever was between the pieces. When you have captures in the split pattern, those capture values are part of the output list:
my #words_and_separators = split /(\s+)/, $x;
Since you know that none of the separators will have vowels, you can make substitutions on them knowing they won't change. This means you can treat them just like the words (that is, there is no special case, which is another thing to think about as you decompose problems). To get your final string with the original spacing, join on the empty string:
my $ending_string = join '', #words_and_separators;
So, here's how that might all look put together. I'll add the /r flag on the substitution so it returns the modified copy instead of working on the original (don't modify the control variable!):
my #words;
foreach my $word ( split /(\s+)/, $x ) {
push #words, $word =~ s/\B[aeiou]+//gr;
}
my $ending_string = join '', #words;
But, that foreach is a bit annoying. This list pipeline is the same, and it's easier to read these bottom to top. Each thing produces a list that flows into the thing above it. This is how I'd probably express it in real code:
my $ending_string =
join '',
map { s/\B[aeiou]+//gr } # each item is in $_
split /(\s+)/, $x;
Now, here's the grand finale. What if we didn't split thing up on whitespace but on whitespace and the first letter of each word? With separator retention mode we know that we only have to affect every other item, so we count them as we do the map:
my $n = 0;
my $ending_string =
join '',
map { ++$n % 2 ? tr/aeiouAEIOU//dr : $_ }
split /((?:^|\s+)[a-z])/i, $x;
But, I wouldn't write this technique in this way because someone would ultimately find me and exact their revenge. Instead, that foreach I found annoying before may soothe the angry masses:
my $n = 0;
foreach ( split /((?:^|\s+)[a-z])/i, $x ) {
print ++$n % 2 ? tr/aeiouAEIOU//dr : $_;
}
This now remembers the actual separators from the original string and leaves alone the first character of the "word" because it's not in the element we will modify.
The code in the foreach doesn't need to use the conditional operator, ?: or some of the other features. The important part is skipping every other element. That split pattern is a bit of a puzzler if you haven't seen it before, but that's what you get with those sorts of requirements. I think modifying a portion of the substring is just as likely to trip up people on a first read.
I mean, if they are going to make you do it the wrong way in the homework, strike back with something that will take up a bit of their time. :)
Oh, this is fun
I had another idea, because tr/// has another task beyond transliteration. It also counts. Because it returns the number of replacements, if you replace anything with itself, you get a count of the occurrences of that thing. You can count vowels, for instance:
my $has_vowels = $string =~ tr/aeiou/aeiou/; # counts vowels
But, with a string of one letter, that means you have a way to tell if it is a vowel:
my $is_vowel = substr( $string, $i, 1 ) =~ tr/aeiou/aeiou/;
You also can know things about the previous character:
my $is_letter = substr( $string, $i - 1, 1 ) =~ tr/a-zA-Z/a-zA-Z/;
Put that together and you can look at any position and know if it's a vowel that follows a letter. If so, you skip that letter. Otherwise, you add that letter to the output:
use v5.10;
$x = "I like apples more than oranges oooooranges\n";
my $output = substr $x, 0, 1; # avoid the -1 trap (end of string!)
for( my $i = 1; $i < length $x; $i++ ) {
if( substr( $x, $i, 1 ) =~ tr/aeiou/aeiou/ ) { # is a vowel
next if substr( $x, $i - 1, 1 ) =~ tr/a-zA-Z/a-zA-Z/;
}
$output .= substr $x, $i, 1;
}
say $output;
This has the fun consequence of using the recommended operator but completely bypassing the intent. But, this is a proper and intended use of tr///.
It appears that you need to put a little more effort into learning Perl before taking on challenges like this. Your example contains a lot of code that simply isn't valid Perl.
$x = "I like apples more than oranges\n"; #the original sentence
foreach $i in #x[1..] {
You assign your text to the scalar variable $x, but then try to use the array variable #x. In Perl, these are two completely separate variables that have no connection whatsoever. Also, in Perl, the range operator (..) needs values at both ends.
If you had an array called #x (and you don't, you have a scalar) then you could do what you're trying to do here with foreach $i (#x)
if $i "AEIOUaeiou";
I'm not sure what you're trying to do here. I guess the nearest useful Perl expression I can see would be something like:
if ($i =~ /^[AEIOUaeiou]$/)
Which would test if $i is a vowel. But that's a regex, so you're not allowed to use it.
Obviously, I'd solve this problem with a regex, but as those are banned, I've reached for some slightly more obscure Perl features in my code below (that's so your teacher won't believe this is your solution if you just cut and paste it):
#!/usr/bin/perl
use strict;
use warnings;
use feature 'say';
my $text = "I like apples more than oranges\n";
# Split the string into an array of words
my #words = split /\s+/, $text;
# For each word...
for (#words) {
# Get a substring that omits the first character
# and use tr/// to remove vowels from that substring
substr($_, 1) =~ tr/AEIOUaeiou//d;
}
# Join the array back together
$text = join ' ', #words;
say $text;
Update: Oh, and notice that I've used tr/AEIUOaeiou//d where you have tr/A E I O U a e i o u//d. It probably won't make any difference here (depending on your approach - but you'll probably be applying it to strings that don't contain spaces) but it's good practice to only include the characters that you want to remove.
We can go over the input string from the end and remove any vowel that's not preceded by a space. We go from right to left so we don't have to adjust the position after each deletion. We don't need to check the very first letter, it shouldn't be ever removed. To remove a vowel, we can use tr///d on the substr of the original string.
for my $i (reverse 1 .. length $x) {
substr($x, $i, 1) =~ tr/aeiouAEIOU//d
if substr($x, $i - 1, 1) ne ' ';
}
Firstly your if statement is wrong.
Secondly this is not a Perl code.
Here is a piece of code that will work, but there is a better way to do it
my $x = "I like apples more than oranges\n";
my $new = "";
my #arr;
foreach my $word (split(' ', $x)) {
#arr = split('', $word);
foreach (my $i; $i<scalar #arr; $i++){
if ($i == 0){
$new .= $arr[$i];
}
elsif (index("AEIOUaeiou", $arr[$i]) == -1) {
$new .= $arr[$i];
}
}
$new .= " ";
}
print "$new\n";
Here I am splitting the string in order to get an array, then I am checking if the given char is a vowel, if it's not, I am appending it to a new string.
Always include
use strict;
use warnings;
on top of your code.
Clearly this is an exercise in lvalues. Obviously. Indubitably!
#!/usr/bin/env perl
# any old perl will do
use 5.010;
use strict;
use warnings;
# This is not idomatic nor fantastic code. Idiotastic?
$_='I am yclept Azure-Orange, queueing to close a query. How are YOU?';
# My little paws typed "local pos" and got
# "Useless localization of match position" :(
# so a busy $b keeps/restores that value
while (/\b./g) {
substr($_,$b=pos,/\b/g && -$b+pos)
# Suggestion to use tr is poetic, not pragmatic,
# ~ tr is sometimes y and y is sometimes a vowel
=~ y/aeiouAEIOU//d;
pos=$b;
}
say
# "say" is the last word.
Was there an embargo against using s/// substitution, or against using all regex? For some reason I thought matching was OK, just not substitution. If matches are OK, I have an idea that "improves" upon this by removing $b through pattern matching side effects. Will see if it pans out. If not, should be pretty easy to replace /\b/ and pos with index and variables, though the definition of word boundary over-simplifies in that case.
(edit) here it is a little more legible with nary a regex
my $text="YO you are the one! The-only-person- asking about double spaces.
Unfortunate about newlines...";
for (my $end=length $text;
$end > 0 && (my $start = rindex $text,' ',$end);
$end = $start-1) {
# y is a beautiful letter, using it for vowels is poetry.
substr($text,2+$start,$end-$start) =~ y/aeiouUOIEA//d;
}
say $text;
Maybe more devious minds will succeed with vec, unpack, open, fork?
You can learn about some of these techniques via
perldoc -f substr
perldoc -f pos
perldoc re
As for my own implementer notes, the least important thing is ending without punctuation so nothing can go after
I'm looping through an array, and I want to test if an element is found in another array.
In pseudo-code, what I'm trying to do is this:
foreach $term (#array1) {
if ($term is found in #array2) {
#do something here
}
}
I've got the "foreach" and the "do something here" parts down-pat ... but everything I've tried for the "if term is found in array" test does NOT work ...
I've tried grep:
if grep {/$term/} #array2 { #do something }
# this test always succeeds for values of $term that ARE NOT in #array2
if (grep(/$term/, #array2)) { #do something }
# this test likewise succeeds for values NOT IN the array
I've tried a couple different flavors of "converting the array to a hash" which many previous posts have indicated are so simple and easy ... and none of them have worked.
I am a long-time low-level user of perl, I understand just the basics of perl, do not understand all the fancy obfuscated code that comprises 99% of the solutions I read on the interwebs ... I would really, truly, honestly appreciate any answers that are explicit in the code and provide a step-by-step explanation of what the code is doing ...
... I seriously don't grok $_ and any other kind or type of hidden, understood, or implied value, variable, or function. I would really appreciate it if any examples or samples have all variables and functions named with clear terms ($term as opposed to $_) ... and describe with comments what the code is doing so I, in all my mentally deficient glory, may hope to possibly understand it some day. Please. :-)
...
I have an existing script which uses 'grep' somewhat succesfully:
$rc=grep(/$term/, #array);
if ($rc eq 0) { #something happens here }
but I applied that EXACT same code to my new script and it simply does NOT succeed properly ... i.e., it "succeeds" (rc = zero) when it tests a value of $term that I know is NOT present in the array being tested. I just don't get it.
The ONLY difference in my 'grep' approach between 'old' script and 'new' script is how I built the array ... in old script, I built array by reading in from a file:
#array=`cat file`;
whereas in new script I put the array inside the script itself (coz it's small) ... like this:
#array=("element1","element2","element3","element4");
How can that result in different output of the grep function? They're both bog-standard arrays! I don't get it!!!! :-(
########################################################################
addendum ... some clarifications or examples of my actual code:
########################################################################
The term I'm trying to match/find/grep is a word element, for example "word123".
This exercise was just intended to be a quick-n-dirty script to find some important info from a file full of junk, so I skip all the niceties (use strict, warnings, modules, subroutines) by choice ... this doesn't have to be elegant, just simple.
The term I'm searching for is stored in a variable which is instantiated via split:
foreach $line(#array1) {
chomp($line); # habit
# every line has multiple elements that I want to capture
($term1,$term2,$term3,$term4)=split(/\t/,$line);
# if a particular one of those terms is found in my other array 'array2'
if (grep(/$term2/, #array2) {
# then I'm storing a different element from the line into a 3rd array which eventually will be outputted
push(#known, $term1) unless $seen{$term1}++;
}
}
see that grep up there? It ain't workin right ... it is succeeding for all values of $term2 even if it is definitely NOT in array2 ... array1 is a file of a couple thousand lines. The element I'm calling $term2 here is a discrete term that may be in multiple lines, but is never repeated (or part of a larger string) within any given line. Array2 is about a couple dozen elements that I need to "filter in" for my output.
...
I just tried one of the below suggestions:
if (grep $_ eq $term2, #array2)
And this grep failed for all values of $term2 ... I'm getting an all or nothing response from grep ... so I guess I need to stop using grep. Try one of those hash solutions ... but I really could use more explanation and clarification on those.
This is in perlfaq. A quick way to do it is
my %seen;
$seen{$_}++ for #array1;
for my $item (#array2) {
if ($seen{$item}) {
# item is in array2, do something
}
}
If letter case is not important, you can set the keys with $seen{ lc($_) } and check with if ($seen{ lc($item) }).
ETA:
With the changed question: If the task is to match single words in #array2 against whole lines in #array1, the task is more complicated. Trying to split the lines and match against hash keys will likely be unsafe, because of punctuation and other such things. So, a regex solution will likely be the safest.
Unless #array2 is very large, you might do something like this:
my $rx = join "|", #array2;
for my $line (#array1) {
if ($line =~ /\b$rx\b/) { # use word boundary to avoid partial matches
# do something
}
}
If #array2 contains meta characters, such as *?+|, you have to make sure they are escaped, in which case you'd do something like:
my $rx = join "|", map quotemeta, #array2;
# etc
You could use the (infamous) "smart match" operator, provided you are on 5.10 or later:
#!/usr/bin/perl
use strict;
use warnings;
my #array1 = qw/a b c d e f g h/;
my #array2 = qw/a c e g z/;
print "a in \#array1\n" if 'a' ~~ #array1;
print "z in \#array1\n" if 'z' ~~ #array1;
print "z in \#array2\n" if 'z' ~~ #array2;
The example is very simple, but you can use an RE if you need to as well.
I should add that not everyone likes ~~ because there are some ambiguities and, um, "undocumented features". Should be OK for this though.
This should work.
#!/usr/bin/perl
use strict;
use warnings;
my #array1 = qw/a b c d e f g h/;
my #array2 = qw/a c e g z/;
for my $term (#array1) {
if (grep $_ eq $term, #array2) {
print "$term found.\n";
}
}
Output:
a found.
c found.
e found.
g found.
#!/usr/bin/perl
#ar = ( '1','2','3','4','5','6','10' );
#arr = ( '1','2','3','4','5','6','7','8','9' ) ;
foreach $var ( #arr ){
print "$var not found\n " if ( ! ( grep /$var/, #ar )) ;
}
Pattern matching is the most efficient way of matching elements. This would do the trick. Cheers!
print "$element found in the array\n" if ("#array" =~ m/$element/);
Your 'actual code' shouldn't even compile:
if (grep(/$term2/, #array2) {
should be:
if (grep (/$term2/, #array2)) {
You have unbalanced parentheses in your code. You may also find it easier to use grep with a callback (code reference) that operates on its arguments (the array.) It helps keep the parenthesis from blurring together. This is optional, though. It would be:
if (grep {/$term2/} #array2) {
You may want to use strict; and use warnings; to catch issues like this.
The example below might be helpful, it tries to see if any element in #array_sp is present in #my_array:
#! /usr/bin/perl -w
#my_array = qw(20001 20003);
#array_sp = qw(20001 20002 20004);
print "#array_sp\n";
foreach $case(#my_array){
if("#array_sp" =~ m/$case/){
print "My God!\n";
}
}
use pattern matching can solve this. Hope it helps
-QC
1. grep with eq , then
if (grep {$_ eq $term2} #array2) {
print "$term2 exists in the array";
}
2. grep with regex , then
if (grep {/$term2/} #array2) {
print "element with pattern $term2 exists in the array";
}
I want to see if I have repeated items in my array, there are over 16.000 so will automate it
There may be other ways but I started with this and, well, would like to finish it unless there is a straightforward command. What I am doing is shifting and pushing from one array into another and this way, check the destination array to see if it is "in array" (like there is such a command in PHP).
So, I got this sub routine and it works with literals, but it doesn't with variables. It is because of the 'eq' or whatever I should need. The 'sourcefile' will contain one or more of the words of the destination array.
// Here I just fetch my file
$listamails = <STDIN>;
# Remove the newlines filename
chomp $listamails;
# open the file, or exit
unless ( open(MAILS, $listamails) ) {
print "Cannot open file \"$listamails\"\n\n";
exit;
}
# Read the list of mails from the file, and store it
# into the array variable #sourcefile
#sourcefile = <MAILS>;
# Close the handle - we've read all the data into #sourcefile now.
close MAILS;
my #destination = ('hi', 'bye');
sub in_array
{
my ($destination,$search_for) = #_;
return grep {$search_for eq $_} #$destination;
}
for($i = 0; $i <=100; $i ++)
{
$elemento = shift #sourcefile;
if(in_array(\#destination, $elemento))
{
print "it is";
}
else
{
print "it aint there";
}
}
Well, if instead of including the $elemento in there I put a 'hi' it does work and also I have printed the value of $elemento which is also 'hi', but when I put the variable, it does not work, and that is because of the 'eq', but I don't know what else to put. If I put == it complains that 'hi' is not a numeric value.
When you want distinct values think hash.
my %seen;
#seen{ #array } = ();
if (keys %seen == #array) {
print "\#array has no duplicate values\n";
}
It's not clear what you want. If your first sentence is the only one that matters ("I want to see if I have repeated items in my array"), then you could use:
my %seen;
if (grep ++$seen{$_} >= 2, #array) {
say "Has duplicates";
}
You said you have a large array, so it might be faster to stop as soon as you find a duplicate.
my %seen;
for (#array) {
if (++$seen{$_} == 2) {
say "Has duplicates";
last;
}
}
By the way, when looking for duplicates in a large number of items, it's much faster to use a strategy based on sorting. After sorting the items, all duplicates will be right next to each other, so to tell if something is a duplicate, all you have to do is compare it with the previous one:
#sorted = sort #sourcefile;
for (my $i = 1; $i < #sorted; ++$i) { # Start at 1 because we'll check the previous one
print "$sorted[$i] is a duplicate!\n" if $sorted[$i] eq $sorted[$i - 1];
}
This will print multiple dupe messages if there are multiple dupes, but you can clean it up.
As eugene y said, hashes are definitely the way to go here. Here's a direct translation of the code you posted to a hash-based method (with a little more Perlishness added along the way):
my #destination = ('hi', 'bye');
my %in_array = map { $_ => 1 } #destination;
for my $i (0 .. 100) {
$elemento = shift #sourcefile;
if(exists $in_array{$elemento})
{
print "it is";
}
else
{
print "it aint there";
}
}
Also, if you mean to check all elements of #sourcefile (as opposed to testing the first 101 elements) against #destination, you should replace the for line with
while (#sourcefile) {
Also also, don't forget to chomp any values read from a file! Lines read from a file have a linebreak at the end of them (the \r\n or \n mentioned in comments on the initial question), which will cause both eq and hash lookups to report that otherwise-matching values are different. This is, most likely, the reason why your code is failing to work correctly in the first place and changing to use sort or hashes won't fix that. First chomp your input to make it work, then use sort or hashes to make it efficient.
I am having quite a bit of trouble with a Perl script I am writing. I want to compare an element of an array to a variable I have to see if they are true. For some reason I cannot seem to get the comparison operation to work correctly. It will either evaluate at true all the time (even when outputting both strings clearly shows they are not the same), or it will always be false and never evaluate (even if they are the same). I have found an example of just this kind of comparison operation on another website, but when I use it it doesn't work. Am I missing something? Is the variable type I take from the file not a string? (Can't be an integer as far as I can tell as it is an IP address).
$ipaddress = '192.43.2.130'
if ($address[0] == ' ')
{
open (FH, "serverips.txt") or die "Crossroads could not find a list of backend servers";
#address = <FH>;
close(FH);
print $address[0];
print $address[1];
}
for ($i = 0; $i < #address; $i++)
{
print "hello";
if ($address[$i] eq $ipaddress)
{print $address[$i];
$file = "server_$i";
print "I got here first";
goto SENDING;}
}
SENDING:
print " I am here";
I am pretty weak in Perl, so forgive me for any rookie mistakes/assumptions I may have made in my very meager bit of code. Thank you for you time.
if ($address[0] == ' ')
{
open (FH, "serverips.txt") or die "Crossroads could not find a list of backend servers";
#address = <FH>;
close(FH);
You have several issues with this code here. First you should use strict because it would tell you that #address is being used before it's defined and you're also using numeric comparison on a string.
Secondly you aren't creating an array of the address in the file. You need to loop through the lines of the file to add each address:
my #address = ();
while( my $addr = <FH> ) {
chomp($addr); # removes the newline character
push(#address, $addr);
}
However you really don't need to push into an array at all. Just loop through the file and find the IP. Also don't use goto. That's what last is for.
while( my $addr = <FH> ) {
chomp($addr);
if( $addr eq $ipaddress ) {
$file = "server_$i";
print $addr,"\n";
print "I got here first"; # not sure what this means
last; # breaks out of the loop
}
}
When you're reading in from a file like that, you should use chomp() when doing a comparison with that line. When you do:
print $address[0];
print $address[1];
The output is on two separate lines, even though you haven't explicitly printed a newline. That's because $address[$i] contains a newline at the end. chomp removes this.
if ($address[$i] eq $ipaddress)
could read
my $currentIP = $address[$i];
chomp($currentIP);
if ($currentIP eq $ipaddress)
Once you're familiar with chomp, you could even use:
chomp(my $currentIP = $address[$i]);
if ($currentIP eq $ipaddress)
Also, please replace the goto with a last statement. That's perl's equivalent of C's break.
Also, from your comment on Jack's answer:
Here's some code you can use for finding how long it's been since a file was modified:
my $secondsSinceUpdate = time() - stat('filename.txt')->mtime;
You probably are having an issue with newlines. Try using chomp($address[$i]).
First of all, please don't use goto. Every time you use goto, the baby Jesus cries while killing a kitten.
Secondly, your code is a bit confusing in that you seem to be populating #address after starting the if($address[0] == '') statement (not to mention that that if should be if($address[0] eq '')).
If you're trying to compare each element of #address with $ipaddress for equality, you can do something like the following
Note: This code assumes that you've populated #address.
my $num_matches=0;
foreach(#address)
{
$num_matches++ if $_ eq $ipaddress;
}
if($num_matches)
{
#You've got a match! Do something.
}
else
{
#You don't have any matches. This may or may not be bad. Do something else.
}
Alternatively, you can use the grep operator to get any and all matches from #address:
my #matches=grep{$_ eq $ipaddress}#address;
if(#matches)
{
#You've got matches.
}
else
{
#Sorry, no matches.
}
Finally, if you're using a version of Perl that is 5.10 or higher, you can use the smart match operator (ie ~~):
if($ipaddress~~#address)
{
#You've got a match!
}
else
{
#Nope, no matches.
}
When you read from a file like that you include the end-of-line character (generally \n) in each element. Use chomp #address; to get rid of it.
Also, use last; to exit the loop; goto is practically never needed.
Here's a rather idiomatic rewrite of your code. I'm excluding some of your logic that you might need, but isn't clear why:
$ipaddress = '192.43.2.130'
open (FH, "serverips.txt") or die "Crossroads could not find a list of backend servers";
while (<FH>) { # loop over the file, using the default input space
chomp; # remove end-of-line
last if ($_ eq $ipaddress); # a RE could easily be used here also, but keep the exact match
}
close(FH);
$file = "server_$."; # $. is the line number - it's not necessary to keep track yourself
print "The file is $file\n";
Some people dislike using perl's implicit variables (like $_ and $.) but they're not that hard to keep track of. perldoc perlvar lists all these variables and explains their usage.
Regarding the exact match vs. "RE" (regular expression, or regexp - see perldoc perlre for lots of gory details) -- the syntax for testing a RE against the default input space ($_) is very simple. Instead of
last if ($_ eq $ipaddress);
you could use
last if (/$ipaddress/);
Although treating an ip address as a regular expression (where . has a special meaning) is probably not a good idea.
I am trying to get a perl loop to work that is working from an array that contains 6 elements. I want the loop to pull out two elements from the array, perform certain functions, and then loop back and pull out the next two elements from the array until the array runs out of elements. Problem is that the loop only pulls out the first two elements and then stops. Some help here would be greatly apperaciated.
my open(infile, 'dnadata.txt');
my #data = < infile>;
chomp #data;
#print #data; #Debug
my $aminoacids = 'ARNDCQEGHILKMFPSTWYV';
my $aalen = length($aminoacids);
my $i=0;
my $j=0;
my #matrix =();
for(my $i=0; $i<2; $i++){
for( my $j=0; $j<$aalen; $j++){
$matrix[$i][$j] = 0;
}
}
The guidelines for this program states that the program should ignore the presence of gaps in the program. which means that DNA code that is matched up with a gap should be ignored. So the code that is pushed through needs to have alignments linked with gaps removed.
I need to modify the length of the array by two since I am comparing two sequence in this part of the loop.
#$lemseqcomp = $lenarray / 2;
#print $lenseqcomp;
#I need to initialize these saclar values.
$junk1 = " ";
$junk2 = " ";
$seq1 = " ";
$seq2 = " ";
This is the loop that is causeing issues. I belive that the first loop should move back to the array and pull out the next element each time it loops but it doesn't.
for($i=0; $i<$lenarray; $i++){
#This code should remove the the last value of the array once and
#then a second time. The sequences should be the same length at this point.
my $last1 =pop(#data1);
my $last2 =pop(#data1);
for($i=0; $i<length($last1); $i++){
my $letter1 = substr($last1, $i, 1);
my $letter2 = substr($last2, $i, 1);
if(($letter1 eq '-')|| ($letter2 eq '-')){
#I need to put the sequences I am getting rid of somewhere. Here is a good place as any.
$junk1 = $letter1 . $junk1;
$junk2 = $letter1 . $junk2;
}
else{
$seq1 = $letter1 . $seq1;
$seq2 = $letter2 . $seq2;
}
}
}
print "$seq1\n";
print "$seq2\n";
print "#data1\n";
I am actually trying to create a substitution matrix from scratch and return the data. The reason why the code looks weird, is because it isn't actually finished yet and I got stuck.
This is the test sequence if anyone is curious.
YFRFR
YF-FR
FRFRFR
ARFRFR
YFYFR-F
YFRFRYF
First off, if you're going to work with sequence data, use BioPerl. Life will be so much easier. However...
Since you know you'll be comparing the lines from your input file as pairs, it makes sense to read them into a datastructure that reflects that. As elsewhere suggested, an array like #data[[line1, line2],[line3,line4]) ensures that the correct pairs of lines are always together.
What I'm not clear on what you're trying to do is:
a) are you generating a consensus
sequence where the 2 sequences are
difference only by gaps
b) are your 2 sequences significantly
different and you're trying to
exclude the non-aligning parts and
then generate a consensus?
So, does the first pair represent your data, or is it more like the second?
ATCG---AAActctgGGGGG--taGC
ATCGcccAAActctgGGGGGTTtaGC
ATCG---AAActctgGGGGG--taGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
ATCGcccAAActctgGGGGGTTtaGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
The problem is that you're using $i as the counter variable for both your loops, so the inner loop modifies the counter out from under the outer loop. Try changing the inner loop's counter to $j, or using my to localize them properly.
Don't store your values as an array, store as a two-dimensional array:
my #dataset = ([$val1, $val2], [$val3, $val4]);
or
my #dataset;
push (#dataset, [$val_n1, $val_n2]);
Then:
for my $value (#dataset) {
### Do stuff with $value->[0] and $value->[1]
}
There are lots of strange things in your code: you are initializing a matrix then not using it; reading a whole file into an array; scanning a string C style but then not doing anything with the unmatched values; and finally, just printing the two last processed values (which, in your case, are the two first elements of your array, since you are using pop.)
Here's a guess.
use strict;
my $aminoacids = 'ARNDCQEGHILKMFPSTWYV';
# Preparing a regular expression. This is kind of useful if processing large
# amounts of data. This will match anything that is not in the string above.
my $regex = qr([^$aminoacids]);
# Our work function.
sub do_something {
my ($a, $b) = #_;
$a =~ s/$regex//g; # removing unwanted characters
$b =~ s/$regex//g; # ditto
# Printing, saving, whatever...
print "Something: $a - $b\n";
return ($a, $b);
}
my $prev;
while (<>) {
chomp;
if ($prev) {
do_something($prev, $_);
$prev = undef;
} else {
$prev = $_;
}
}
print STDERR "Warning: trailing data: $prev\n"
if $prev;
Since you are a total Perl/programming newbie, I am going to show a rewrite of your first code block, then I'll offer you some general advice and links.
Let's look at your first block of sample code. There is a lot of stuff all strung together, and it's hard to follow. I, personally, am too dumb to remember more than a few things at a time, so I chop problems into small pieces that I can understand. This is (was) known as 'chunking'.
One easy way to chunk your program is use write subroutines. Take any particular action or idea that is likely to be repeated or would make the current section of code long and hard to understand, and wrap it up into a nice neat package and get it out of the way.
It also helps if you add space to your code to make it easier to read. Your mind is already struggling to grok the code soup, why make things harder than necessary? Grouping like things, using _ in names, blank lines and indentation all help. There are also conventions that can help, like making constant values (values that cannot or should not change) all capital letters.
use strict; # Using strict will help catch errors.
use warnings; # ditto for warnings.
use diagnostics; # diagnostics will help you understand the error messages
# Put constants at the top of your program.
# It makes them easy to find, and change as needed.
my $AMINO_ACIDS = 'ARNDCQEGHILKMFPSTWYV';
my $AMINO_COUNT = length($AMINO_ACIDS);
my $DATA_FILE = 'dnadata.txt';
# Here I am using subroutines to encapsulate complexity:
my #data = read_data_file( $DATA_FILE );
my #matrix = initialize_matrix( 2, $amino_count, 0 );
# now we are done with the first block of code and can do more stuff
...
# This section down here looks kind of big, but it is mostly comments.
# Remove the didactic comments and suddenly the code is much more compact.
# Here are the actual subs that I abstracted out above.
# It helps to document your subs:
# - what they do
# - what arguments they take
# - what they return
# Read a data file and returns an array of dna strings read from the file.
#
# Arguments
# data_file => path to the data file to read
sub read_data_file {
my $data_file = shift;
# Here I am using a 3 argument open, and a lexical filehandle.
open( my $infile, '<', $data_file )
or die "Unable to open dnadata.txt - $!\n";
# I've left slurping the whole file intact, even though it can be very inefficient.
# Other times it is just what the doctor ordered.
my #data = <$infile>;
chomp #data;
# I return the data array rather than a reference
# to keep things simple since you are just learning.
#
# In my code, I'd pass a reference.
return #data;
}
# Initialize a matrix (or 2-d array) with a specified value.
#
# Arguments
# $i => width of matrix
# $j => height of matrix
# $value => initial value
sub initialize_matrix {
my $i = shift;
my $j = shift;
my $value = shift;
# I use two powerful perlisms here: map and the range operator.
#
# map is a list contsruction function that is very very powerful.
# it calls the code in brackets for each member of the the list it operates against.
# Think of it as a for loop that keeps the result of each iteration,
# and then builds an array out of the results.
#
# The range operator `..` creates a list of intervening values. For example:
# (1..5) is the same as (1, 2, 3, 4, 5)
my #matrix = map {
[ ($value) x $i ]
} 1..$j;
# So here we make a list of numbers from 1 to $j.
# For each member of the list we
# create an anonymous array containing a list of $i copies of $value.
# Then we add the anonymous array to the matrix.
return #matrix;
}
Now that the code rewrite is done, here are some links:
Here's a response I wrote titled "How to write a program". It offers some basic guidelines on how to approach writing software projects from specification. It is aimed at beginners. I hope you find it helpful. If nothing else, the links in it should be handy.
For a beginning programmer, beginning with Perl, there is no better book than Learning Perl.
I also recommend heading over to Perlmonks for Perl help and mentoring. It is an active Perl specific community site with very smart, friendly people who are happy to help you. Kind of like Stack Overflow, but more focused.
Good luck!
Instead of using a C-style for loop, you can read data from an array two elements at a time using splice inside a while loop:
while (my ($letter1, $letter2) = splice(#data, 0, 2))
{
# stuff...
}
I've cleaned up some of your other code below:
use strict;
use warnings;
open(my $infile, '<', 'dnadata.txt');
my #data = <$infile>;
close $infile;
chomp #data;
my $aminoacids = 'ARNDCQEGHILKMFPSTWYV';
my $aalen = length($aminoacids);
# initialize a 2 x 21 array for holding the amino acid data
my $matrix;
foreach my $i (0 .. 1)
{
foreach my $j (0 .. $aalen-1)
{
$matrix->[$i][$j] = 0;
}
}
# Process all letters in the DNA data
while (my ($letter1, $letter2) = splice(#data, 0, 2))
{
# do something... not sure what?
# you appear to want to look up the letters in a reference table, perhaps $aminoacids?
}