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
To achieve below task I have written below C like perl program (As I am new to Perl), But I am not sure if this is the best way to achieve.
Can someone please guide?
Note: Not with the full program, But where I can make improvement.
Thanks in advance
Input :
$str = "mail1, local<mail1#mail.local>, mail2#mail.local, <mail3#mail.local>, mail4 local<mail4#mail.local>"
Expected Output :
mail1, local<mail1#mail.local>
mail2#mail.local
<mail3#mail.local>
mail4, local<mail4#mail.local>
Sample Program
my $str="mail1, \#local<mail1\#mail.local>, mail2\#mail.local, <mail3\#mail.local>, mail4, local<mail4\#mail.local>";
my $count=0, #array, $flag=0, $tempStr="";
for my $c (split (//,$str)) {
if( ($count eq 0) and ($c eq ' ') ) {
next;
}
if($c) {
if( ($c eq ',') and ($flag eq 1) ) {
push #array, $tempStr;
$count=0;
$flag1=0;
$tempStr="";
next;
}
if( ($c eq '>' ) or ( $c eq '#' ) ) {
$flag=1;
}
$tempStr="$tempStr$c";
$count++;
}
}
if($count>0) {
push #array, $tempStr;
}
foreach my $var (#array) {
print "$var\n";
}
Edit:
Input:
Input is the output of above code.
Expected Output :
"mail1, local"<mail1#mail.local>
"mail4, local"<mail4#mail.local>
Sample Code:
$str =~ s/([^#>]+[#>][^,]+),\s*/$1\n/g;
my #addresses = split('\n',$str);
if(scalar #addresses) {
foreach my $address (#addresses) {
if (($address =~ /</) and ($address !~ /\"/) and ($address !~ /^</)){
$address="\"$address";
$address=~ s/</\"</g;
}
}
$str = join(',',#addresses);
}
print "$str\n";
As I see, you want to replace each:
comma and following spaces,
occurring after either # or >,
with a newline.
To make such replacement, instead of writing a parsing program, you can use
a regex.
The search part can be as follows:
([^#>]+[#>][^,]+),\s*
Details:
( - Start of the 1st capturing group.
[^#>]+ - A non-empty sequence of chars other than # or >.
[#>] - Either # or >.
[^,]+ - A non-empty sequence of chars other than a comma.
) - End of the 1st capturing group.
,\s* - A comma and optional sequence of spaces.
The replace part should be:
$1 - The 1st capturing group.
\n - A newline.
So the whole program, much shorter than yours, can be as follows:
my $str='mail1, local<mail1#mail.local>, mail2#mail.local, <mail3#mail.local>, mail4, local<mail4#mail.local>';
print "Before:\n$str\n";
$str =~ s/([^#>]+[#>][^,]+),\s*/$1\n/g;
print "After:\n$str\n";
To replace all needed commas I used g option.
Note that I put the source string in single quotes, otherwise Perl
would have complained about Possible unintended interpolation of #mail.
Edit
Your modified requirements must be handled different way.
"Ordinary" replacement is not an option, because now there are some
fragments to match and some framents to ignore.
So the basic idea is to write a while loop with a matching regex:
(\w+),?\s+(\w+)(<[^>]+>), meaning:
(\w+) - First capturing group - a sequence of word chars (e.g. mail1).
,?\s+ - Optional comma and a sequence of spaces.
(\w+) - Second capturing group - a sequence of word chars (e.g. local).
(<[^>]+>) - Third capturing group - a sequence of chars other than >
(actual mail address), enclosed in angle brackets, e.g. <mail1#mail.local>.
Within each execution of the loop you have access to the groups
captured in this particular match ($1, $2, ...).
So the content of this loop is to print all these captured groups,
with required additional chars.
The code (again much shorter than yours) should look like below:
my $str = 'mail1, local<mail1#mail.local>, mail2#mail.local, <mail3#mail.local>, mail4 local<mail4#mail.local>';
while ($str =~ /(\w+),?\s+(\w+)(<[^>]+>)/g) {
print "\"$1, $2\"$3\n";
}
Here is an approach using split, which in this case also needs a careful regex
use warnings;
use strict;
use feature 'say';
my $string = # broken into two parts for readabililty
q(mail1, local<mail1#mail.local>, mail2#mail.local, )
. q(<mail3#mail.local>, mail4, local<mail4#mail.local>);
my #addresses = split /#.+?\K,\s*/, $string;
say for #addresses;
The split takes a full regex in its delimiter specification. In this case I figure that each record is delimited by a comma which comes after the email address, so #.+?,
To match a pattern only when it is preceded by another brings to mind a negative lookbehind before the comma. But those can't be of variable length, which is precisely the case here.
We can instead normally match the pattern #.+? and then use the \K form (of the lookbehind) which drops all previous matches so that they are not taken out of the string. Thus the above splits on ,\s* when that is preceded by the email address, #... (what isn't consumed).
It prints
mail1, local<mail1#mail.local>
mail2#mail.local
<mail3#mail.local>
mail4, local<mail4#mail.local>
The edit asks about quoting the description preceding <...> when it's there. A simple way is to make another pass once addresses have been parsed out of the string as above. For example
my #addresses = split /#.+?\K,\s*/, $string; #/ stop syntax highlight
s/(.+?,\s*.+?)</"$1"</ for #addresses;
say for #addresses;
The regex in a loop is one way to change elements of an array. I use it for its efficiency (changes elements in place), conciseness, and as a demonstration of the following properties.
In a foreach loop the index variable (or $_) is an alias for the currently processed element – so changing it changes that element. This is a known source of bugs when allowed unknowingly, which was another reason to show it in the above form.
The statement also uses the statement modifier and it is equivalent to
foreach my $elem (#addresses) {
$elem =~ s/(.+?,\s*.+?)</"$1"</;
}
This is often considered a more proper way to write it but I find that the other form emphasizes more clearly that elements are being changed, when that is the sole purpose of the foreach.
I'm trying to use an array and a loop to print out the following (basically for each letter of the alphabet, print each letter of the alphabet after it and then move on to the next letter). I'm new to perl, anyone have any quick words of :
aa
ab
ac
ad
...
ba
bb
bc
bd
...
ca
cb
...
Currently I have this, but it only prints a single character alphabet...
#arr = ("a","b","c","d","e","f","g","h","i","j","k","l","m","n","o","p","q","r","s","t","u","v","w","x","y","z");
$i = #arr;
while ($i)
{
print $arr[$i];
$i--;
}
Using the range operator and the ranges you want to target:
use strict;
use warnings;
my #elements = ("aa" .. "zz");
for my $combo (#elements)
{
print "$combo\n";
}
You can utilize the initial 2 letters till the ending 2 letters you want as ending and the for will take care of everything.
This really isn't multi-dimensional array work, if it were you'd be working with stuff like:
my #foo = (
[1,2,3],
[4,7,8,1,2,3],
[2,3],
);
This is really a very basic how do I make a nested loop that iterates over the same array. I'll bet this is homework.
So, I'll let you figure out the nesting bits, but give some help with Perl's loop operators.
!! for/foreach
for (the each is optional) is the real heavy hitter for looping in perl. Use it like so:
for my $var ( #array ) {
#do stuff with $var
}
Each element in #array will be aliased to the $var variable, and the block of code will be executed. The fact that we are aliasing, rather than copying means that if alter the value of $var, #array will be changed as well. The stuff between the parenthesis may be any expression. The expression will be evaluated in list context. So if you put a file handle in the parens, the entire file will be read into memory and processed.
You can also leave off naming the loop variable, and $_ will be used instead. In general, DO NOT DO THIS.
!! C-Style for
Every once in a while you need to keep track of indexes as you loop over an array. This is when a C style for loop comes in handy.
for( my $i=0; $i<#array; $i++ ) {
# do stuff with $array[$i]
}
!! While/Until
While and until operate with boolean loop conditions. That means that the loop will repeat as long as the appropriate boolean value if found for the condition ( TRUE for while, and FALSE for until). In addition to the obvious cases where you are looking for a particular condition, while is great for processing a file one line at a time.
while ( my $line = <$fh> ) {
# Do stuff with $line.
}
!! map
map is an amazingly useful bit of functional programming kung-fu. It is used to turn one list into another. You pass an anonymous code reference that is used to enact the transformation.
# Multiply all elements of #old by two and store them in #new.
my #new = map { $_ * 2 } #old;
So how do you solve your particular problem? There are many ways. Which is best depends on how you want to use the results. If you want to create a new array of the letter pairs, use map. If you are interested primarily in a side effect (say printing a variable) use for. If you need to work with really big lists that come from sort of interator (like lines from a filehandle) use while.
Here's a solution. I wouldn't turn it in to your professor until you understand how it works.
print map { my $letter=$_; map "$letter$_\n", "a".."z" } "a".."z";
Look at perldoc articles, perlsyn for info on the looping constructs, perlfunc for info on map and look at perlop for info on the range operator (..).
Good luck.
Use the range operator (..) for your initialization. The range operator basically grabs a range of values such as numbers or characters.
Then use a nested loop to go through the array one time per character for a total of 26^2 iterations.
Rather than a while loop I've used a foreach loop to go through each item in the array. You could also put 'a' .. 'z' instead of declared #arr as the argument to the foreach loop. The foreach loops below set $char or $char2 to each value in #arr in turn.
my #arr = ('a' .. 'z');
for my $char (#arr) {
for my $char2 (#arr) {
print "$char$char2\n";
}
}
If all you really want to do is print the 676 strings you describe, then:
#!/usr/bin/perl
use warnings;
use strict;
my $str = 'aa';
while (length $str < 3) {
print $str++, "\n";
}
But I smell an "XY problem"...
What I want to do is check an array of strings against my search string and get the corresponding key so I can store it. Is there a magical way of doing this with Perl, or am I doomed to using a loop? If so, what is the most efficient way to do this?
I'm relatively new to Perl (I've only written 2 other scripts), so I don't know a lot of the magic yet, just that Perl is magic =D
Reference Array: (1 = 'Canon', 2 = 'HP', 3 = 'Sony')
Search String: Sony's Cyber-shot DSC-S600
End Result: 3
UPDATE:
Based on the results of discussion in this question, depending on your intent/criteria of what constitutes "not using a loop", the map based solution below (see "Option #1) may be the most concise solution, provided that you don't consider map a loop (the short version of the answers is: it's a loop as far as implementation/performance, it's not a loop from language theoretical point of view).
Assuming you don't care whether you get "3" or "Sony" as the answer, you can do it without a loop in a simple case, by building a regular expression with "or" logic (|) from the array, like this:
my #strings = ("Canon", "HP", "Sony");
my $search_in = "Sony's Cyber-shot DSC-S600";
my $combined_search = join("|",#strings);
my #which_found = ($search_in =~ /($combined_search)/);
print "$which_found[0]\n";
Result from my test run: Sony
The regular expression will (once the variable $combined_search is interpolated by Perl) take the form /(Canon|HP|Sony)/ which is what you want.
This will NOT work as-is if any of the strings contain regex special characters (such as | or ) ) - in that case you need to escape them
NOTE: I personally consider this somewhat cheating, because in order to implement join(), Perl itself must do a loop somewhere inside the interpeter. So this answer may not satisfy your desire to remain loop-less, depending on whether you wanted to avoid a loop for performance considerations, of to have cleaner or shorter code.
P.S. To get "3" instead of "Sony", you will have to use a loop - either in an obvious way, by doing 1 match in a loop underneath it all; or by using a library that saves you from writing the loop yourself but will have a loop underneath the call.
I will provide 3 alternative solutions.
#1 option: - my favorite. Uses "map", which I personally still consider a loop:
my #strings = ("Canon", "HP", "Sony");
my $search_in = "Sony's Cyber-shot DSC-S600";
my $combined_search = join("|",#strings);
my #which_found = ($search_in =~ /($combined_search)/);
print "$which_found[0]\n";
die "Not found" unless #which_found;
my $strings_index = 0;
my %strings_indexes = map {$_ => $strings_index++} #strings;
my $index = 1 + $strings_indexes{ $which_found[0] };
# Need to add 1 since arrays in Perl are zero-index-started and you want "3"
#2 option: Uses a loop hidden behind a nice CPAN library method:
use List::MoreUtils qw(firstidx);
my #strings = ("Canon", "HP", "Sony");
my $search_in = "Sony's Cyber-shot DSC-S600";
my $combined_search = join("|",#strings);
my #which_found = ($search_in =~ /($combined_search)/);
die "Not Found!"; unless #which_found;
print "$which_found[0]\n";
my $index_of_found = 1 + firstidx { $_ eq $which_found[0] } #strings;
# Need to add 1 since arrays in Perl are zero-index-started and you want "3"
#3 option: Here's the obvious loop way:
my $found_index = -1;
my #strings = ("Canon", "HP", "Sony");
my $search_in = "Sony's Cyber-shot DSC-S600";
foreach my $index (0..$#strings) {
next if $search_in !~ /$strings[$index]/;
$found_index = $index;
last; # quit the loop early, which is why I didn't use "map" here
}
# Check $found_index against -1; and if you want "3" instead of "2" add 1.
Here is a solution that builds a regular expression with embedded code to increment the index as perl moves through the regex:
my #brands = qw( Canon HP Sony );
my $string = "Sony's Cyber-shot DSC-S600";
use re 'eval'; # needed to use the (?{ code }) construct
my $index = -1;
my $regex = join '|' => map "(?{ \$index++ })\Q$_" => #brands;
print "index: $index\n" if $string =~ $regex;
# prints 2 (since Perl's array indexing starts with 0)
The string that is prepended to each brand first increments the index, and then tries to match the brand (escaped with quotemeta (as \Q) to allow for regex special characters in the brand names).
When the match fails, the regex engine moves past the alternation | and then the pattern repeats.
If you have multiple strings to match against, be sure to reset $index before each. Or you can prepend (?{$index = -1}) to the regex string.
An easy way is just to use a hash and regex:
my $search = "your search string";
my %translation = (
'canon' => 1,
'hp' => 2,
'sony' => 3
);
for my $key ( keys %translation ) {
if ( $search =~ /$key/i ) {
return $translation{$key};
)
}
Naturally the return can just as easily be a print. You can also surround the entire thing in a while loop with:
while(my $search = <>) {
#your $search is declared = to <> and now gets its values from STDIN or strings piped to this script
}
Please also take a look at perl's regex features at perlre
and take a look at perl's data structures at perlref
EDIT
as was just pointed out to me you were trying to steer away from using a loop. Another method would be to use perl's map function. Take a look here.
You can also take a look at Regexp::Assemble, which will take a collection of sub-regexes and build a single super-regex from them that can then be used to test for all of them at once (and gives you the text which matched the regex, of course). I'm not sure that it's the best solution if you're only looking at three strings/regexes that you want to match, but it's definitely the way to go if you have a substantially larger target set - the project I initially used it on has a library of some 1500 terms that it's matching against and it performs very well.
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?
}