Please bear with me.
Write a program that reads a series of words (with one word per line)1 until end-of-input, then print a summary of how many times each word was seen. (Hint: remember that when an undefined value is used as if it were a number, Perl automatically converts it to 0. It may help to look back at the earlier exercise that kept a running total.) If the input words were fred, barney, fred, dino, wilma, fred (all on separate lines), the output should tell us that fred was seen 3 times. For extra credit, sort the summary words in ASCII order in the output.
[1] It has to be one word per line because we still haven't shown you how to extract individual words from a line of input.
This one should use a hash. And I can't figure out how. I can only think of using an array and using 2 loops to compare duplicates. I guess I didn't understand the problem right. Here's my code using an array.
#! usr/bin/perl
use warnings;
use strict;
chomp(my #input = <STDIN>);
foreach my $name (#input) {
my $count;
foreach my $compare_name (#input) {
if ($name eq $compare_name) {
$count += 1;
}
}
print "$name seen $count times\n";
}
but this prints say for example:
myname
myname
myname
it prints:
myname seen 3 times
myname seen 3 times
myname seen 3 times
can somebody guide me on how to use a hash on this one? Thanks
You are trying to find out how many times you've seen a word, which is to say you're trying to access the count associated with a word.
If only you could use the word as the index into an array and store the count in that array element...
Well, that's exactly what a hash is. It's no surprise it was recommended by the exercise.
$counts{$word} # Retrieves the count associated with a word.
++$counts{$word}; # Increment the number of times you've seen a word.
keys(%counts) # Returns a list of the words you have encountered.
It is three times, because you have three iterations of the outer loop, each yielding same results (3 times).
A much simple way is:
my %occurs;
while (<STDIN>) {
chomp($_);
$occurs{$_}++;
}
foreach my $occur (sort keys %occurs) {
print "$occur seen $occurs{$occur} times\n";
}
Here is one way to do:
#!/usr/bin/perl -w
use v5.14;
use strict;
my %map;
chomp(my #words = <STDIN>);
foreach my $word (#words) {
$map{$word} += 1;
}
foreach my $key (sort keys %map) {
say "$key occurs $map{$key} times."
}
It's simple, readable and easy to maintain.
Related
I have an array, each element is a string which consists of several words. The first word is identifier, which will not be considered. The rest part of the string would be number or alphabet only. I want to sort the alphabet part and then output the whole element. Following are my codes.
#!/usr/bin/perl
use strict;
use warnings;
my #log=("a1 9 2 3 1","gl cct car","zo4 4 7", "abl off key dog","a8 act zoo");
my #values;
my #letter_log;
my #letter_idf;
my #dig_log;
my $i;
$i=0;
foreach(#log)
{
#values=split(/\s+/,$_);chomp(#values);
#_= m/$values[0]\s/;
print "25 \$'=$';\n";
if($' =~ /\D\s+/){$letter_idf[$i]=$values[0];$letter_log[$i]="$'";}
else{$dig_log[$i]=$_;}
$i++;
}
#_=sort { $letter_log[$a] cmp $letter_log[$b] } 0..$#letter_log;
chomp(#_);
enter code here
for($i=0;$i<=$#letter_log;$i++){print"$letter_idf[$_[$i]]"."$letter_log[$_[$i]];\t";}
foreach(#dig_log){print "$_;\t";}
print "\n";
I hope the output is like below
( "g1 act car"; "a8 act zoo"; "ab1 off key dog"; "a1 9 2 3 1"; "zo4 4 7")
However, my #letter_log is empty. I highly appreciate it if you could point out the errors and provide a correct solution.
PLEASE DO NOT USE MODULES, LIKE
import Scalar::Util qw(look_like_number);
I tried to avoid the modules because I want to study how to tell if a string is a number or not. Thanks!
The provided code that demonstrates your intention is not a perfect match for the title since it does a lot more. I would like to address only the main question in the title here.
If you can first define what a number is (instead of using a indirect definition of "whatever perl think a numbers is"), it becomes an easier problem.
For example, if you define the number you are looking for as a string with multiple characters of digit 0..9, then a simple regular expression /^[0-9]+$/ can serve your purpose.
Thanks for comments ikegami and melpomene.
The reason why I want to try it because the module is a "program" as well. I want to learn how to realize it by myself. After all, we meet all kinds of data which need to handle.
After many failures and tests, I figured it out and share it here.
first, the system variable "$'"changed before I assign it in if statement. I save it into another variable.
Second, I use an alternative way to realize it because the sequence numbers with spaces must be string. So, I only take one "character" to test it. It proves that this operation is correct. Do not forget the statements in my original post
"The first word is identifier, which will not be considered. The rest part of the string would be number or alphabet only. "
Here are my revised scripts. "NOTHING IS IMPOSSIBLE."
#!/usr/bin/perl -w
use strict;
use warnings;
#import Scalar::Util qw(look_like_number);
my #log=("a1 9 2 3 1","gl act car","zo4 4 7", "abl off key dog","a8 act zoo");
print "original log:\n";
$"=";\t"; #control array's delimiter
print "#log\n";
my #values;
my #letter_log;
my #letter_idf;
my #dig_log;
my $s;
my $i;
my $s_r;
$i=0;
foreach(#log)
{
#values=split(/\s+/,$_);chomp(#values);
#_= m/$values[0]\s/;
print "25 \$'=$';\n";
$s=$';
$s_r=substr($s,0,1);
if($s_r =~ /\D/)
{ print"26.0: $'\ts=$s\ts_r=$s_r\n";
$letter_idf[$i]=$values[0];
$letter_log[$i]=$s;
print "26: $letter_idf[$i]\t$letter_log[$i]\n";$i++;
}
else{$dig_log[$i]=$_;}
}
#_=sort { $letter_log[$a] cmp $letter_log[$b] } 0..$#letter_log;
chomp(#_);
print"35: srt letter log: #letter_log\n";
#foreach(#letter_log){print "$_;\t";}
print"38: nsrt letter log: ";
for($i=0;$i<=$#letter_log;$i++){print"$letter_idf[$_[$i]] "."$letter_log[$_[$i]];\t";}
print"\n";
print"41: digital log:";
foreach(#dig_log){print "$_;\t";}
print "\n";
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"...
I am new to Perl, by the way. I have a Perl script that needs to count the number of times a string appears in the file. The script gets the word from the file itself.
I need it to grab the first word in the file and then search the rest of the file to see if it is repeated anywhere else. If it is repeated I need it to return the amount of times it was repeated. If it was not repeated, it can return 0. I need it to then get the next word in the file and check this again.
I will grab the first word from the file, search the file for repeats of that word, grab the second word from
the file, search the file for repeats of that word, grab the third word from the file, search the file for repeats of that word.
So far I have a while loop that is grabbing each word I need, but I do not know how to get it to search for repeats without resetting the position of my current line. So how do I do this? Any ideas or suggestions are greatly appreciated! Thanks in advance!
while (<theFile>) {
my $line1 = $_;
my $startHere = rindex($line1, ",");
my $theName = substr($line1, $startHere + 1, length($line1) - $startHere);
#print "the name: ".$theName."\n";
}
Use a hashtable;
my %wordcount = ();
while(my $line = <theFile>)
{
chomp($line);
my #words = split(' ', $line);
foreach my $word(#words)
{
$wordCount{$word} += 1;
}
}
# output
foreach my $key(keys %wordCount)
{
print "Word: $key Repeat_Count: " . ($wordCount{$key} - 1) . "\n";
}
The $wordCount{$key} - 1 in the output accounts for the first time a word was seen; Words that only apprear once in the file will have a count of 0
Unless this is actually homework and/or you have to achieve the results in the specific manor you describe, this is going to be FAR more efficient.
Edit: From your comment below:
Each word i am searching for is not "the first word" it is a certain word on the line. Basically i have a csv file and i am skipping to the third value and searching for repeats of it.
I would still use this approach. What you would want to do is:
split on , since this is a CSV file
Pull out the 3rd word in the array on each line and store the words you are interested in in their own hash table
At the end, iterate through the "search word" hash table, and pull out the counts from the wordcount table
So:
my #words = split(',', $line);
$searchTable{#words[2]} = 1;
...
foreach my $key(keys %searchTable)
{
print "Word: $key Repeat_Count: " . ($wordCount{$key} - 1) . "\n";
}
you'll have to adjust according to what rules you have around counting words that repeat in the third column. You could just remove them from #words before the loop that inserts into your wordCount hash.
my $word = <theFile>
chomp($word); #`assuming word is by itself.
my $wordcount = 0;
foreach my $line (<theFile>) {
$line =~ s/$word/$wordcount++/eg;
}
print $wordcount."\n";
Look up the regex flag 'e' for more on what this does. I didn't test the code, but something like it should work. For clarification, the 'e' flag evaluates the second part of the regex (the substitution) as code before replacing, but it's more than that, so with that flag you should be able to make this work.
Now that I understand what you are asking for, the above solution won't work. What you can do, is use sysread to read the entire file into a buffer, and run the same substition after that, but you will have to get the first word off manually, or you can just decrement after the fact. This is because the sysread filehandle and the regular filehandle are handled differently, so try this:
my $word = <theFile>
chomp($word); #`assuming word is by itself.
my $wordcount = 0;
my $srline = '';
#some arbitrary very long length, longer than file
#Looping also possible.
sysread(theFile,$srline,10000000)
$srline =~ s/$word/$wordcount++/eg;
$wordcount--; # I think that the first word will still be in here, causing issues, you should test.
print $wordcount."\n";
Now, given that I read your comment responding to your question, I don't think that your current algorithm is optimal, and you probably want a hash storing up all of the counts for words in a file. This would probably be best done using something like the following:
my %counts = ();
foreach my $line (<theFile>) {
$line =~ s/(\w+)/$counts{$1}++/eg;
}
# now %counts contains key-value pair words for everything in the file.
To find count of all words present in the file you can do something like:
#!/usr/bin/perl
use strict;
use warnings;
my %count_of;
while (my $line = <>) { #read from file or STDIN
foreach my $word (split /\s+/, $line) {
$count_of{$word}++;
}
}
print "All words and their counts: \n";
for my $word (sort keys %count_of) {
print "'$word': $count_of{$word}\n";
}
__END__
What does it mean when you try to print an array or hash and you see the following; Array(0xd3888) or HASH(0xd3978)?
EXAMPLE
CODE
my #data = (
['1_TEST','1_T','1_TESTER'],
['2_TEST','2_T','2_TESTER'],
['3_TEST','3_T','3_TESTER'],
['4_TEST','4_T','4_TESTER'],
['5_TEST','5_T','5_TESTER'],
['6_TEST','6_T','^_TESTER']
);
foreach my $line (#data) {
chomp($line);
#random = split(/\|/,$line);
print "".$random[0]."".$random[1]."".$random[2]."","\n";
}
RESULT
ARRAY(0xc1864)
ARRAY(0xd384c)
ARRAY(0xd3894)
ARRAY(0xd38d0)
ARRAY(0xd390c)
ARRAY(0xd3948)
It's hard to tell whether you meant it or not, but the reason why you're getting array references is because you're not printing what you think you are.
You started out right when iterating over the 'rows' of #data with:
foreach my $line (#data) { ... }
However, the next line is a no-go. It seems that you're confusing text strings with an array structure. Yes, each row contains strings, but Perl treats #data as an array, not a string.
split is used to convert strings to arrays. It doesn't operate on arrays! Same goes for chomp (with an irrelevant exception).
What you'll want to do is replace the contents of the foreach loop with the following:
foreach my $line (#data) {
print $line->[0].", ".$line->[1].", ".$line->[2]."\n";
}
You'll notice the -> notation, which is there for a reason. $line refers to an array. It is not an array itself. The -> arrows deference the array, allowing you access to individual elements of the array referenced by $line.
If you're not comfortable with the idea of deferencing with arrows (and most beginners usually aren't), you can create a temporary array as shown below and use that instead.
foreach my $line (#data) {
my #random = #{ $line };
print $random[0].", ".$random[1].", ".$random[2]."\n";
}
OUTPUT
1_TEST, 1_T, 1_TESTER
2_TEST, 2_T, 2_TESTER
3_TEST, 3_T, 3_TESTER
4_TEST, 4_T, 4_TESTER
5_TEST, 5_T, 5_TESTER
6_TEST, 6_T, ^_TESTER
A one-liner might go something like print "#$_\n" for #data; (which is a bit OTT), but if you want to just print the array to see what it looks like (say, for debugging purposes), I'd recommend using the Data::Dump module, which pretty-prints arrays and hashes for you without you having to worry about it too much.
Just put use Data::Dump 'dump'; at beginning of your script, and then dump #data;. As simple as that!
It means you do not have an array; you have a reference to an array.
Note that an array is specified with round brackets - as a list; when you use the square bracket notation, you are creating a reference to an array.
foreach my $line (#data)
{
my #array = #$line;
print "$array[0] - $array[1] - $array[2]\n";
}
Illustrating the difference:
my #data = (
['1_TEST','1_T','1_TESTER'],
['2_TEST','2_T','2_TESTER'],
['3_TEST','3_T','3_TESTER'],
['4_TEST','4_T','4_TESTER'],
['5_TEST','5_T','5_TESTER'],
['6_TEST','6_T','^_TESTER']
);
# Original print loop
foreach my $line (#data)
{
chomp($line);
#random = split(/\|/,$line);
print "".$random[0]."".$random[1]."".$random[2]."","\n";
}
# Revised print loop
foreach my $line (#data)
{
my #array = #$line;
print "$array[0] - $array[1] - $array[2]\n";
}
Output
ARRAY(0x62c0f8)
ARRAY(0x649db8)
ARRAY(0x649980)
ARRAY(0x649e48)
ARRAY(0x649ec0)
ARRAY(0x649f38)
1_TEST - 1_T - 1_TESTER
2_TEST - 2_T - 2_TESTER
3_TEST - 3_T - 3_TESTER
4_TEST - 4_T - 4_TESTER
5_TEST - 5_T - 5_TESTER
6_TEST - 6_T - ^_TESTER
You're printing a reference to the hash or array, rather than the contents OF that.
In the particular code you're describing I seem to recall that Perl automagically makes the foreach looping index variable (my $line in your code) into an "alias" (a sort of reference I guess) of the value at each stage through the loop.
So $line is a reference to #data[x] ... which is, at each iteration, some array. To get at one of the element of #data[0] you'd need the $ sigil (because the elements of the array at #data[0] are scalars). However $line[0] is a reference to some package/global variable that doesn't exist (use warnings; use strict; will tell you that, BTW).
[Edited after Ether pointed out my ignorance]
#data is a list of anonymous array references; each of which contains a list of scalars. Thus you have to use the sort of explicit de-referencing I describe below:
What you need is something more like:
print ${$line}[0], ${$line}[1], ${$line}[2], "\n";
... notice that the ${xxx}[0] is ensuring that the xxx is derefenced, then indexing is performed on the result of the dereference, which is then extracted as a scalar.
I testing this as well:
print $$line[0], $$line[1], $$line[2], "\n";
... and it seems to work. (However, I think that the first form is more clear, even if it's more verbose).
Personally I chalk this up to yet another gotchya in Perl.
[Further editorializing] I still count this as a "gotchya." Stuff like this, and the fact that most of the responses to this question have been technically correct while utterly failing to show any effort to actually help the original poster, has once again reminded me why I shifted to Python so many years ago. The code I posted works, of course, and probably accomplishes what the OP was attempting. My explanation was wholly wrong. I saw the word "alias" in the `perlsyn` man page and remembered that there were some funky semantics somewhere there; so I totally missed the part that [...] is creating an anonymous reference. Unless you drink from the Perl Kool-Aid in deep drafts then even the simplest code cannot be explained.
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?
}