Perl subroutines - hash

Here I fixed most of my mistakes and thank you all, any other advice please with my hash at this point and how can I clear each word and puts the word and its frequency in a hash, excluding the empty words.. I think my code make since now.

So you can focus on the key part of the algorithm, how about accepting input on STDIN and output to STDOUT. That way there's no argument checking, etc. Just a simple:
$ prog < words.txt
All you really need is a very simple algorithm:
Read a line
Split it into words
Record a count of the word
When done, display the counts
Here's a sample program
#! /usr/bin/perl -w
use strict;
my (%data);
while (<STDIN>) {
chomp;
my(#words) = split(/\s+/);
foreach my $word (#words) {
if (!defined($data{$word})) {
$data{$word} = 0;
}
$data{$word}++;
}
}
foreach (sort(keys(%data))) {
print "$_: $data{$_}\n";
}
Once you understand this and have it working in your environment, you can extend it to meet your other requirements:
remove non-alphabetic characters from each word
print three results per line
use input and output files
put the algorithm into a subroutine

I agree that starting with dave's answer would be more productive, but if you are interested in your mistakes, here is what I see:
You assign the return value of checkArgs to a scalar variable $checkArgs, but return an array value. It means that $checkArgs will always contain 2 (the size of the array) after this call (because the program dies if the number of arguments is not 2). It is not very bad since you do not use the value later, but why you need it at all in this case?
You open files and close them immediately without reading from them. Does not make sense.
Statement
while (<>)
reads either from standard output or from all files in the command line arguments. The latter variant is like what you want, but your second argument is the output file, not input. The diamond operator will try to read from it too. You have two options: a) use only one file name in the command line arguments, read the file with <>, use standard output for output, and redirect output to a file in shell; b) use
while(<$file1>)
instead, of course, before closing files. Option a) is the traditional Unix- and Perl-style, but b) provides for clearer code for beginners.
Statements
return $word;
and
return $str, $hash{$str};
return corresponding values on the first iterations of the loops, all other data remain unprocessed. In the first case, you should create a local array, store all $word in it and return the array as a whole. In the second case, you already have such local %hash, it is enough to return this hash. In both cases, you need should assign the return values of the functions not to scalars, but to an array and a hash correspondingly. Now, you actually lose all you data.

Related

How do I group values from a file into a hash according to specific Regular Expressions in Perl?

I have a .txt file with data in one column like so:
state_1
state_2
state_3
input_11
input_12
input_13
input_21
input_22
input_31
And I want to group these tags into a hash according to their names and numbers:
state_1: # For state_1, we have all "input1x" data tags
-input_11
-input_12
-input_13
state_2: # For state_2, we have all "input2x" data tags
-input_21
-input_22
state_3: # For state_3, we have all "input3x" data tags
-input_31
I tried using the push function like in this case to try and force the values into the hashes as arrays with push #{ $state{$inputs} }, $_;, but I am stuck finding a way to loop and get the desired hash according to the regular expressions.
I have also researched how to group my data according to regex, but I still cannot find a way to group the data as I get it from the .txt file.
My question is, what am I looking for to be able to group these tags accordingly?
In short, extract that index (1 or 2...) from a line of data and use it to form the right key and add the line to that key's arraref, also relying on autovivification
push #{$data{"state_$1"}}, $line if $line =~ /input_([0-9])/;
On lines with data input_NN the regex extracts the first number after input_, and adds that line to the arrayref at its suitable key. The key name to add to is built using the captured number and the fixed prefix. The very first time round for a key, before it's ever been seen and so it isn't in the hash yet, it is made by the mechanism/feature called autovivification.†
Then there are a few details -- if what is there in real data, instead of the token names input and state, isn't known ahead of time then it can be extracted from the first line of data, and then used as above. The linefeed need be removed as the line is read. Altogether
use warnings;
use strict;
use feature 'say';
use Data::Dump qw(dd); # to see complex data; or, use core Data::Dumper
my %data;
while (<>) { # reads line by line the files given on command line
chomp;
push #{$data{"state_$1"}}, $_ if /input_([0-9])/;
}
dd \%data;
This assumes that the keys/data have fixed prefixes and that those are known (state, input).
A one-liner example
perl -MData::Dump -wnlE'push #{$h{"state_$1"}}, $_ if /input_([0-9])/; }{ dd \%h' file
where file contains what is given in the question. That }{ starts the END phase -- code after that is executed once all lines have been read and processing completed, the RUN phase finished and the program is about to exit.
† This is a feature whereby a needed object is created when an undefined value (where the object would be) is dereferenced in an "lvalue context" (where it need be "modifiable").
A specific example above: we "use" (dereference) a key state_1 (etc) by adding the the arrayref that is its value, push #{ $data{state_1} }, $value -- but there is no such key there the first time! Well, it's made for us on the fly.
See for instance an article from The Effective Perler, and then there is far more of it around. Here are some generic examples and discussion, and here is a trickier example of when it kicks in or not.
Entry from perlglossary
In Perl, storage locations (lvalues) spontaneously generate themselves as needed, including the creation of any hard reference values to point to the next level of storage. The assignment $a[5][5][5][5][5] = "quintet" potentially creates five scalar storage locations, plus four references (in the first four scalar locations) pointing to four new anonymous arrays (to hold the last four scalar locations). But the point of autovivification is that you don’t have to worry about it.

How is a Perl filehandle a scalar if it can return multiple lines?

I have kind of fundamental question about scalars in Perl. Everything I read says scalars hold one value:
A scalar may contain one single value in any of three different
flavors: a number, a string, or a reference. Although a scalar may not
directly hold multiple values, it may contain a reference to an array
or hash which in turn contains multiple values.
--from perldoc
Was curious how the code below works
open( $IN, "<", "phonebook.txt" )
or die "Cannot open the file\n";
while ( my $line = <$IN> ) {
chomp($line);
my ( $name, $area, $phone ) = split /\|/, $line;
print "$name $phone $phone\n";
}
close $IN;
Just to clarify the code above is opening a pipe delimited text file in the following format name|areacode|phone
It opens the file up and then it splits them into $name $area $phone; how does it go through the multiple lines of the file and print them out?
Going back to the perldoc quote from above "A scalar may contain a single value of a string, number, reference." I am assuming that it has to be a reference, but doesn't even really seem like a reference and if it is looks like it would a reference of a scalar? so I am wondering what is going on internally that allows Perl to iterate through all of the lines in the code?
Nothing urgent, just something I noticed and was curious about. Thanks.
It looks like Borodin zeroed in on the part you wanted, but I'll add to it.
There are variables, which store things for us, and there are operators, which do things for us. A file handle, the thing you have in $IN, isn't the file itself or the data in the file. It's a connection that the program to use to get information from the file.
When you use the line input operator, <>, you give it a file handle to tell it where to grab the next line from. By itself, it defaults to ARGV, but you can put any file handle in there. In this case, you have <$IN>. Borodin already explained the reference and bareword stuff.
So, when you use the line input operator, it look at the connection you give in then gets a line from that file and returns it. You might be able to grok this more easily with it's function form:
my $line = readline( $IN );
The thing you get back doesn't come out of $IN, but the thing it points to. Along the way, $IN keeps track of where it is in the file. See seek and tell.
Along the same lines are Perl's regexes. Many people call something like /foo.*bar/ a regular expression. They are slightly wrong. There's a regular expression inside the pattern match operator //. The pattern is the instructions, but it doesn't do anything by itself until the operator uses it.
I find in my classes if I emphasize the difference between the noun and verb parts of the syntax, people have a much easier time with this sort of stuff.
Old Answer
Through each iteration of the while loop, exactly one value is put into the scalar variables. When the loop is done with a line, everything is reset.
The value in $line is a single value: the entire line which you have not broken up yet. Perl doesn't care what that single value looks like. With each iteration, you deal with exactly one line and that's what's in $line. Remember, these are variables, which means you can modify and replace their values, so they can only hold one thing at a time, but there can be multiple times.
The scalars $name, $area, and $phone have single values, each produced by split. Those are lexical variables (my), so they are only visible inside the specific loop iteration where they are defined.
Beyond that, I'm not sure which scalar you might be confused about.
The old-fashioned way of opening files is to use a bare name for the file handle, like so
open IN, 'phonebook.txt'
A file handle is a special type of value, like scalar, hash, array etc. but it has no prefix symbol to differentiate it. (This isn't actually the full extent of the truth, but I am worried about confusing you if I add even more detail.)
Perl still works like this, but it is best avoided for a couple of reasons.
All such file handles are global, and there is no way to restrict access to them by scope
There is no way to pass the value to a subroutine or store it in a data structure
So Perl was enhanced several years ago so that you can use references to file handles. These can be stored in scalar variables, arrays, or hashes, and can be passed as subroutine parameters.
What happens now when you write
open my $in, '<', 'phonebook.txt'
is that perl autovivifies an anonymous file handle, and puts a reference to it in variable $in, so yes, you were right, it is a reference. (Another thing that was changed about the same time was the move to three-parameter open calls, which allow you to open a file called, say, >.txt for input.)
I hope that helps you to understand. It's an unnecessary level of detail, but it can often help you to remember the way Perl works to understand the underlying details.
Incidentally, it is best to keep to lower-case letters for lexical variables, even for file handle references. I often add fh to the end to indicate that the variable holds a file handle, like $in_fh. But there's no need to use capitals, which are generally reserved for global variables like Package::Names.
Update - The Rest of the Story
I thought I should add something to explain what I have mised out, for fear of misleading people who care about the gory detail.
Perl keeps a symbol table hash - a stash - that work very like ordinary Perl hashes. There is one such stash for each package, including the default package main. Note that this hash nothing to do with lexical variables - declared with my - which are stored entirely separately.
Ther indexes for the stashes are the names of the package variables, without the initial symbol. So, for example, if you have
our $val;
our #val;
our %val;
then the stash will have only a single element, with a key of val and a value which is a reference to an intermediate structure called a typeglob. This is another hash structure, with one element for each different type of variable that has been declared. In this case our val typeglob will have three elements, for the scalar, array, and hash varieties of the val variables.
One of these elements may also be an IO variable type, which is where file handles are kept. But, for historical reasons, the value that is passed around as a file handle is in fact a reference to the typeglob that contains it. That is why, if you write open my $in, '<', 'phonebook.txt' and then print $in you will see something like GLOB(0x269581c) - the GLOB being short for typeglob.
Apart from that, the account above is accurate. Perl autovivifies an anonymous typeglob in the current package, and uses only its IO slot for the file handle.
Scalars in Perl are denoted by a $ and they can indeed contain the type of values you mention in your questions but next to that they can also contain a file handle. You can create file handles in Perl in two ways one way is Lexical
open my $filehandle, '>', '/path/to/file' or die $!;
and the other is global
open FILEHANDLE, '>', '/path/to/file' or die $!;
You should use the Lexical version which is what you're doing.
The while loop in your code uses the <> operator on your lexical filehandle which returns a line out of your file every time it's called, until it's out of lines (when End Of File is reached) in which case it returns false.
I went into a bit more detail on file handles as it seems it's a concept you're not completely clear on.

A better variable naming system?

A newbie to programming. The task is to extract a particular data from a string and I chose to write the code as follows -
while ($line =<IN>) {
chomp $line;
#tmp=(split /\t/, $line);
next if ($tmp[0] !~ /ch/);
#tgt1=#tmp[8..11];
#tgt2=#tmp[12..14];
#tgt3=#tmp[15..17];
#tgt4=#tmp[18..21];
foreach (1..4) {
print #tgt($_), "\n";
}
I thought #tgt($_) would be interpreted as #tgt1, #tgt2, #tgt3, #tgt4 but I still get the error message that #tgt is a global symbol (#tgt1, #tgt2, #tgt3, #tgt4` have been declared).
Q1. Did I misunderstand foreach loop?
Q2. Why couldn't perl see #tgt($_) as #tgt1, #tgt2 ..etc?
Q2. From the experience this is probably a bad way to name variables. What would be a preferred way to name variables that have similar features?
Q2. Why couldn't perl see #tgt($_) as #tgt1, #tgt2 ..etc?
Q2. From the experience this is probably a bad way to name variables. What would be a preferred way to name variables that have similar features?
I'll asnswer both together.
#tgt($_) does NOT mean what you hope it means
First off, it's an invalid syntax (you can't use () after an array name, perl interpeter will produce a compile error).
What you're trying to do is access distinct variables by accessing a variable via an expression resulting in its name (aka symbolic references). This IS possible to do; but is typically a bad idea and poor-style Perl (as in, you CAN but you SHOULD NOT do it, without a very very good reason).
To access element $_ the way you tried, you use #{"tgt$_"} syntax. But I repeat - Do Not Do That, even if you can.
A correct idiomatic solution: use an array of arrayrefs, with your 1-4 (or rather 0-3) indexing the outer array:
# Old bad code: #tgt1=#tmp[8..11];
# New correct code:
$tgt[0]=[ #tmp[8..11] ]; # [] creates an array reference from a list.
# etc... repeat 4 times - you can even do it in a smart loop later.
What this does is, it stores a reference to an array slice into a zeroth element of a single #tgt array.
At the end, #tgt array has 4 elements , each an array reference to an array containing one of the slices.
Q1. Did I misunderstand foreach loop?
Your foreach loop (as opposed to its contents - see above) was correct, with one style caveat - again, while you CAN use a default $_ variable, you should almost never use it, instead always use named variables for readability.
You print the abovementioned array of arrayrefs as follows (ask separately if any of the syntax is unclear - this is a mid-level data structure handling, not for beginners):
foreach my $index (0..3) {
print join(",", #{ $tgt[$index]}) . "\n";
}

Perl Program to Mimic RNA Synthesis

Looking for suggestions on how to approach my Perl programming homework assignment to write an RNA synthesis program. I've summed and outlined the program below. Specifically, I'm looking for feedback on the blocks below (I'll number for easy reference). I've read up to chapter 6 in Elements of Programming with Perl by Andrew Johnson (great book). I've also read the perlfunc and perlop pod-pages with nothing jumping out on where to start.
Program Description: The program should read an input file from the command line, translate it into RNA, and then transcribe the RNA into a sequence of uppercase one-letter amino acid names.
Accept a file named on the command line
here I will use the <> operator
Check to make sure the file only contains acgt or die
if ( <> ne [acgt] ) { die "usage: file must only contain nucleotides \n"; }
Transcribe the DNA to RNA (Every A replaced by U, T replaced by A, C replaced by G, G replaced by C)
not sure how to do this
Take this transcription & break it into 3 character 'codons' starting at the first occurance of "AUG"
not sure but I'm thinking this is where I will start a %hash variables?
Take the 3 character "codons" and give them a single letter Symbol (an uppercase one-letter amino acid name)
Assign a key a value using (there are 70 possibilities here so I'm not sure where to store or how to access)
If a gap is encountered a new line is started and process is repeated
not sure but we can assume that gaps are multiples of threes.
Am I approaching this the right way? Is there a Perl function that I'm overlooking that can simplify the main program?
Note
Must be self contained program (stored values for codon names & symbols).
Whenever the program reads a codon that has no symbol this is a gap in the RNA, it should start a new line of output and begin at the next occurance of "AUG". For simplicity we can assume that gaps are always multiples of threes.
Before I spend any additional hours on research I am hoping to get confirmation that I'm taking the right approach. Thanks for taking time to read and for sharing your expertise!
1. here I will use the <> operator
OK, your plan is to read the file line by line. Don't forget to chomp each line as you go, or you'll end up with newline characters in your sequence.
2. Check to make sure the file only contains acgt or die
if ( <> ne [acgt] ) { die "usage: file must only contain nucleotides \n"; }
In a while loop, the <> operator puts the line read into the special variable $_, unless you assign it explicitly (my $line = <>).
In the code above, you're reading one line from the file and discarding it. You'll need to save that line.
Also, the ne operator compares two strings, not one string and one regular expression. You'll need the !~ operator here (or the =~ one, with a negated character class [^acgt]. If you need the test to be case-insensitive, look into the i flag for regular expression matching.
3. Transcribe the DNA to RNA (Every A replaced by U, T replaced by A, C replaced by G, G replaced by C).
As GWW said, check your biology. T->U is the only step in transcription. You'll find the tr (transliterate) operator helpful here.
4. Take this transcription & break it into 3 character 'codons' starting at the first occurance of "AUG"
not sure but I'm thinking this is where I will start a %hash variables?
I would use a buffer here. Define an scalar outside the while(<>) loop. Use index to match "AUG". If you don't find it, put the last two bases on that scalar (you can use substr $line, -2, 2 for that). On the next iteration of the loop append (with .=) the line to those two bases, and then test for "AUG" again. If you get a hit, you'll know where, so you can mark the spot and start translation.
5. Take the 3 character "codons" and give them a single letter Symbol (an uppercase one-letter amino acid name)
Assign a key a value using (there are 70 possibilities here so I'm not sure where to store or how to access)
Again, as GWW said, build a hash table:
%codons = ( AUG => 'M', ...).
Then you can use (for eg.) split to build an array of the current line you're examining, build codons three elements at a time, and grab the correct aminoacid code from the hash table.
6.If a gap is encountered a new line is started and process is repeated
not sure but we can assume that gaps are multiples of threes.
See above. You can test for the existence of a gap with exists $codons{$current_codon}.
7. Am I approaching this the right way? Is there a Perl function that I'm overlooking that can simplify the main program?
You know, looking at the above, it seems way too complex. I built a few building blocks; the subroutines read_codon and translate: I think they help the logic of the program immensely.
I know this is a homework assignment, but I figure it might help you get a feel for other possible approaches:
use warnings; use strict;
use feature 'state';
# read_codon works by using the new [state][1] feature in Perl 5.10
# both #buffer and $handle represent 'state' on this function:
# Both permits abstracting reading codons from processing the file
# line-by-line.
# Once read_colon is called for the first time, both are initialized.
# Since $handle is a state variable, the current file handle position
# is never reset. Similarly, #buffer always holds whatever was left
# from the previous call.
# The base case is that #buffer contains less than 3bp, in which case
# we need to read a new line, remove the "\n" character,
# split it and push the resulting list to the end of the #buffer.
# If we encounter EOF on the $handle, then we have exhausted the file,
# and the #buffer as well, so we 'return' undef.
# otherwise we pick the first 3bp of the #buffer, join them into a string,
# transcribe it and return it.
sub read_codon {
my ($file) = #_;
state #buffer;
open state $handle, '<', $file or die $!;
if (#buffer < 3) {
my $new_line = scalar <$handle> or return;
chomp $new_line;
push #buffer, split //, $new_line;
}
return transcribe(
join '',
shift #buffer,
shift #buffer,
shift #buffer
);
}
sub transcribe {
my ($codon) = #_;
$codon =~ tr/T/U/;
return $codon;
}
# translate works by using the new [state][1] feature in Perl 5.10
# the $TRANSLATE state is initialized to 0
# as codons are passed to it,
# the sub updates the state according to start and stop codons.
# Since $TRANSLATE is a state variable, it is only initialized once,
# (the first time the sub is called)
# If the current state is 'translating',
# then the sub returns the appropriate amino-acid from the %codes table, if any.
# Thus this provides a logical way to the caller of this sub to determine whether
# it should print an amino-acid or not: if not, the sub will return undef.
# %codes could also be a state variable, but since it is not actually a 'state',
# it is initialized once, in a code block visible form the sub,
# but separate from the rest of the program, since it is 'private' to the sub
{
our %codes = (
AUG => 'M',
...
);
sub translate {
my ($codon) = #_ or return;
state $TRANSLATE = 0;
$TRANSLATE = 1 if $codon =~ m/AUG/i;
$TRANSLATE = 0 if $codon =~ m/U(AA|GA|AG)/i;
return $codes{$codon} if $TRANSLATE;
}
}
I can give you a few hints on a few of your points.
I think your first goal should be to parse the file character by character, ensuring each one is valid, group them into sets of three nucleotides and then work on your other goals.
I think your biology is a bit off as well, when you transcribe DNA to RNA you need to think about what strands are involved. You may not need to "complement" your bases during your transcription step.
2. You should check this as your parse the file character by character.
3. You could do this with a loop and some if statements or hash
4. This could probably be done with a counter as you read the file character by character. Since you need to insert a space after every 3rd character.
5. This would be a good place to use a hash that's based on the amino acid codon table.
6. You'll have to look for the gap character as you parse the file. This seems to contradict your #2 requirement since the program says your text can only contain ATGC.
There are a lot of perl functions that could make this easier. There are also perl modules such as bioperl. But I think using some of these could defeat the purpose of your assignment.
Look at BioPerl and browse the source-modules for indicators on how to go about it.

Can someone suggest how this Perl script works?

I have to maintain the following Perl script:
#!/usr/bin/perl -w
die "Usage: $0 <file1> <file2>\n" unless scalar(#ARGV)>1;
undef $/;
my #f1 = split(/(?=(?:SERIAL NUMBER:\s+\d+))/, <>);
my #f2 = split(/(?=(?:SERIAL NUMBER:\s+\d+))/, <>);
die "Error: file1 has $#f1 serials, file2 has $#f2\n" if ($#f1 != $#f2);
foreach my $g (0 .. $#f1) {
print (($f2[$g] =~ m/RESULT:\s+PASS/) ? $f2[$g] : $f1[$g]);
}
print STDERR "$#f1 serials found\n";
I know pretty much what it does, but how it's done is difficult to follow. The calls to split() are particulary puzzling.
It's fairly idiomatic Perl and I would be grateful if a Perl expert could make a few clarifying suggestions about how it does it, so that if I need to use it on input files it can't deal with, I can attempt to modify it.
It combines the best results from two datalog files containing test results. The datalog files contain results for various serial numbers and the data for each serial number begins and ends with SERIAL NUMBER: n (I know this because my equipment creates the input files)
I could describe the format of the datalog files, but I think the only important aspect is the SERIAL NUMBER: n because that's all the Perl script checks for
The ternary operator is used to print a value from one input file or the other, so the output can be redirected to a third file.
This may not be what I would call "idiomatic" (that would be use Module::To::Do::Task) but they've certainly (ab)used some language features here. I'll see if I can't demystify some of this for you.
die "Usage: $0 <file1> <file2>\n" unless scalar(#ARGV)>1;
This exits with a usage message if they didn't give us any arguments. Command-line arguments are stored in #ARGV, which is like C's char **argv except the first element is the first argument, not the program name. scalar(#ARGV) converts #ARGV to "scalar context", which means that, while #ARGV is normally a list, we want to know about it's scalar (i.e. non-list) properties. When a list is converted to scalar context, we get the list's length. Therefore, the unless conditional is satisfied only if we passed no arguments.
This is rather misleading, because it will turn out your program needs two arguments. If I wrote this, I would write:
die "Usage: $0 <file1> <file2>\n" unless #ARGV == 2;
Notice I left off the scalar(#ARGV) and just wrote #ARGV. The scalar() function forces scalar context, but if we're comparing equality with a number, Perl can implicitly assume scalar context.
undef $/;
Oof. The $/ variable is a special Perl built-in variable that Perl uses to tell what a "line" of data from a file is. Normally, $/ is set to the string "\n", meaning when Perl tries to read a line it will read up until the next linefeed (or carriage return/linefeed on Windows). Your writer has undef-ed the variable, though, which means when you try to read a "line", Perl will just slurp up the whole file.
my #f1 = split(/(?=(?:SERIAL NUMBER:\s+\d+))/, <>);
This is a fun one. <> is a special filehandle that reads line-by-line from each file given on the command line. However, since we've told Perl that a "line" is an entire file, calling <> once will read in the entire file given in the first argument, and storing it temporarily as a string.
Then we take that string and split() it up into pieces, using the regex /(?=(?:SERIAL NUMBER:\s+\d+))/. This uses a lookahead, which tells our regex engine "only match if this stuff comes after our match, but this stuff isn't part of our match," essentially allowing us to look ahead of our match to check on more info. It basically splits the file into pieces, where each piece (except possibly the first) begins with "SERIAL NUMBER:", some arbitrary whitespace (the \s+ part), and then some digits (the \d+ part). I can't teach you regexes, so for more info I recommend reading perldoc perlretut - they explain all of that better than I ever will.
Once we've split the string into a list, we store that list in a list called #f1.
my #f2 = split(/(?=(?:SERIAL NUMBER:\s+\d+))/, <>);
This does the same thing as the last line, only to the second file, because <> has already read the entire first file, and storing the list in another variable called #f2.
die "Error: file1 has $#f1 serials, file2 has $#f2\n" if ($#f1 != $#f2);
This line prints an error message if #f1 and #f2 are different sizes. $#f1 is a special syntax for arrays - it returns the index of the last element, which will usually be the size of the list minus one (lists are 0-indexed, like in most languages). He uses this same value in his error message, which may be deceptive, as it will print 1 fewer than might be expected. I would write it as:
die "Error: file $ARGV[0] has ", $#f1 + 1, " serials, file $ARGV[1] has ", $#f2 + 1, "\n"
if $#f1 != $#f2;
Notice I changed "file1" to "file $ARGV[0]" - that way, it will print the name of the file you specified, rather than just the ambiguous "file1". Notice also that I split up the die() function and the if() condition on two lines. I think it's more readable that way. I also might write unless $#f1 == $#f2 instead of if $#f1 != $#f2, but that's just because I happen to think != is an ugly operator. There's more than one way to do it.
foreach my $g (0 .. $#f1) {
This is a common idiom in Perl. We normally use for() or foreach() (same thing, really) to iterate over each element of a list. However, sometimes we need the indices of that list (some languages might use the term "enumerate"), so we've used the range operator (..) to make a list that goes from 0 to $#f1, i.e., through all the indices of our list, since $#f1 is the value of the highest index in our list. Perl will loop through each index, and in each loop, will assign the value of that index to the lexically-scoped variable $g (though why they didn't use $i like any sane programmer, I don't know - come on, people, this tradition has been around since Fortran!). So the first time through the loop, $g will be 0, and the second time it will be 1, and so on until the last time it is $#f1.
print (($f2[$g] =~ m/RESULT:\s+PASS/) ? $f2[$g] : $f1[$g]);
This is the body of our loop, which uses the ternary conditional operator ?:. There's nothing wrong with the ternary operator, but if the code gives you trouble we can just change it to an if(). Let's just go ahead and rewrite it to use if():
if($f2[$g] =~ m/RESULT:\s+PASS/) {
print $f2[$g];
} else {
print $f1[$g];
}
Pretty simple - we do a regex check on $f2[$g] (the entry in our second file corresponding to the current entry in our first file) that basically checks whether or not that test passed. If it did, we print $f2[$g] (which will tell us that test passed), otherwise we print $f1[$g] (which will tell us the test that failed).
print STDERR "$#f1 serials found\n";
This just prints an ending diagnostic message telling us how many serials were found (minus one, again).
I personally would rewrite that whole hairy bit where he hacks with $/ and then does two reads from <> to be a loop, because I think that would be more readable, but this code should work fine, so if you don't have to change it too much you should be in good shape.
The undef $/ line deactivates the input record separator. Instead of reading records line by line, the interpreter will read whole files at once after that.
The <>, or 'diamond operator' reads from the files from the command line or standard input, whichever makes sense. In your case, the command line is explicitely checked, so it will be files. Input record separation has been deactivated, so each time you see a <>, you can think of it as a function call returning a whole file as a string.
The split operators take this string and cut it in chunks, each time it meets the regular expression in argument. The (?= ... ) construct means "the delimiter is this, but please keep it in the chunked result anyway."
That's all there is to it. There would always be a few optimizations, simplifications, or "other ways to do it," but this should get you running.
You can get quick glimpse how the script works, by translating it into java or scala. The inccode.com translator delivers following java code:
public class script extends CRoutineProcess implements IInProcess
{
VarArray arrF1 = new VarArray();
VarArray arrF2 = new VarArray();
VarBox call ()
{
// !/usr/bin/perl -w
if (!(BoxSystem.ProgramArguments.scalar().isGT(1)))
{
BoxSystem.die(BoxString.is(VarString.is("Usage: ").join(BoxSystem.foundArgument.get(0
).toString()).join(" <file1> <file2>\n")
)
);
}
BoxSystem.InputRecordSeparator.empty();
arrF1.setValue(BoxConsole.readLine().split(BoxPattern.is("(?=(?:SERIAL NUMBER:\\s+\\d+))")));
arrF2.setValue(BoxConsole.readLine().split(BoxPattern.is("(?=(?:SERIAL NUMBER:\\s+\\d+))")));
if ((arrF1.length().isNE(arrF2.length())))
{
BoxSystem.die("Error: file1 has $#f1 serials, file2 has $#f2\n");
}
for (
VarBox varG : VarRange.is(0,arrF1.length()))
{
BoxSystem.print((arrF2.get(varG).like(BoxPattern.is("RESULT:\\s+PASS"))) ? arrF2.get(varG) : arrF1.get(varG)
);
}
return STDERR.print("$#f1 serials found\n");
}
}