Can someone suggest how this Perl script works? - perl

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");
}
}

Related

Perl subroutines

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.

What happens internally when you have < FH >, <>, or < * > in perl?

I apologize if this question sounds simple, my intention is to understand in depth how this (these?) particular operator(s) works and I was unable to find a satisfactory description in the perldocs (It probably exists somewhere, I just couldn't find it for the life of me)
Particularly, I am interested in knowing if
a) <>
b) <*> or whatever glob and
c) <FH>
are fundamentally similar or different, and how they are used internally.
I built my own testing functions to gain some insight on this (presented below). I still don't have a full understanding (my understanding might even be wrong) but this is what I've concluded:
<>
In Scalar Context: Reads the next line of the "current file" being read (provided in #ARGV). Questions: This seems like a very particular scenario, and I wonder why it is the way it is and whether it can be generalized or not. Also what is the "current file" that is being read? Is it in a file handle? What is the counter?
In List Context: Reads ALL of the files in #ARGV into an array
<list of globs>
In Scalar Context: Name of the first file found in current folder that matches the glob. Questions: Why the current folder? How do I change this? Is the only way to change this doing something like < /home/* > ?
In List Context: All the files that match the glob in the current folder.
<FH> just seems to return undef when assigned to a variable.
Questions: Why is it undef? Does it not have a type? Does this behave similarly when the FH is not a bareword filehandle?
General Question: What is it that handles the value of <> and the others during execution? In scalar context, is any sort of reference returned, or are the variables that we assign them to, at that point identical to any other non-ref scalar?
I also noticed that even though I am assigning them in sequence, the output is reset each time. i.e. I would have assumed that when I do
$thing_s = <>;
#thing_l = <>;
#thing_l would be missing the first item, since it was already received by $thing_s. Why is this not the case?
Code used for testing:
use strict;
use warnings;
use Switch;
use Data::Dumper;
die "Call with a list of files\n" if (#ARGV<1);
my #whats = ('<>','<* .*>','<FH>');
my $thing_s;
my #thing_l;
for my $what(#whats){
switch($what){
case('<>'){
$thing_s = <>;
#thing_l = <>;
}
case('<* .*>'){
$thing_s = <* .*>;
#thing_l = <* .*>;
}
case('<FH>'){
open FH, '<', $ARGV[0];
$thing_s = <FH>;
#thing_l = <FH>;
}
}
print "$what in scalar context is: \n".Dumper($thing_s)."\n";
print "$what in list context is: \n".Dumper(#thing_l)."\n";
}
The <> thingies are all iterators. All of these variants have common behaviour:
Used in list context, all remaining elements are returned.
Used in scalar context, only the next element is returned.
Used in scalar context, it returns undef once the iterator is exhausted.
These last two properties make it suitable for use as a condition in while loops.
There are two kinds of iterators that can be used with <>:
Filehandles. In this case <$fh> is equivalent to readline $fh.
Globs, so <* .*> is equivalent to glob '* .*'.
The <> is parsed as a readline when it contains either nothing, a bareword, or a simple scalar. More complex expression can be embedded like <{ ... }>.
It is parsed as a glob in all other cases. This can be made explicit by using quotes: <"* .*"> but you should really be explicit and use the glob function instead.
Some details differ, e.g. where the iterator state is kept:
When reading from a file handle, the file handle holds that iterator state.
When using the glob form, each glob expression has its own state.
Another part is if the iterator can restart:
glob restarts after returning one undef.
filehandles can only be restarted by seeking – not all FHs support this operation.
If no file handle is used in <>, then this defaults to the special ARGV file handle. The behaviour of <ARGV> is as follows:
If #ARGV is empty, then ARGV is STDIN.
Otherwise, the elements of #ARGV are treated as file names. The following pseudocode is executed:
$ARGV = shift #ARGV;
open ARGV, $ARGV or die ...; # careful! no open mode is used
The $ARGV scalar holds the filename, and the ARGV file handle holds that file handle.
When ARGV would be eof, the next file from #ARGV is opened.
Only when #ARGV is completely empty can <> return undef.
This can actually be used as a trick to read from many files:
local #ARGV = qw(foo.txt bar.txt baz.txt);
while (<>) {
...;
}
What is it that handles the value of <> and the others during execution?
The Perl compiler is very context-aware, and often has to choose between multiple ambiguous interpretations of a code segment. It will compile <> as a call to readline or to glob depending on what is inside the brackets.
In scalar context, is any sort of reference returned, or are the variables that we assign them to, at that point identical to any other non-ref scalar?
I'm not sure what you're asking here, or why you think the variables that take the result of a <> should be any different from other variables. They are always simple string values: either a filename returned by glob, or some file data returned by readline.
<FH> just seems to return undef when assigned to a variable. Questions: Why is it undef? Does it not have a type? Does this behave similarly when the FH is not a bareword filehandle?
This form will treat FH as a filehandle, and return the next line of data from the file if it is open and not at eof. Otherwise undef is returned, to indicate that nothing valid could be read. Perl is very flexible with types, but undef behaves as its own type, like Ruby's nil. The operator behaves the same whether FH is a global file handle or a (variable that contains) a reference to a typeglob.

How to get rid of use of an uninitialized value within an 'if' construct using a Perl regex

How do I get rid of use of an uninitialized value within an if construct using a Perl regex?
When using the code below, I get use of uninitialized value messages.
if($arrayOld[$i] =~ /-(.*)/ || $arrayOld[$i] =~ /\#(.*)/)
When using the code below, I get no output.
if(defined($arrayOld[$i]) =~ /-(.*)/ || defined($arrayOld[$i]) =~ /\#(.*)/)
What is the proper way to check if a variable has a value given the code above?
Try:
if($arrayOld[$i] && $arrayOld[$i] =~ /-|\#(.*)/)
This first checks $arrayOld[$i] for a value before running a regx against it.
(Have also combined the || into the regex.)
From the error message in your comment, you're accessing an element of #arrayOld that isn't defined. Without seeing the rest of the code, this could indicate a bug in your program, or it could just be expected behavior.
If you understand why $arrayOld[$i] is undef, and you want to allow that without getting a warning, there's a couple of things you can do. Perl 5.10.0 introduced the defined-or operator //, which you can use to substitute the empty string for undef:
use 5.010;
...
if(($arrayOld[$i] // '') =~ /-(.*)/ || ($arrayOld[$i] // '') =~ /\#(.*)/)
Or, you can just turn off the warning:
if (do { no warnings 'uninitalized';
$arrayOld[$i] =~ /-(.*)/ || $arrayOld[$i] =~ /\#(.*)/ })
Here, I'm using do to limit the time the warning is disabled. However, turning off the warning also suppresses the warning you'd get if $i were undef. Using // allows you to specify exactly what is allowed to be undef, and exactly what value should be used instead of undef.
Note: defined($arrayOld[$i]) =~ /-(.*)/ is running a pattern match on the result of the defined function, which is just going to be a true/false value; not the string you want to test.
To answer your question narrowly, you can prevent undefined-value warnings in that line of code with
if (defined $i && defined $arrayOld[$i]
&& ($arrayOld[$i] =~ /-(.*)/ || $arrayOld[$i] =~ /\#(.*)/))
{
...;
}
That is, evaluating either $i or the expression $arrayOld[$i] may result in an undefined value. Note the additional layer of parentheses that are necessary as written above because of the difference in precedence between && and ||, with the former binding more tightly. For the particular patterns in your question, you could sidestep this precedence issue by combining your patterns into one regex, but this can be tricky to do in the general case.
I recommend against using the unpleasing code above. Read on to see an elegant solution to your problem that has Perl do the work for you and is much easier to read.
Looking back
From the slightly broader context of your earlier question, $i is a loop variable and by construction will certainly be defined, so testing $i is overkill. Your code blindly pulls elements from #arrayOld, and Perl happily obliges. In cases where nothing is there, you get the undefined value.
This sort of one-by-one peeking and poking is common in C programs, but in Perl, it is almost always a red flag that you could express your algorithm more elegantly. Consider the complete, working example below.
Working demonstration
#! /usr/bin/env perl
use strict;
use warnings;
use 5.10.0; # given/when
*FILEREAD = *DATA; # for demo only
my #interesting_line = (qr/-(.*)/, qr/\#(.*)/);
$/ = ""; # paragraph mode
while(<FILEREAD>) {
chomp;
my #arrayOld = split /\n/;
my #arrayNewLines;
for (1 .. #arrayOld) {
given (shift #arrayOld) {
push #arrayNewLines, $_ when #interesting_line;
push #arrayOld, $_;
}
}
print "\#arrayOld:\n", map("$_\n", #arrayOld), "\n",
"\#arrayNewLines:\n", map("$_\n", #arrayNewLines);
}
__DATA__
#SCSI_test # put this line into #arrayNewLines
kdkdkdkdkdkdkdkd
dkdkdkdkdkdkdkdkd
- ccccccccccccccc # put this line into #arrayNewLines
Front matter
The line
use 5.10.0;
enables Perl’s given/when switch statement, and this makes for a nice way to decide which array gets a given line of input.
As the comment indicates
*FILEREAD = *DATA; # for demo only
is for the purpose of this Stack Overflow demonstration. In your real code, you have open FILEREAD, .... Placing the input from your question into Perl’s DATA filehandle allows presenting code and input in one self-contained unit, and then we alias FILEREAD to DATA so the rest of the code will drop into yours with no fuss.
The main event
The core of the processing is
for (1 .. #arrayOld) {
given (shift #arrayOld) {
push #arrayNewLines, $_ when #interesting_line;
push #arrayOld, $_;
}
}
Notice that there are no defined checks or even explicit regex matches! There’s no $i or $arrayOld[$i]! What’s going on?
You start with #arrayOld containing all the lines from the current paragraph and want to end with the interesting lines in #arrayNewLines and everything else staying in #arrayOld. The code above takes the next line out of #arrayOld with shift. If the line is interesting, we push it onto the end of #arrayNewLines. Otherwise, we put it back on the end of #arrayOld.
The statement modifier when #interesting_line performs an implicit smart-match with the topic from given. As explained in “Smart matching in detail,” when smart matching against an array, Perl implicitly loops over it and stops on the first match. In this case, the array #interesting_line contains compiled regexes that match lines you want to move to #arrayNewLines. If the current line (in $_ thanks to given) does not match any of those patterns, it goes back in #arrayOld.
We do the preceding process exactly scalar #arrayOld times, that is, once for each line in the current paragraph. This way, we process everything exactly once and do not have to worry about fussy bookkeeping over where the current array index is. Whatever is left in #arrayOld after that many shifts must be the lines we pushed back onto it, which are the uninteresting lines in the order that the occurred in the input.
Sample output
For the input in your question, the output is
#arrayOld:
kdkdkdkdkdkdkdkd
dkdkdkdkdkdkdkdkd
#arrayNewLines:
#SCSI_test # put this line into #arrayNewLines
- ccccccccccccccc # put this line into #arrayNewLines

Need more explanation about what's being done here?

print reverse <>;
print sort <>;
What's the exact steps perl handles with these operations?
It seems for the 1st one,perl not just reverses the order of invocation parameters,but also the contents of each file...
print reverse <>;
<> is evaluated in an array context, meaning it "slurps" the file. It reads the entire file. In the case of the magic file represented by the files named in #ARGV, it will read the contents of all files in the order referenced by the command line arguments (#ARGV).
reverse then reverses the order of the array, meaning the last line from the last file comes first, and the first line from the last file comes last.
print then prints the array.
From your notes, you might want something like this:
perl -e 'sub BEGIN { #ARGV=reverse #ARGV; } print <>;' /etc/motd /etc/passwd
This is described in the docs for I/O operators. Here's an excerpt from the docs:
The null filehandle <> is special: it can be used to emulate the behavior of sed and awk. Input from <> comes either from standard input, or from each file listed on the command line. Here's how it works: the first time <> is evaluated, the #ARGV array is checked, and if it is empty, $ARGV[0] is set to "-", which when opened gives you standard input. The #ARGV array is then processed as a list of filenames.
It's worth reading the entire doc, as it provides equivalent "non-magical" Perl code equivalent to <> in various use cases.

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.