Why do I get a syntax error in the following script?
print "Enter Sequence:";
$a = <STDIN>;
if ($a=="A")|| ($a== "T")|| ( $a == "C")|| ($a== "G")
{
print $a;
}
else
{
print "Error";
}
First, you have a syntax error: The condition expression of an if statement must be in parens.
The second error is found by using use strict; use warnings;, something you should always do. The error is the use of numerical comparison (==) where string comparison (eq) is called for.
The final problem is that $a will almost surely contain a string ending with a newline, so a chomp is in order.
The immediate problem is that he entire logical expression for an if must be in parentheses.
In addition
You must use eq instead of == for comparing strings
Your input string will have a trailing newline, so it will look like "C\n" and will not match a simple one-character string. You need to chomp the input before you compare it
It is generally better to read from STDIN using <> rather than <STDIN>. That way you can specify an input file on the command line, or read from the STDIN if no input was provided
You must always put use strict and use warnings at the top of your program. That will catch many simple errors that you may otherwise overlook
You shouldn't use $a as a variable name. It is a symbol reserved by Perl itself, and says nothing about the purpose of the variable
It is best to use a regular expression for simple comparisons like this. It makes your code much easier to read and will usually make the execution very much faster
Please take a look at this program, which I think does what you want.
use strict;
use warnings;
print "Enter Sequence: ";
my $input = <>;
chomp $input;
if ( $input =~ /^[ATCG]$/i ) {
print $input, "\n";
}
else {
print "Error";
}
Related
Suppose I have a function that dynamically generates regular expressions and then matches against them.
For example, in the following function match_here a \G anchor is inserted at the beginning of the regex. This simplifies the API because the caller does not need to remember to include the pos anchor in the pattern.
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Data::Dumper;
sub match_here {
my ($str, $index, $rg) = #_;
pos($str) = $index;
croak "index ($index) out of bounds" unless pos($str) == $index;
my $out;
if ($str =~ /\G$rg/) {
$out = $+[0];
}
return $out;
}
# no match starting at position 0
# prints '$VAR1 = undef;'
print Dumper(match_here("abc", 0, "b+"));
# match from 1 to 2
# prints '$VAR1 = 2;'
print Dumper(match_here("abc", 1, "b+"));
I'm wondering whether an anonymous regex object is "compiled" every time the function is evaluated or if there's some caching so that identical strings will not cause additional regex objects to be compiled.
Also, assuming that no caching is done by the Perl interpreter, is compiling a regex object expensive enough to be worth caching (possibly in an XS extension)?
From perlop(1), under the m// operator:
PATTERN may contain variables, which will be interpolated every time the pattern search is evaluated
[...]
Perl will not recompile the pattern unless an interpolated variable that it contains changes. You can force Perl to skip the test and never recompile by adding a "/o" (which stands for "once") after the trailing delimiter. Once upon a time, Perl would recompile regular expressions unnecessarily, and this modifier was useful to tell it not to do so, in the interests of speed.
So yes, there is a cache, and you can even force the use of the cache even when it's invalid by saying /o, but you really shouldn't do that.
But that cache only stores one compiled regexp per instance of the m// or s/// operator, so it only helps if the regexp is used with the same variables (e.g. your $rg) many times consecutively. If you alternate between calling it with $rg='b+' and $rg='c+' you will get a recompile every time.
For that kind of situation, you can do your own caching with the qr// operator. It explicitly compiles the regexp and returns an object that you can store and use to execute the regexp later. That could be incorporated into your match_here like this:
use feature 'state';
sub match_here {
my ($str, $index, $rg) = #_;
pos($str) = $index;
croak "index ($index) out of bounds" unless pos($str) == $index;
my $out;
state %rg_cache;
my $crg = $rg_cache{$rg} ||= qr/\G$rg/;
if ($str =~ /$crg/) {
$out = $+[0];
}
return $out;
}
To add more detail on the basic cache (when not using qr//): the fact that $rg is a newly allocated lexical variable each time makes no difference. It only matters that the value is the same as the previous one.
Here's an example to prove the point:
use re qw(Debug COMPILE);
while(<>) {
chomp;
# Insane interpolation. Do not use anything remotely like this in real code
print "MATCHED: $_\n" if /^${\(`cat refile`)}/;
}
Every time the match operator executes, it reads refile. The regular expression is ^ followed by the contents of refile. The debugging output shows that it is recompiled only if the contents of the file have changed. If the file still has the same contents as the last time, the operator notices that the same string is being passed to the regexp compiler again, and reuses the cached result.
Or try this less dramatic example:
use re qw(Debug COMPILE);
#patterns = (
'\d{3}',
'\d{3}',
'[aeiou]',
'[aeiou]',
'\d{3}',
'\d{3}'
);
for ('xyz', '123', 'other') {
for $i (0..$#patterns) {
if(/$patterns[$i]/) {
print "$_ matches $patterns[$i]\n";
} else {
print "$_ does not match $patterns[$i]\n";
}
}
}
in which there are 18 compilations and 11 of them are cache hits, even though the same "variable" (the same element of the #patterns array) is never used twice in a row.
I'm just starting in Perl and I'm quite enjoying it. I'm writing some basic functions, but what I really want to be able to do is to use those functions intelligently using console commands. For example, say I have a function adding two numbers. I'd want to be able to type in console "add 2, 4" and read the first word, then pass the two numbers as parameters in an "add" function. Essentially, I'm asking for help in creating some basic scripting using Perl ^^'.
I have some vague ideas about how I might do this in VB, but Perl, I have no idea where I'd start, or what functions would be useful to me. Is there something like VB.net's "Split" function where you can break down the contents of a scalar into an array? Is there a simple way to analyse one word at a time in a scalar, or iterate through a scalar until you hit a separator, for example?
I hope you can help, any suggestions are appreciated! Bear in mind, I'm no expert, I started Perl all of a few weeks ago, and I've only been doing VB.net half a year.
Thank you!
Edit: If you're not sure what to suggest and you know any simple/intuitive resources that might be of help, that would also be appreciated.
Its rather easy to make a script which dispatches to a command by name. Here is a simple example:
#!/usr/bin/env perl
use strict;
use warnings;
# take the command name off the #ARGV stack
my $command_name = shift;
# get a reference to the subroutine by name
my $command = __PACKAGE__->can($command_name) || die "Unknown command: $command_name\n";
# execute the command, using the rest of #ARGV as arguments
# and print the return with a trailing newline
print $command->(#ARGV);
print "\n";
sub add {
my ($x, $y) = #_;
return $x + $y;
}
sub subtract {
my ($x, $y) = #_;
return $x - $y;
}
This script (say its named myscript.pl) can be called like
$ ./myscript.pl add 2 3
or
$ ./myscript.pl subtract 2 3
Once you have played with that for a while, you might want to take it further and use a framework for this kind of thing. There are several available, like App::Cmd or you can take the logic shown above and modularize as you see fit.
You want to parse command line arguments. A space serves as the delimiter, so just do a ./add.pl 2 3 Something like this:
$num1=$ARGV[0];
$num2=$ARGV[1];
print $num1 + $num2;
will print 5
Here is a short implementation of a simple scripting language.
Each statement is exactly one line long, and has the following structure:
Statement = [<Var> =] <Command> [<Arg> ...]
# This is a regular grammar, so we don't need a complicated parser.
Tokens are seperated by whitespace. A command may take any number of arguments. These can either be the contents of variables $var, a string "foo", or a number (int or float).
As these are Perl scalars, there is no visible difference between strings and numbers.
Here is the preamble of the script:
#!/usr/bin/perl
use strict;
use warnings;
use 5.010;
strict and warnings are essential when learning Perl, else too much weird stuff would be possible. The use 5.010 is a minimum version, it also defines the say builtin (like a print but appends a newline).
Now we declare two global variables: The %env hash (table or dict) associates variable names with their values. %functions holds our builtin functions. The values are anonymous functions.
my %env;
my %functions = (
add => sub { $_[0] + $_[1] },
mul => sub { $_[0] * $_[1] },
say => sub { say $_[0] },
bye => sub { exit 0 },
);
Now comes our read-eval-loop (we don't print by default). The readline operator <> will read from the file specified as the first command line argument, or from STDIN if no filename is provided.
while (<>) {
next if /^\s*\#/; # jump comment lines
# parse the line. We get a destination $var, a $command, and any number of #args
my ($var, $command, #args) = parse($_);
# Execute the anonymous sub specified by $command with the #args
my $value = $functions{ $command }->(#args);
# Store the return value if a destination $var was specified
$env{ $var } = $value if defined $var;
}
That was fairly trivial. Now comes some parsing code. Perl “binds” regexes to strings with the =~ operator. Regexes may look like /foo/ or m/foo/. The /x flags allows us to include whitespace in our regex that doesn't match actual whitespace. The /g flag matches globally. This also enables the \G assertion. This is where the last successful match ended. The /c flag is important for this m//gc style parsing to consume one match at a time, and to prevent the position of the regex engine in out string to being reset.
sub parse {
my ($line) = #_; # get the $line, which is a argument
my ($var, $command, #args); # declare variables to be filled
# Test if this statement has a variable declaration
if ($line =~ m/\G\s* \$(\w+) \s*=\s* /xgc) {
$var = $1; # assign first capture if successful
}
# Parse the function of this statement.
if ($line =~ m/\G\s* (\w+) \s*/xgc) {
$command = $1;
# Test if the specified function exists in our %functions
if (not exists $functions{$command}) {
die "The command $command is not known\n";
}
} else {
die "Command required\n"; # Throw fatal exception on parse error.
}
# As long as our matches haven't consumed the whole string...
while (pos($line) < length($line)) {
# Try to match variables
if ($line =~ m/\G \$(\w+) \s*/xgc) {
die "The variable $1 does not exist\n" if not exists $env{$1};
push #args, $env{$1};
}
# Try to match strings
elsif ($line =~ m/\G "([^"]+)" \s*/xgc) {
push #args, $1;
}
# Try to match ints or floats
elsif ($line =~ m/\G (\d+ (?:\.\d+)? ) \s*/xgc) {
push #args, 0+$1;
}
# Throw error if nothing matched
else {
die "Didn't understand that line\n";
}
}
# return our -- now filled -- vars.
return $var, $command, #args;
}
Perl arrays can be handled like linked list: shift removes and returns the first element (pop does the same to the last element). push adds an element to the end, unshift to the beginning.
Out little programming language can execute simple programs like:
#!my_little_language
$a = mul 2 20
$b = add 0 2
$answer = add $a $b
say $answer
bye
If (1) our perl script is saved in my_little_language, set to be executable, and is in the system PATH, and (2) the above file in our little language saved as meaning_of_life.mll, and also set to be executable, then
$ ./meaning_of_life
should be able to run it.
Output is obviously 42. Note that our language doesn't yet have string manipulation or simple assignment to variables. Also, it would be nice to be able to call functions with the return value of other functions directly. This requires some sort of parens, or precedence mechanism. Also, the language requires better error reporting for batch processing (which it already supports).
I'm a little noobish to perl coding conventions, could someone help explain:
why are there / and /< in front of perl variables?
what does\= and =~ mean, and what is the difference?
why does the code require an ending / before the ;, e.g. /start=\'([0-9]+)\'/?
The 1st 3 sub-questions were sort of solved by really the perldocs, but what does the following line means in the code?
push(#{$Start{$start}},$features);
i understand that we are pushing the $features into a #Start array but what does #$Start{$start} mean? Is it the same as:
#Start = ($start);
Within the code there is something like this:
use FileHandle;
sub open_infile {
my $file = shift;
my $in = FileHandle->new($file,"<:encoding(UTF-8)")
or die "ERROR: cannot open $file: $!\n" if ($Opt_utf8);
$in = new FileHandle("$file")
or die "ERROR: cannot open $file: $!\n" if (!$Opt_utf8);
return $in;
}
$uamf = shift #ARGV;
$uamin = open_infile($uamf);
while (<$uamin>) {
chomp;
if(/<segment /){
/start=\'([0-9]+)\'/;
/end=\'([0-9]+)\'/;
/features=\'([^\']+)\'/;
$features =~ s/annotation;//;
push(#{$Start{$start}},$features);
push(#{$End{$end}},$features);
}
}
EDITED
So after some intensive reading of the perl doc, here's somethings i've gotten
The /<segment / is a regex check that checks whether the readline
in while (<$uamin>) contains the following string: <segment.
Similarly the /start=\'([0-9]+)\'/ has nothing to to do with
instantiating any variable, it's a regex check to see whether the
readline in while (<$uamin>) contains start=\'([0-9]+)\' which
\'([0-9]+)\' refers to a numeric string.
In $features =~ s/annotation;// the =~ is use because the string
replacement was testing a regular expression match. See
What does =~ do in Perl?
Where did you see this syntax (or more to the point: have you edited stuff out of what you saw)? /foo/ represents the match operator using regular expressions, not variables. In other words, the first line is checking to see if the input string $_ contains the character sequence <segment.
The subsequent three lines essentially do nothing useful, in the sense that they run regular expression matches and then discard the results (there are side-effects, but subsequent regular expressions discard the side-effects, too).
The last line does a substitution, replacing the first occurance of the characters annotation; with the empty string in the string $features.
Run the command perldoc perlretut to learn about regex in Perl.
I am having quite a bit of trouble with a Perl script I am writing. I want to compare an element of an array to a variable I have to see if they are true. For some reason I cannot seem to get the comparison operation to work correctly. It will either evaluate at true all the time (even when outputting both strings clearly shows they are not the same), or it will always be false and never evaluate (even if they are the same). I have found an example of just this kind of comparison operation on another website, but when I use it it doesn't work. Am I missing something? Is the variable type I take from the file not a string? (Can't be an integer as far as I can tell as it is an IP address).
$ipaddress = '192.43.2.130'
if ($address[0] == ' ')
{
open (FH, "serverips.txt") or die "Crossroads could not find a list of backend servers";
#address = <FH>;
close(FH);
print $address[0];
print $address[1];
}
for ($i = 0; $i < #address; $i++)
{
print "hello";
if ($address[$i] eq $ipaddress)
{print $address[$i];
$file = "server_$i";
print "I got here first";
goto SENDING;}
}
SENDING:
print " I am here";
I am pretty weak in Perl, so forgive me for any rookie mistakes/assumptions I may have made in my very meager bit of code. Thank you for you time.
if ($address[0] == ' ')
{
open (FH, "serverips.txt") or die "Crossroads could not find a list of backend servers";
#address = <FH>;
close(FH);
You have several issues with this code here. First you should use strict because it would tell you that #address is being used before it's defined and you're also using numeric comparison on a string.
Secondly you aren't creating an array of the address in the file. You need to loop through the lines of the file to add each address:
my #address = ();
while( my $addr = <FH> ) {
chomp($addr); # removes the newline character
push(#address, $addr);
}
However you really don't need to push into an array at all. Just loop through the file and find the IP. Also don't use goto. That's what last is for.
while( my $addr = <FH> ) {
chomp($addr);
if( $addr eq $ipaddress ) {
$file = "server_$i";
print $addr,"\n";
print "I got here first"; # not sure what this means
last; # breaks out of the loop
}
}
When you're reading in from a file like that, you should use chomp() when doing a comparison with that line. When you do:
print $address[0];
print $address[1];
The output is on two separate lines, even though you haven't explicitly printed a newline. That's because $address[$i] contains a newline at the end. chomp removes this.
if ($address[$i] eq $ipaddress)
could read
my $currentIP = $address[$i];
chomp($currentIP);
if ($currentIP eq $ipaddress)
Once you're familiar with chomp, you could even use:
chomp(my $currentIP = $address[$i]);
if ($currentIP eq $ipaddress)
Also, please replace the goto with a last statement. That's perl's equivalent of C's break.
Also, from your comment on Jack's answer:
Here's some code you can use for finding how long it's been since a file was modified:
my $secondsSinceUpdate = time() - stat('filename.txt')->mtime;
You probably are having an issue with newlines. Try using chomp($address[$i]).
First of all, please don't use goto. Every time you use goto, the baby Jesus cries while killing a kitten.
Secondly, your code is a bit confusing in that you seem to be populating #address after starting the if($address[0] == '') statement (not to mention that that if should be if($address[0] eq '')).
If you're trying to compare each element of #address with $ipaddress for equality, you can do something like the following
Note: This code assumes that you've populated #address.
my $num_matches=0;
foreach(#address)
{
$num_matches++ if $_ eq $ipaddress;
}
if($num_matches)
{
#You've got a match! Do something.
}
else
{
#You don't have any matches. This may or may not be bad. Do something else.
}
Alternatively, you can use the grep operator to get any and all matches from #address:
my #matches=grep{$_ eq $ipaddress}#address;
if(#matches)
{
#You've got matches.
}
else
{
#Sorry, no matches.
}
Finally, if you're using a version of Perl that is 5.10 or higher, you can use the smart match operator (ie ~~):
if($ipaddress~~#address)
{
#You've got a match!
}
else
{
#Nope, no matches.
}
When you read from a file like that you include the end-of-line character (generally \n) in each element. Use chomp #address; to get rid of it.
Also, use last; to exit the loop; goto is practically never needed.
Here's a rather idiomatic rewrite of your code. I'm excluding some of your logic that you might need, but isn't clear why:
$ipaddress = '192.43.2.130'
open (FH, "serverips.txt") or die "Crossroads could not find a list of backend servers";
while (<FH>) { # loop over the file, using the default input space
chomp; # remove end-of-line
last if ($_ eq $ipaddress); # a RE could easily be used here also, but keep the exact match
}
close(FH);
$file = "server_$."; # $. is the line number - it's not necessary to keep track yourself
print "The file is $file\n";
Some people dislike using perl's implicit variables (like $_ and $.) but they're not that hard to keep track of. perldoc perlvar lists all these variables and explains their usage.
Regarding the exact match vs. "RE" (regular expression, or regexp - see perldoc perlre for lots of gory details) -- the syntax for testing a RE against the default input space ($_) is very simple. Instead of
last if ($_ eq $ipaddress);
you could use
last if (/$ipaddress/);
Although treating an ip address as a regular expression (where . has a special meaning) is probably not a good idea.
I have a line of code along the lines of:
print $somehash{$var}{fh} "foo";
The hash contains the filehandle a few levels down. The error is:
String found where operator expected at test.pl line 10, near "} "foo""
I can fix it by doing this:
my $fh = $somehash{$var}{fh};
print $fh "foo";
...but is there a one-liner?
see http://perldoc.perl.org/functions/print.html
Note that if you're storing
FILEHANDLEs in an array, or if you're
using any other expression more
complex than a scalar variable to
retrieve it, you will have to use a
block returning the filehandle value
instead: ...
So, in your case, you would use a block like this:
print { $somehash{$var}{fh} } "foo";
If you have anything other than a simple scalar as your filehandle, you need to wrap the reference holding the filehandle in braces so Perl knows how to parse the statement:
print { $somehash{$var}{fh} } $foo;
Part of Perl Best Practices says to always wrap filehandles in braces just for this reason, although I don't get that nutty with it.
The syntax is odd because print is an indirect method on a filehandle object:
method_name Object #arguments;
You might have seen this in old-school CGI.pm. Here are two indirect method calls:
use CGI;
my $cgi_object = new CGI 'cat=Buster&bird=nightengale';
my $value = param $cgi_object 'bird';
print "Indirect value is $value\n";
That almost works fine (see Schwern's answer about the ambiguity) as long as the object is in a simple scalar. However, if I put the $cgi_object in a hash, I get the same syntax error you got with print. I can put the braces around the hash access to make it work out. Continuing with the previous code:
my %hash;
$hash{animals}{cgi} = $cgi_object;
# $value = param $hash{animals}{cgi} 'cat'; # syntax error
$value = param { $hash{animals}{cgi} } 'cat';
print "Braced value is $value\n";
That's all a bit clunky so just use the arrow notation for everything instead:
my $cgi_object = CGI->new( ... );
$cgi_object->param( ... );
$hash{animals}{cgi}->param( ... );
You can do the same with filehandles, although you have to use the IO::Handle module to make it all work out:
use IO::Handle;
STDOUT->print( 'Hello World' );
open my( $fh ), ">", $filename or die ...;
$fh->print( ... );
$hash{animals}{fh} = $fh;
$hash{animals}{fh}->print( ... );
The above answers are all correct. The reason they don't allow a full expression in there is print FH LIST is already pretty weird syntax. To put anything more complicated in there would introduce a ton of ambiguous syntax. The block removed that ambiguity.
To see where this madness leads to, consider the horror that is indirect object syntax.
foo $bar; # Is that foo($bar) or $bar->foo()? Good luck!