Hopefully you can help a scientist to decipher whats wrong with the code I'm trying to run to clean up some NGS results. The Perl file itself comes from https://github.com/mtokuyama/ERVmap, though I am posting the code below for reference. The other Perl files in the package work just fine and, while I have built a passing ability to use the linux terminal, Perl is a little beyond me.
The linux terminal I'm using is currently running: Ubuntu 16.04.6 LTS
This is the Perl code I'm trying to run using the following command line on linux as instructed by their GitHub page:
perl clean_htseq.pl ./ c c2 __
#!/usr/bin/env perl
#$Id: run_clean_htseq.pl,v 1.2 2015/03/02 17:24:35 yk336 Exp $
#
# create pbs file
#
use warnings;
use strict;
use File::Basename;
use POSIX;
my $dir = shift;
my $e1 = shift;
my $e2 = shift;
my $stop = shift;
die "$e1 eq $e2" if ($e1 eq $e2);
my $find = "find $dir -name \"*${e1}\"";
my $out = `$find`;
my #files = split(/\n/, $out);
for my $f (#files) {
my $o = $f;
$o =~ s/${e1}$/$e2/;
my $cmd = "./clean_htseq.pl $stop $f > $o";
print "$cmd\n";
system($cmd);
}
The first error that I had was that the _clean_htseq.pl_ wasn't found (line 30, already altered to solution) which i solved by adding the ./ in front of it and giving the software permission to use the script file.
My current issue with the code/command line is the following error:
Use of uninitialized value $e2 in string eq at ./clean_htseq.pl line 18.
find: warning: Unix filenames usually don't contain slashes (though pathnames do). That means that '-name ‘*./SRR7251667.c’' will probably evaluate to false all the time on this system. You might find the '-wholename' test more useful, or perhaps '-samefile'. Alternatively, if you are using GNU grep, you could use 'find ... -print0 | grep -FzZ ‘*./SRR7251667.c’'.
This has been tracked down to the "__" at the end of the command line, while i'm sure this is supposed to mean something to the script I removed it and resulted in the following error:
Use of uninitialized value $stop in concatenation (.) or string at clean_htseq.pl line 30.
./clean_htseq.pl ./SRR7251667.c > ./SRR7251667.c2
Use of uninitialized value $e1 in string eq at ./clean_htseq.pl line 18.
Use of uninitialized value $e2 in string eq at ./clean_htseq.pl line 18.
Use of uninitialized value $e1 in concatenation (.) or string at ./clean_htseq.pl line 18.
Use of uninitialized value $e2 in concatenation (.) or string at ./clean_htseq.pl line 18.
eq at ./clean_htseq.pl line 18.
An error occurs too when I remove the "." from "./" but it comes back with an error about not finding the _clean_htseq.pl_ file which is in the working directory.
Your problem seems to be here:
my $dir = shift;
my $e1 = shift;
my $e2 = shift;
my $stop = shift;
Outside of a subroutine, shift works on #ARGV—the array that holds the command line arguments. You shift four times, so you need four arguments:
perl clean_htseq.pl ./ c c2 __
You only seem to give it two, and $stop has no value (so you are giving it less than two):
./clean_htseq.pl $stop $f
You can't just remove arguments and hope things still work out. Likely you're going to have to look at the source to see what those things mean (which should motivate you as a scientist to use good variable names and document code—Best Practices for Scientific Computing).
A first step may be to set defaults. The defined-or operator does well here:
use v5.10;
my $dir = shift // 'default_dir';
my $e1 = shift // 'default_value';
my $e2 = shift // 'default_value';
my $stop = shift // 'default_value';
Or, you could just give up if there aren't enough arguments. An array in scalar context gives you the number of elements in the array (although it doesn't guarantee anything about their values):
die "Need four arguments!\n" unless #ARGV == 4;
There are various other improvements which would help this script, some of which I go through in the "Secure Programming Techniques" chapter in Mastering Perl. Taking unchecked user input and passing it to another program is generally not a good idea.
Related
I am trying to pass arguments from one Perl script to another. Some of the arguments contain spaces.
I am reading in a comma-delimited text file and splitting each line on the comma.
my ($jockey, $racecourse, $racenum, $hnamenum, $trainer, $TDRating, $PRO) = split(/,/, $line);
The data in the comma-delimited text file look as follows:
AARON LYNCH,WARRNAMBOOL,RACE 1,DAREBIN (8),ERIC MUSGROVE,B,1
When I print out each variable, from the parent script, they look fine (as above).
print "$jockey\n";
print "$racecourse\n";
print "$racenum\n";
print "$hnamenum\n";
print "$trainer\n";
print "$TDRating\n";
print "$PRO\n";
AARON LYNCH
WARRNAMBOOL
RACE 1
DAREBIN (8)
ERIC MUSGROVE
B
1
When I pass the arguments to the child script (as follows), the arguments are passed incorrectly.
system("perl \"$bindir\\narrative4.pl\" $jockey $racecourse $racenum $hnamenum $trainer $TDRating $PRO");
AARON
LYNCH
WARRNAMBOOL
RACE
1
DAREBIN
(8)
As you can see, $ARGV[0] becomes AARON, $ARGV[1] becomes LYNCH, $ARGV[2] becomes WARRNAMBOOL, and so on.
I have investigated adding quotes to the arguments using qq, quotemeta and Win32::ShellQuote, unfortunately, even if I pass qq{"$jockey"}, the quotes are still stripped before they reach the child script, so they must be protected in some way.
I not sure if either of the aforementioned solutions is the correct but I'm happy to be corrected.
I'd appreciate any suggestions. Thanks in advance.
Note: I am running this using Strawberry Perl on a Windows 10 PC.
Note2: I purposely left out use strict; & use warnings; in these examples.
Parent Script
use Cwd;
$dir = getcwd;
$bin = "bin"; $bindir = "$dir/$bin";
$infile = "FINAL-SORTED-JOCKEY-RIDES-FILE.list";
open (INFILE, "<$infile") or die "Could not open $infile $!\n";
while (<INFILE>)
{
$line = $_;
chomp($line);
my ($jockey, $racecourse, $racenum, $hnamenum, $trainer, $TDRating, $PRO) = split(/,/, $line);
print "$jockey\n";
print "$racecourse\n";
print "$racenum\n";
print "$hnamenum\n";
print "$trainer\n";
print "$TDRating\n";
print "$PRO\n";
system("perl \"$bindir\\narrative4.pl\" $jockey $racecourse $racenum $hnamenum $trainer $TDRating $PRO");
sleep (1);
}
close INFILE;
exit;
Child Script
$passedjockey = $ARGV[0];
$passedracecourse = $ARGV[1];
$passedracenum = $ARGV[2];
$passedhnamenum = $ARGV[3];
$passedtrainer = $ARGV[4];
$passedTDRating = $ARGV[5];
$passedPRO = $ARGV[6];
print "$passedjockey\n";
print "$passedracecourse\n";
print "$passedracenum\n";
print "$passedhnamenum\n";
print "$passedtrainer\n";
print "$passedTDRating\n";
print "$passedPRO\n\n";
That whole double-quoted string that is passed to system is first evaluated and thus all variables are interpolated -- so the intended multi-word arguments become merely words in a list. So in the end the string has a command to run with individual words as arguments.
Then, even if you figure out how to stick which quotes in there just right, so to keep those multi-word arguments "together," there's still a chance of a shell being invoked, in which case those arguments again get broken up into words before being passed to the program.
Instead of all this use the LIST form of system. The first argument is then the name of the program that will be directly executed without a shell (see docs for some details on that), and the remaining arguments are passed as they are to that program.
parent
use warnings;
use strict;
use feature 'say';
my #args = ('first words', 'another', 'two more', 'final');
my $prog = 'print_args.pl';
system($prog, #args) == 0
or die "Error w/ system($prog, #args): $!";
and the invoked print_args.pl
use warnings;
use strict;
use feature 'say';
say for #ARGV;
The #ARGV contains arguments passed to the program at invocation. There's more that can be done to inspect the error, see docs and links in them.†
By what you show you indeed don't need a shell and the LIST form is generally easy to recommend as a basic way to use system, when the shell isn't needed. If you were to need shell's capabilities for something in that command then you'd have to figure out how to protect those spaces.
† And then there are modules for running external programs that are far better than system & Co. From ease-of-use to features and power:
IPC::System::Simple, Capture::Tiny, IPC::Run3, IPC::Run.
I get the following error:
Use of uninitialized value $_ in concatenation (.) or string at checkfornewfiles.pl line 34.
when attempting to run the following code :
#!/usr/bin/perl -w
#Author: mimo
#Date 3/2015
#Purpose: monitor directory for new files...
AscertainStatus();
######### start of subroutine ########
sub AscertainStatus {
my $DIR= "test2";
####### open handler #############
opendir (HAN1, "$DIR") || die "Problem: $!";
########## assign theoutput of HAN1 to array1 ##########
my #array1= readdir(HAN1);
######## adding some logic #########
if ("$#array1" > 1) { #### if files exists (more than 1) in the directory #######
for (my $i=0; $i<2; $i++) {shift #array1;} ####### for i in position 0 (which is the . position) loop twice and add one (the position ..) get rid of them #######
MailNewFiles(#array1);
} else { print "No New Files\n";}
}
sub MailNewFiles {
$mail= "sendmail";
open ($mail, "| /usr/lib/sendmail -oi -t" ) ||die "errors with sendmail $!"; # open handler and pipe it to sendmail
print $mail <<"EOF"; #print till the end of fiEOF
From: "user";
To: "root";
Subject: "New Files Found";
foreach (#_) {print $mail "new file found:\n $_\n";}
EOF
close($mail);
}
#End
I am new to perl and I don't know what's going wrong. Can anyone help me ?
A few suggestions:
Perl isn't C. Your main program loop shouldn't be a declared subroutine which you then execute. Eliminate the AscertainStatus subroutine.
Always, always use strict; and use warnings;.
Indent correctly. It makes it much easier for people to read your code and help analyze what you did wrong.
Use a more modern Perl coding style. Perl is an old language, and over the years new coding style and techniques have been developed to help you eliminate basic errors and help others read your code.
Don't use system commands when there are Perl modules that can do this for you in a more standard way, and probably do better error checking. Perl comes with the Net::SMTP that handles mail communication for you. Use that.
The error Use of uninitialized value $_ in concatenation (.) or string is exactly what it says. You are attempting to use a value of a variable that hasn't been set. In this case, the variable is the #_ variable in your foreach statement. Your foreach isn't a true foreach, but part of your print statement since your EOF is after your for statement. This looks like an error.
Also, what is the value of #_? This variable contains a list of values that have been passed to your subroutine. If none are passed, it will be undefined. Even if #_ is undefined, foreach (undef) will simply skip the loop. However, since foreach (#_) { is a string to print, your Perl program will crash without #_ being defined.
If you remove the -w from #!/usr/bin/perl, your program will actually "work" (Note the quotes), and you'll see that your foreach will literally print.
I do not recommend you not to use warnings which is what -w does. In fact, I recommend you use warnings; rather than -w. However, in this case, it might help you see your error.
You have EOF after the line with foreach. It contains $_ which is interpolated here but $_ is not initialized yet because it is not in foreach loop. It is not code but just text. Move EOF before foreach.
But probably you would like
sub MailNewFiles {
$mail= "sendmail";
open ($mail, "| /usr/lib/sendmail -oi -t" ) ||die "errors with sendmail $!"; # open handler and pipe it to sendmail
local $"="\n"; # " make syntax highlight happy
print $mail <<"EOF"; #print till the end of fiEOF
From: "user";
To: "root";
Subject: "New Files Found";
New files found:
#_
EOF
close($mail);
}
See perlvar for more informations about $".
The message
Use of uninitialized value $xxx in ...
is very straightforward. When you encounter it, it means that you are using a variable ($xxx) in any way, but that the variable has not ever been initialized.
Sometimes, adding an initialization command at the start of you code is enough :
my $str = '';
my $num = 0;
Sometimes, your algorithm is wrong, or you just mistyped your variable, like in :
my $foo = 'foo';
my $bar = $ffo . 'bar'; # << There is a warning on this line
# << because you made a mistake on $foo ($ffo)
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).
syntax error at bioinfo2.pl line 24, near ");"
syntax error at bioinfo2.pl line 26, near "}"
Execution of bioinfo2.pl aborted due to compilation errors.
print "Enter file name......\n\n";
chomp($samplefile = <STDIN>);
open(INFILE,"$samplefile") or die "Could not open $samplefile";
#residue_name= ();
#residue_count= ();
while($newline = <INFILE>)
{
if ($newline =~ /^ATOM/)
{
chomp $newline;
#columns = split //, $newline;
$res = join '', $columns[17], $columns[18], $columns[19];
splice #columns,0;
$flag=0
for ($i = 0; $i<scalar(#residue_name); $i++;)
{
if (#residue_name[i] == $res)
{
#residue_count[i] = #residue_count[i] + 1;
$flag=1;
}
}
if($flag==0)
{
push(#residue_name, $res);
}
for ($i = 0; $i<scalar(#residue_name); $i++)
{
print (#residue_name[i], "-------", #residue_count[i], "\n");
}
}
}
It might be advisable to use strict; use warnings. That forces you to declare your variables (you can do so with my), and rules out many possible errors.
Here are a few things that I noticed:
In Perl5 v10 and later, you can use the say function (use 5.010 or use feature 'say'). This works like print but adds a newline at the end.
Never use the two-arg form of open. This opens some security issues. Provide an explicit open mode. Also, you can use scalars as filehandles; this provides nice features like auto-closing of files.
open my $INFILE, '<', $samplefile or die "Can't open $samplefile: $!";
The $! variable contains the reason why the open failed.
If you want to retrieve a list of elements from an array, you can use a slice (multiple subscripts):
my $res = join '', #columns[17 .. 19]; # also, range operator ".."
Note that the sigil is now an #, because we take multiple elems.
The splice #columns, 0 is a fancy way of saying “delete all elements from the array, and return them”. This is not neccessary (you don't read from that variable later). If you use lexical variables (declared with my), then each iteration of the while loop will receive a new variable. If you really want to remove the contents, you can undef #columns. This should be more efficient.
Actual error: You require a semicolon after $flag = 0 to terminate the statement before you can begin a loop.
Actual error: A C-style for-loop contains three expressions contained in parens. Your last semicolon divides them into 4 expressions, this is an error. Simply remove it, or look at my next tip:
C-style loops (for (foo; bar; baz) {}) are painful and error-prone. If you only iterate over a range (e.g. of indices), then you can use the range operator:
for my $i (0 .. $#residue_name) { ... }
The $# sigil gives the last index of an array.
When subscripting arrays (accessing array elements), then you have to include the sigil of the index:
$residue_name[$i]
Note that the sigil of the array is $, because we access only one element.
The pattern $var = $var + 1 can be shortened to $var++. This uses the increment operator.
The $flag == 0 could be abbreviated to !$flag, as all numbers except zero are considered true.
Here is a reimplementation of the script. It takes the filename as a command line argument; this is more flexible than prompting the user.
#!/usr/bin/perl
use strict; use warnings; use 5.010;
my $filename = $ARGV[0]; # #ARGV holds the command line args
open my $fh, "<", $filename or die "Can't open $filename: $!";
my #residue_name;
my #residue_count;
while(<$fh>) { # read into "$_" special variable
next unless /^ATOM/; # start a new iteration if regex doesn't match
my $number = join "", (split //)[17 .. 19]; # who needs temp variables?
my $push_number = 1; # self-documenting variable names
for my $i (0 .. $#residue_name) {
if ($residue_name[$i] == $number) {
$residue_count[$i]++;
$push_number = 0;
}
}
push #residue_name, $number if $push_number;
# are you sure you want to print this after every input line?
# I'd rather put this outside the loop.
for my $i (0 .. $#residue_name) {
say $residue_name[$i], ("-" x 7), $residue_count[$i]; # "x" repetition operator
}
}
And here is an implementation that may be faster for large input files: We use hashes (lookup tables), instead of looping through arrays:
#!/usr/bin/perl
use strict; use warnings; use 5.010;
my $filename = $ARGV[0]; # #ARGV holds the command line args
open my $fh, "<", $filename or die "Can't open $filename: $!";
my %count_residue; # this hash maps the numbers to counts
# automatically guarantees that every number has one count only
while(<$fh>) { # read into "$_" special variable
next unless /^ATOM/; # start a new iteration if regex doesn't match
my $number = join "", (split //)[17 .. 19]; # who needs temp variables?
if (exists $count_residue{$number}) {
# if we already have an entry for that number, we increment:
$count_residue{$number}++;
} else {
# We add the entry, and initialize to zero
$count_residue{$number} = 0;
}
# The above if/else initializes new numbers (seen once) to zero.
# If you want to count starting with one, replace the whole if/else by
# $count_residue{$number}++;
# print out all registered residues in numerically ascending order.
# If you want to sort them by their count, descending, then use
# sort { $count_residue{$b} <=> $count_residue{$a} } ...
for my $num (sort {$a <=> $b} keys %count_residue) {
say $num, ("-" x 7), $count_residue{$num};
}
}
It took me a while to chance down all the various errors. As others have said, use use warnings; and use strict;
Rule #1: Whenever you see syntax error pointing to a perfectly good line, you should always see if the line before is missing a semicolon. You forgot the semicolon after $flag=0.
In order to track down all the issues, I've rewritten your code into a more modern syntax:
#! /usr/bin/env perl
use strict;
use warnings;
use autodie;
print "Enter file name......\n\n";
chomp (my $samplefile = <STDIN>);
open my $input_file, '<:crlf', $samplefile;
my #residue_name;
my #residue_count;
while ( my $newline = <$input_file> ) {
chomp $newline;
next if $newline !~ /^ATOM/; #Eliminates the internal `if`
my #columns = split //, $newline;
my $res = join '', $columns[17], $columns[18], $columns[19];
my $flag = 0;
for my $i (0..$#residue_name) {
if ( $residue_name[$i] == $res ) {
$residue_count[$i]++;
$flag = 1;
}
}
if ( $flag == 0 ) {
push #residue_name, $res;
}
for my $i (0..$#residue_name) {
print "$residue_name[$i] ------- $residue_count[$i]\n";
}
}
close $input_file;
Here's a list of changes:
Lines 2 & 3: Always use use strict; and use warnings;. These will help you track down about 90% of your program errors.
Line 4: Use use autodie;. This will eliminate the need for checking whether a file opened or not.
Line 7 (and others): Using use strict; requires you to predeclare variables. Thus, you'll see my whenever a variable is first used.
Line 8: Use the three parameter open and use local variables for file handles instead of globs (i.e. $file_handle vs. FILE_HANDLE). The main reasons is that local variables are easier to pass into subroutines than globs.
Lines 9 & 10: No need to initialize the arrays, just declare them is enough.
Line 13: Always chomp as soon as you read in.
Line 14: Doing this eliminates an entire inner if statement that's embraces your entire while loop. Code blocks (such as if, while, and for) get hard to figure out when they get too long and too many embedded inside each other. Using next in this way allows me to eliminate the if block.
Line 17: Here's where you missed the semicolon which gave you your first syntax error. The main thing is I eliminated the very confusing splice command. If you want to zero out your array, you could have simply said #columns = (); which is much clearer. However, since #columns is now in scope only in the while loop, I no longer have to blank it out since it will be redefined for each line of your file.
Line 18: This is a much cleaner way of looping through all lines of your array. Note that $#residue_name gives you the last index of $#residue_name while scalar #resudue_name gives you the number of elements. This is a very important distinction! If I have an #array = (0, 1, 2, 3, 4), $#array will be 4, but scalar #array will be 5. Using the C style for loop can be a bit confusing when doing this. Should you use > or >=? Using (0..$#residue) name is obvious and eliminate the chance of errors which included the extra semi-colon inside your C style for statement. Because of the chance of errors and the complexity of the syntax, The developers who created Python have decided not allow for C style for loops.
Line 19 (and others): Using warnings pointed out that you did #residue_name[i] and it had several issues. First of all, you should use $residue_name[...] when indexing an array, and second of all, i is not an integer. You meant $i. Thus #residue_name[i] becomes $residue_name[$i].
Line 20: If you're incrementing a variable, use $foo++; or $foo += 1; and not $foo = $foo + 1;. The first two make it easier to see that you're incrementing a variable and not recalculating it's value.
Line 29: One of the great features of Perl is that variables can be interpolated inside quotes. You can put everything inside a single set of quotes. By the way, you should use . and not , if you do break up a print statement into multiple pieces. The , is a list operation. This means that what you print out is dependent upon the value of $,. The $, is a Perl variable that says what to print out between each item of a list when you interpolate a list into a string.
Please don't take this as criticism of your coding abilities. Many Perl books that teach Perl, and many course that teach Perl seem to teach Perl as it was back in the Perl 3.0 days. When I first learned Perl, it was at Perl 3.0, and much of my syntax would have looked like yours. However, Perl 5.x has been out for quite a while and contains many features that made programming easier and cleaner to read.
It took me a while to get out of Perl 3.0 habits and into Perl 4.0 and later Perl 5.0 habits. You learn by looking at what others do, and asking questions on forums like Stack Overflow.
I still can't say your code will work. I don't have your input, so I can't test it against that. However, by using this code as the basis of your program, debugging these errors should be pretty easy.
I am getting the an error while reading a file and below is the script.
#!/bin/bash
$file = "SampleLogFile.txt"; #--- line 2
open(MYINPUTFILE,$file); #--- line 3
while(<**MYINPUTFILE**>) {
# Good practice to store $_ value because
# subsequent operations may change it.
my($line) = $_;
# Good practice to always strip the trailing
# newline from the line.
chomp($line);
# Convert the line to upper case.
print "$line" if $line = ~ /sent/;
}
close (MYINPUTFILE);
Output :
PerlTesting_New.ksh[2]: =: not found
PerlTesting_New.ksh[3]: syntax error at line 3 : `(' unexpected
Any idea what the issue is ?
Change
#!/bin/bash
to
#!/usr/bin/perl
Otherwise Perl will not be interpreting your script. Change path accordingly as per your system
Okay, whoever is teaching you to write Perl like this needs to move out of the nineties.
#!/usr/bin/perl
use strict; # ALWAYS
use warnings; # Also always.
# When you learn more you can selectively turn off bits of strict and warnings
# functionality on an as needed basis.
use IO::File; # A nice OO module for working with files.
my $file_name = "SampleLogFile.txt"; # note that we have to declare $file now.
my $input_fh = IO::File->new( $file_name, '<' ); # Open the file read-only using IO::File.
# You can avoid assignment through $_ by assigning to a variable, even when you use <$fh>
while( my $line = $input_fh->getline() ) {
# chomp($line); # Chomping is usually a good idea.
# In this case it does nothing but screw up
# your output, so I commented it out.
# This does nothing of the sort:
# Convert the line to upper case.
print "$line" if $line = ~ /sent/;
}
You can also do this with a one liner:
perl -pe '$_ = "" unless /sent/;' SampleLogFile.txt
See perlrun for more info on one-liners.
hmm, your first line : #!/bin/bash
/bin/bash : This is the Bash shell.
You may need to change to
!/usr/bin/perl