How do I print on a single line all content between certain start- and stop-lines? - perl

Question

while(<FILE>)
{
chomp $_;
$line[$i]=$_;
++$i;
}
for($j=0;$j<$i;++$j)
{
if($line[$j]=~/Syn_Name/)
{
do
{
print OUT $line[$j],"\n";
++$j;
}
until($line[$j]=~/^\s*$/)
}
}
This is my code I am trying to print data between Syn_Name and a blank line.
My code extracts the chunk that I need.
But the data between the chunk is printed line by line. I want the data for each chunk to get printed on a single line.

Answer 1

Simplification of your code. Using the flip-flop operator to control the print. Note that printing the final line will not add a newline (unless the line contained more than one newline). At best, it prints the empty string. At worst, it prints whitespace.
You do not need a transition array for the lines, you can use a while loop. In case you want to store the lines anyway, I added a commented line with how that is best done.
#chomp(my #line = <FILE>);
while (<FILE>) {
chomp;
if(/Syn_Name/ .. /^\s*$/) {
print OUT;
print "\n" if /^\s*$/;
}
}

Answer 2

Contents
Idiomatic Perl
Make errors easier to fix
Warnings about common programming errors
Don't execute unless variable names are consistent
Developing this habit will save you lots of time
Perl's range operator
Working demos
Print chomped lines immediately
Join lines with spaces
One more edge case
Idiomatic Perl
You seem to have a background with the C family of languages. This is fine because it gets the job done, but you can let Perl handle the machinery for you, namely
chomp defaults to $_ (also true with many other Perl operators)
push adds an element to the end of an array
to simplify your first loop:
while (<FILE>)
{
chomp;
push #line, $_;
}
Now you don't have update $i to keep track of how many lines you've already added to the array.
On the second loop, instead of using a C-style for loop, use a foreach loop:
The foreach loop iterates over a normal list value and sets the variable VAR to be each element of the list in turn …
The foreach keyword is actually a synonym for the for keyword, so you can use foreach for readability or for for brevity. (Or because the Bourne shell is more familiar to you than csh, so writing for comes more naturally.) If VAR is omitted, $_ is set to each value.
This way, Perl handles the bookkeeping for you.
for (#line)
{
# $_ is the current element of #line
...
}
Make errors easier to fix
Sometimes Perl can be too accommodating. Say in the second loop you made an easy typographical error:
for (#lines)
Running your program now produces no output at all, even if the input contains Syn_Name chunks.
A human can look at the code and see that you probably intended to process the array you just created and pluralized the name of the array by mistake. Perl, being eager to help, creates a new empty #lines array, which leaves your foreach loop with nothing to do.
You may delete the spurious s at the end of the array's name but still have a program produces no output! For example, you may have an unhandled combination of inputs that doesn't open the OUT filehandle.
Perl has a couple of easy ways to spare you these (and more!) kinds of frustration from dealing with silent failures.
Warnings about common programming errors
You can turn on an enormous list of warnings that help diagnose common programming problems. With my imagined buggy version of your code, Perl could have told you
Name "main::lines" used only once: possible typo at ./synname line 16.
and after fixing the typo in the array name
print() on unopened filehandle OUT at ./synname line 20, <FILE> line 8.
print() on unopened filehandle OUT at ./synname line 20, <FILE> line 8.
print() on unopened filehandle OUT at ./synname line 20, <FILE> line 8.
print() on unopened filehandle OUT at ./synname line 20, <FILE> line 8.
print() on unopened filehandle OUT at ./synname line 20, <FILE> line 8.
Right away, you see valuable information that may be difficult or at least tedious to spot unaided:
variable names are inconsistent, and
the program is trying to produce output but needs a little more plumbing.
Don't execute unless variable names are consistent
Notice that even with the potential problems above, Perl tried to execute anyway. With some classes of problems such as the variable-naming inconsistency, you may prefer that Perl not execute your program but stop and make you fix it first. You can tell Perl to be strict about variables:
This generates a compile-time error if you access a variable that wasn't declared via our or use vars, localized via my, or wasn't fully qualified.
The tradeoff is you have to be explicit about which variables you intend to be part of your program instead of allowing them to conveniently spring to life upon first use. Before the first loop, you would declare
my #line;
to express your intent. Then with the bug of a mistakenly pluralized array name, Perl fails with
Global symbol "#lines" requires explicit package name at ./synname line 16.
Execution of ./synname aborted due to compilation errors.
and you know exactly which line contains the error.
Developing this habit will save you lots of time
I begin almost every non-trivial Perl program I write with
#! /usr/bin/env perl
use strict;
use warnings;
The first is the shebang line, an ordinary comment as far as Perl is concerned. The use lines enable the strict pragma and the warnings pragma.
Not wanting to be a strict-zombie, as Mark Dominus chided, I'll point out that use strict; as above with no option makes Perl strict in dealing with three error-prone areas:
strict vars, as described above;
strict refs, disallows use of symbolic references; and
strict subs, requires the programmer to be more careful in referring to subroutines.
This is a highly useful default. See the strict pragma's documentation for more details.
Perl's range operator
The perlop documentation describes .., Perl's range operator, that can help you greatly simplify the logic in your second loop:
In scalar context, .. returns a boolean value. The operator is bistable, like a flip-flop, and emulates the line-range (comma) operator of sed, awk, and various editors. Each .. operator maintains its own boolean state, even across calls to a subroutine that contains it. It is false as long as its left operand is false. Once the left operand is true, the range operator stays true until the right operand is true, AFTER which the range operator becomes false again. It doesn't become false till the next time the range operator is evaluated.
In your question, you wrote that you want “data between Syn_Name and a blank line,” which in Perl is spelled
/Syn_Name/ .. /^\s*$/
In your case, you also want to do something special at the end of the range, and .. provides for that case too, ibid.
The final sequence number in a range has the string "E0" appended to it, which doesn't affect its numeric value, but gives you something to search for if you want to exclude the endpoint.
Assigning the value returned from .. (which I usually do to a scalar named $inside or $is_inside) allows you to check whether you're at the end, e.g.,
my $is_inside = /Syn_Name/ .. /^\s*$/;
if ($is_inside =~ /E0$/) {
...
}
Writing it this way also avoids duplicating the code for your terminating condition (the right-hand operand of ..). This way if you need to change the logic, you change it in only one place. When you have to remember, you'll forget sometimes and create bugs.
Working demos
See below for code you can copy-and-paste to get working programs. For demo purposes, they read input from the built-in DATA filehandle and write output to STDOUT. Writing it this way means you can transfer my code into yours with little or no modification.
Print chomped lines immediately
As defined in your question, there's no need for one loop to collect the lines in a temporary array and then another loop to process the array. Consider the following code
#! /usr/bin/env perl
use strict;
use warnings;
# for demo only
*FILE = *DATA;
*OUT = *STDOUT;
while (<FILE>)
{
chomp;
if (my $is_inside = /Syn_Name/ .. /^\s*$/) {
my $is_last = $is_inside =~ /E0$/;
print OUT $_, $is_last ? "\n" : ();
}
}
__DATA__
ERROR IF PRESENT IN OUTPUT!
Syn_Name
foo
bar
baz
ERROR IF PRESENT IN OUTPUT!
whose output is
Syn_Namefoobarbaz
We always print the current line, stored in $_. When we're at the end of the range, that is, when $is_last is true, we also print a newline. When $is_last is false, the empty list in the other branch of the ternary operator is the result—meaning we print $_ only, no newline.
Join lines with spaces
You didn't show us an example input, so I wonder whether you really want to butt the lines together rather than joining them with spaces. If you want the latter behavior, then the program becomes
#! /usr/bin/env perl
use strict;
use warnings;
# for demo only
*FILE = *DATA;
*OUT = *STDOUT;
my #lines;
while (<FILE>)
{
chomp;
if (my $is_inside = /Syn_Name/ .. /^\s*$/) {
push #lines, $_;
if ($is_inside =~ /E0$/) {
print OUT join(" ", #lines), "\n";
#lines = ();
}
}
}
__DATA__
ERROR IF PRESENT IN OUTPUT!
Syn_Name
foo
bar
baz
ERROR IF PRESENT IN OUTPUT!
This code accumulates in #lines only those lines within a Syn_Name chunk, prints the chunk, and clears out #lines when we see the terminator. The output is now
Syn_Name foo bar baz
One more edge case
Finally, what happens if we see Syn_Name at the end of the file but without a terminating blank line? That may be impossible with your data, but in case you need to handle it, you'll want to use Perl's eof operator.
eof FILEHANDLE
eof
Returns 1 if the next read on FILEHANDLE will return end of file or if FILEHANDLE is not open … An eof without an argument uses the last file read.
So we terminate on either a blank line or end of file.
#! /usr/bin/env perl
use strict;
use warnings;
# for demo only
*FILE = *DATA;
*OUT = *STDOUT;
my #lines;
while (<FILE>)
{
s/\s+$//;
#if (my $is_inside = /Syn_Name/ .. /^\s*$/) {
if (my $is_inside = /Syn_Name/ .. /^\s*$/ || eof) {
push #lines, $_;
if ($is_inside =~ /E0$/) {
print OUT join(" ", #lines), "\n";
#lines = ();
}
}
}
__DATA__
ERROR IF PRESENT IN OUTPUT!
Syn_Name
foo
bar
YOU CANT SEE ME!
Syn_Name
quux
potrzebie
Output:
Syn_Name foo bar
Syn_Name quux potrzebie
Here instead of chomp, the code removes any trailing invisible whitespace at the ends of lines. This will make sure spacing between joined lines is uniform even if the input is a little sloppy.
Without the eof check, the program does not print the latter line, which you can see by commenting out the active conditional and uncommenting the other.

Answer 3

Another simplified version:
foreach (grep {chomp; /Syn_Name/ .. /^\s*$/ } <FILE>) {
print OUT;
print OUT "\n" if /^\s*$/;
}