I would like to read a file in perl, after, the user can input any string and grep will try to find the string inputted in the file read. It will only exit when the user input nothing or any space character. Here's my code which is not working:
#! usr/bin/perl
use warnings;
use strict;
open MATCHSTRING,"matchstring";
my #lines = <MATCHSTRING>;
while (<>) {
chomp;
my #match = grep {/\b$_\b/s} #lines;
print #match;
}
I'm still lacking the condition where it will exit once nothing is inputted or a newline or any space character.
while (<>)
means
while (defined($_ = <>))
so need to press Ctrl-D (unix) or Ctrl-Z, Enter (Windows) to signal end of input. Or you could add a check for a blank line:
while (<>) {
chomp;
last if $_ eq "";
print grep /\b$_\b/s, #lines;
}
There is possible problem in your example with my #match = grep {/\b$_\b/s} #lines; as grep is not working with user input, but only with content of #lines. What it does is this:
grep { $lines[index] =~ /\b$lines[index]\b/s }
and you probably want this:
while (my $input = <>) {
chomp($input);
last if $input =~ /^ \s* $/x; # exit loop if no input or only whitespaces
my #match = grep { /\b$input\b/s } #lines;
print #match;
}
Related
I have the below file
file1:
abc def host 123 host 869 host
I wrote below script to count the occurrence of a "host" keyword in each line.
I tried all the ways(refer the ones which are commented) still it does not seem to work. sed command worked in command line but not inside the perl script
#!/usr/bin/perl
open(SOURCE,"</home/amp/surevy01/file1");
open(DESTINATION,"</home/amp/surevy01/file2");
while(my $line = <SOURCE>)
{
while(my $line1 = <DESTINATION>)
{
#chomp($line);
#chomp($line1);
if ($line =~ "host")
{
#my $count = grep {host} $line;
#my $count = `sed -i {s/host/host\n/g} $line1 | grep -c {host}`;
#my $count = `perl -pi -e 's/host/host\n/g' $line1 | grep -c host`;
#my $count grep ("host" ,$line);
print "$count";
print "match found \n";
next;
}
else
{
print "match not found \n";
exit;
}
}
}
I'm a beginner to perl. Looking for your valuable suggestions
Your own solution will match instances like hostages and Shostakovich
grep is the canonical way to count elements of a list, and split will turn your line into a list of words, giving
my $count = grep { $_ eq 'host' } split ' ', $line
I don't know why you're looping through two files in your example, but you can use the /g (global) flag:
my $line = "abc def host 123 host 869 host";
my $x = 0;
while ($line =~ /host/g){
$x++;
}
print "$x\n"; # 3
When you run a regex with /g in scalar context (as is the conditional in the while statement), it will keep track of the location of the last match and restart from there. Therefore, /host/g in a loop as above will find each occurence of host. You can also use the /g in list contexts:
my $line = "abc def host 123 host 869 host";
my #matches = $contents =~ /host/g;
print scalar #matches; # 3 again
In this case, #matches will contain all matches of the regexp against the string, which will be ('host', 'host', 'host') since the query is a simple string. Then, scalar(#matches) will yield the length of the list.
This produces the number of instances of host in $line:
my $count = () = $line =~ /host/g;
But that also matches hosting. To avoid that, the following will probably do the trick:
my $count = () = $line =~ /\bhost\b/g;
=()= this is called Perl secret Goatse operator. More info
Here is a part of my script:
foreach $i ( #contact_list ) {
print "$i\n";
$e = "zcat $file_list2| grep $i";
print "$e\n";
$f = qx($e);
print "$f";
}
$e prints properly but $f gives a blank line even when $file_list2 has a match for $i.
Can anyone tell me why?
Always is better to use Perl's grep instead of using pipe :
#lines = `zcat $file_list2`; # move output of zcat to array
die('zcat error') if ($?); # will exit script with error if zcat is problem
# chomp(#lines) # this will remove "\n" from each line
foreach $i ( #contact_list ) {
print "$i\n";
#ar = grep (/$i/, #lines);
print #ar;
# print join("\n",#ar)."\n"; # in case of using chomp
}
Best solution is not calling zcat, but using zlib library :
http://perldoc.perl.org/IO/Zlib.html
use IO::Zlib;
# ....
# place your defiiniton of $file_list2 and #contact list here.
# ...
$fh = new IO::Zlib; $fh->open($file_list2, "rb")
or die("Cannot open $file_list2");
#lines = <$fh>;
$fh->close;
#chomp(#lines); #remove "\n" symbols from lines
foreach $i ( #contact_list ) {
print "$i\n";
#ar = grep (/$i/, #lines);
print (#ar);
# print join("\n",#ar)."\n"; #in case of using chomp
}
Your question leaves us guessing about many things, but a better overall approach would seem to be opening the file just once, and processing each line in Perl itself.
open(F, "zcat $file_list |") or die "$0: could not zcat: $!\n";
LINE:
while (<F>) {
######## FIXME: this could be optimized a great deal still
foreach my $i (#contact_list) {
if (m/$i/) {
print $_;
next LINE;
}
}
}
close (F);
If you want to squeeze out more from the inner loop, compile the regexes from #contact_list into a separate array before the loop, or perhaps combine them into a single regex if all you care about is whether one of them matched. If, on the other hand, you want to print all matches for one pattern only at the end when you know what they are, collect matches into one array per search expression, then loop them and print when you have grepped the whole set of input files.
Your problem is not reproducible without information about what's in $i, but I can guess that it contains some shell metacharacter which causes it to be processed by the shell before the grep runs.
I have a sample file here http://pastebin.com/m5m40nGF
What I want to do is add a line after every instance of protein_id.
protein_id always has the same pattern:
TAB-TAB-TAB-protein_id-TAB-gnl|CorradiLab|M715_#SOME_NUMBER
What I need to do is to add this after every line of protein_id:
TAB-TAB-TAB-transcript_id-TAB-gnl|CorradiLab|M715_mRNA_#SOME_NUMBER
The catch is that #SOME_NUMBER has to stay the same.
In the first case, it would look like this:
94 1476 CDS
protein_id gnl|CorradiLab|M715_ECU01_0190
transcript_id gnl|CorradiLab|M715_mRNA_ECU01_0190
product serine hydroxymethyltransferase
label serine hydroxymethyltransferase
Thanks! Adrian
I tried a perl solution, but I get an error.
open(IN, $in); while(<IN>){
print $_;
if ($_ ~= /gnl\|CorradiLab\|/) {
$_ =~ s/tprotein_id/transcript_id/;
print $_;
}
}
Error:
syntax error at test.pl line 3, near "$_ ~"
syntax error at test.pl line 7, near "}"
Execution of test.pl aborted due to compilation errors.
The following perl script worked
my $in=shift;
open(IN, $in); while(<IN>){
print $_;
if ($_ =~ /gnl\|CorradiLab\|/) {
my $tmp = $_;
$tmp =~ s/protein_id/transcript_id/;
print $tmp;
}
}
Offering an update on existing answer because I feel it can be improved further:
Generally - the precise problem in the OP is this line:
if ($_ ~= /gnl\|CorradiLab\|/) {
Because you've got ~= not =~. That's what syntax error at test.pl line 3, near "$_ ~" is trying to tell you.
I would offer that improving on:
my $in=shift;
open(IN, $in); while(<IN>){
print $_;
if ($_ =~ /gnl\|CorradiLab\|/) {
my $tmp = $_;
$tmp =~ s/protein_id/transcript_id/;
print $tmp;
}
}
while ( my $tmp = <IN> ) { skips the need to assign $_.
3 argument open with lexical filehandle is preferable. E.g. open ( my $in, "<", "$input_filename" ) or die $!; (You should test whether the open worked too)
Explicit open may well be unnecessary if you're just reading a filename from command line. Using <> either reads filenames (opening and processing) or STDIN, which means your script becomes a bit more versatile.
Thus I would rewrite as:
#!/usr/bin/perl
use strict;
use warnings;
while ( my $line = <> ) {
print $line;
if ( $line =~ /gnl\|CorradiLab\|/ ) {
$line =~ s/protein_id/transcript_id/;
print $line;
}
}
Or alternatively:
#!/usr/bin/perl
use strict;
use warnings;
while (<>) {
print;
if (m/gnl\|CorradiLab\|/) {
s/protein_id/transcript_id/;
print;
}
}
I wrote this code and it works fine, it should find lines in which there's no string like 'SID' and append a pipe | at the beginning of the line, so like this: find all lines in which there's no 'SID' and append a pipe | at the beginning of the line. But how I wrote it, I can just output the lines which were changed and have a pipe. What I actually want: leave the file as it is and just append the pipes to the lines which match. Thank you.
#!usr/bin/perl
use strict;
use warnings;
use autodie;
my $fh;
open $fh, '<', 'file1.csv';
my $out = 'file2.csv';
open(FILE, '>', $out);
my $myline = "";
while (my $line = <$fh>) {
chomp $line;
unless ($line =~ m/^SID/) {
$line =~ m/^(.*)$/;
$myline = "\|$1";
}
print FILE $myline . "\n";
}
close $fh;
close FILE;
my file example:
SID,bla
foo bar <- my code adds the pipe to the beginning of this line
output should be like this:
SID,bla
| foo bar
but in my case I only print $myline, I know:
| foo bar
The line
$line =~ m/^(.*)$/
is misguided: all it does is put the contents of $line into $1, so the following statement
$myline = "\|$1"
may as well be
$myline = "|$line"
(The pipe | doesn't need escaping unless it is part of a regular expression.)
Since you are printing $myline at the end of your loop you are never seeing the contents of unmodified lines.
You can fix that by printing $line or $myline according to which one contains the required output, like this
while (my $line = <$fh>) {
chomp $line;
if ($line =~ m/^SID/) {
print "$line\n";
}
else {
my $myline = "|$line";
print "$myline\n";
}
}
or, much more simply, by dropping the intermediate variable and using the default $_ for the input lines, like this
while (<$fh>) {
print '|' unless /^SID/;
print;
}
Note that I have also removed the chomp as it just means you have to put the newline back on the end of the string when you print it.
Instead of creating a new variable $myline, use the one you already have:
while (my $line =<$fh>) {
$line = '|' . $line if $line !~ /^SID/;
print FILE $line;
}
Also, you can use lexical filehandle for the output file as well. Moreover, you should check the return value of open:
open my $OUT, '>', $out or die $!;
A perl script I'm writing needs to parse a file that has continuation lines like a Makefile. i.e. lines that begin with whitespace are part of the previous line.
I wrote the code below but don't feel like it is very clean or perl-ish (heck, it doesn't even use "redo"!)
There are many edge cases: EOF at odd places, single-line files, files that start or end with a blank line (or non-blank line, or continuation line), empty files. All my test cases (and code) are here: http://whatexit.org/tal/flatten.tar
Can you write cleaner, perl-ish, code that passes all my tests?
#!/usr/bin/perl -w
use strict;
sub process_file_with_continuations {
my $processref = shift #_;
my $nextline;
my $line = <ARGV>;
$line = '' unless defined $line;
chomp $line;
while (defined($nextline = <ARGV>)) {
chomp $nextline;
next if $nextline =~ /^\s*#/; # skip comments
$nextline =~ s/\s+$//g; # remove trailing whitespace
if (eof()) { # Handle EOF
$nextline =~ s/^\s+/ /;
if ($nextline =~ /^\s+/) { # indented line
&$processref($line . $nextline);
}
else {
&$processref($line);
&$processref($nextline) if $nextline ne '';
}
$line = '';
}
elsif ($nextline eq '') { # blank line
&$processref($line);
$line = '';
}
elsif ($nextline =~ /^\s+/) { # indented line
$nextline =~ s/^\s+/ /;
$line .= $nextline;
}
else { # non-indented line
&$processref($line) unless $line eq '';
$line = $nextline;
}
}
&$processref($line) unless $line eq '';
}
sub process_one_line {
my $line = shift #_;
print "$line\n";
}
process_file_with_continuations \&process_one_line;
How about slurping the whole file into memory and processing it using regular expressions. Much more 'perlish'. This passes your tests and is much smaller and neater:
#!/usr/bin/perl
use strict;
use warnings;
$/ = undef; # we want no input record separator.
my $file = <>; # slurp whole file
$file =~ s/^\n//; # Remove newline at start of file
$file =~ s/\s+\n/\n/g; # Remove trailing whitespace.
$file =~ s/\n\s*#[^\n]+//g; # Remove comments.
$file =~ s/\n\s+/ /g; # Merge continuations
# Done
print $file;
If you don't mind loading the entire file in memory, then the code below passes the tests.
It stores the lines in an array, adding each line either to the previous one (continuation) or at the end of the array (other).
#!/usr/bin/perl
use strict;
use warnings;
my #out;
while( <>)
{ chomp;
s{#.*}{}; # suppress comments
next unless( m{\S}); # skip blank lines
if( s{^\s+}{ }) # does the line start with spaces?
{ $out[-1] .= $_; } # yes, continuation, add to last line
else
{ push #out, $_; } # no, add as new line
}
$, = "\n"; # set output field separator
$\ = "\n"; # set output record separator
print #out;