I want to rename my temporary file "file3.c" to user input file name.
Using rename or move command from File::copy doesn't rename it.
use strict;
use warnings;
use File::Copy;
#input header file
print "Input file1:\n";
$input = <>;
open(FILE1, $input) || die "couldn't open the file!";
open(FILE3, '>>file3.c') || die "couldn't open the file!";
...
#some work on file3.c
...
close(FILE1);
close(FILE3);
#renaming prepended temporary file name to original file name
rename("file3.c", "$input");
OUTPUT
no renaming occurs
How do I rename it?
You probably only need to chomp your input to remove the newline:
chomp(my $input = <>);
And you should always check for an error $! when performing file operations:
rename($foo, $bar) or die "Cannot rename: $!";
Also, you should most often use or instead of ||, since || has higher precedence. For example, this is a common beginner mistake, that is rather hard to discover:
open my $fh, "<", $file || die $!; # WRONG!
Because logical or || has higher precedence than comma ,, the die statement will never happen, unless $file happens to be a false value.
Related
This is my script count.pl, I am trying to count the number of lines in a file.
The script's code :
chdir $filepath;
if (-e "$filepath"){
$total = `wc -l < file.list`;
printf "there are $total number of lines in file.list";
}
i can get a correct output, but i do not want to count blank lines and anything in the file that start with #. any idea ?
As this is a Perl program already open the file and read it, filtering out lines that don't count with
open my $fh, '<', $filename or die "Can't open $filename: $!";
my $num_lines = grep { not /^$|^\s*#/ } <$fh>;
where $filename is "file.list." If by "blank lines" you mean also lines with spaces only then chagne regex to /^\s*$|^\s*#/. See grep, and perlretut for regex used in its condition.
That filehandle $fh gets closed when the control exits the current scope, or add close $fh; after the file isn't needed for processing any more. Or, wrap it in a block with do
my $num_lines = do {
open my $fh, '<', $filename or die "Can't open $filename: $!";
grep { not /^$|^\s*#/ } <$fh>;
};
This makes sense doing if the sole purpose of opening that file is counting lines.
Another thing though: an operation like chdir should always be checked, and then there is no need for the race-sensitive if (-e $filepath) either. Altogether
# Perhaps save the old cwd first so to be able to return to it later
#my $old_cwd = Cwd::cwd;
chdir $filepath or die "Can't chdir to $filepath: $!";
open my $fh, '<', $filename or die "Can't open $filename: $!";
my $num_lines = grep { not /^$|^\s*#/ } <$fh>;
A couple of other notes:
There is no reason for printf. For all normal prints use say, for which you need use feature qw(say); at the beginning of the program. See feature pragma
Just in case, allow me to add: every program must have at the beginning
use warnings;
use strict;
Perhaps the original intent of the code in the question is to allow a program to try a non-existing location, and not die? In any case, one way to keep the -e test, as asked for
#my $old_cwd = Cwd::cwd;
chdir $filepath or warn "Can't chdir to $filepath: $!";
my $num_lines;
if (-e $filepath) {
open my $fh, '<', $filename or die "Can't open $filename: $!";
$num_lines = grep { not /^$|^\s*#/ } <$fh>;
}
where I still added a warning if chdir fails. Remove that if you really don't want it. I also added a declaration of the variable that is assigned the number of lines, with my $total_lines;. If it is declared earlier in your real code then of course remove that line here.
perl -ne '$n++ unless /^$|^#/ or eof; print "$n\n" if eof'
Works with multiple files too.
perl -ne '$n++ unless /^$|^#/ or eof; END {print "$n\n"}'
Better for a single file.
open(my $fh, '<', $filename);
my $n = 0;
for(<$fh>) { $n++ unless /^$|^#/}
print $n;
Using sed to filter out the "unwanted" lines in a single file:
sed '/^\s*#/d;/^\s*$/d' infile | wc -l
Obviously, you can also replace infile with a list of files.
The solution is very simple, no any magic.
use strict;
use warnings;
use feature 'say';
my $count = 0;
while( <> ) {
$count++ unless /^\s*$|^\s*#/;
}
say "Total $count lines";
Reference:
<>
My program is trying to search a string from multiple files in a directory. The code searches for single patterns like perl but fails to search a long string like Status Code 1.
Can you please let me know how to search for strings with multiple words?
#!/usr/bin/perl
my #list = `find /home/ad -type f -mtime -1`;
# printf("Lsit is $list[1]\n");
foreach (#list) {
# print("Now is : $_");
open(FILE, $_);
$_ = <FILE>;
close(FILE);
unless ($_ =~ /perl/) { # works, but fails to find string "Status Code 1"
print "found\n";
my $filename = 'report.txt';
open(my $fh, '>>', $filename) or die "Could not open file '$filename' $!";
say $fh "My first report generated by perl";
close $fh;
} # end unless
} # end For
There are a number of problems with your code
You must always use strict and use warnings at the top of every Perl program. There is little point in delcaring anything with my without strict in place
The lines returned by the find command will have a newline at the end which must be removed before Perl can find the files
You should use lexical file handles (my $fh instead of FILE) and the three-parameter form of open as you do with your output file
$_ = <FILE> reads only the first line of the file into $_
unless ($_ =~ /perl/) is inverted logic, and there's no need to specify $_ as it is the default. You should write if ( /perl/ )
You can't use say unless you have use feature 'say' at the top of your program (or use 5.010, which adds all features available in Perl v5.10)
It is also best to avoid using shell commands as Perl is more than able to do anything that you can using command line utilities. In this case -f $file is a test that returns true if the file is a plain file, and -M $file returns the (floating point) number of days since the file's modification time
This is how I would write your program
#!/usr/bin/perl
use strict;
use warnings;
use 5.010;
for my $file ( glob '/home/ad/*' ) {
next unless -f $file and int(-M $file) == 1;
open my $fh, '<', $file or die $!;
while ( <$fh> ) {
if ( /perl/ ) {
print "found\n";
my $filename = 'report.txt';
open my $out_fh, '>>', $filename or die "Could not open file '$filename': $!";
say $fh "My first report generated by perl";
close $out_fh;
last;
}
}
}
it should have matched unless $_ contains text in different case.
try this.
unless($_ =~ /Status\s+Code\s+1/i) {
Change
unless ($_ =~ /perl/) {
to:
unless ($_ =~ /(Status Code 1)/) {
I am certain the above works, except it's case sensitive.
Since you question it, I rewrote your script to make more sense of what you're trying to accomplish and implement the above suggestion. Correct me if I am wrong, but you're trying to make a script which matches "Status Code 1" in a bunch of files where last modified within 1 day and print the filename to a text file.
Anyways, below is what I recommend:
#!/usr/bin/perl
use strict;
use warnings;
my $output_file = 'report.txt';
my #list = `find /home/ad -type f -mtime -1`;
foreach my $filename (#list) {
print "PROCESSING: $filename";
open (INCOMING, "<$filename") || die "FATAL: Could not open '$filename' $!";
foreach my $line (<INCOMING>) {
if ($line =~ /(Status Code 1)/) {
open( FILE, ">>$output_file") or die "FATAL: Could not open '$output_file' $!";
print FILE sprintf ("%s\n", $filename);
close(FILE) || die "FATAL: Could not CLOSE '$output_file' $!";
# Bail when we get the first match
last;
}
}
close(INCOMING) || die "FATAL: Could not close '$filename' $!";
}
I want to alter the names in a phylip file using information from another file. The phylip is just one continuous string of information, and the names I want to alter (e.g. aaaaaaabyd) are embedded in it. Like so
((aaaaaaabyd:0.23400159127856412500,(((aaaaaaaaxv:0.44910864993667892753,aaaaaaaagf:0.51328033054009691849):0.06090419044604544752,((aaaaaaabyc:0.11709094683204501752,aaaaaaafzz:0.04488198976629347720):0.09529995111708353117,((aaaaaaadbn:0.34408087090010841536,aaaaaaaafj:0.47991503739434709930):0.06859184769990583908,((aaaaaaaabk:0.09244297511609228524,aaaaaaaete:0.12568841555837687030):0.28431
(there are no new lines)
The names within are like aaaaaaaabk.
The other file has the information change to, like so in the other file,
aaaaaaaabk;Ciona savignyi
aaaaaaaete;Homo sapiens
aaaaaaaafj;Cryptosporidium hominis
aaaaaaaaad;Strongylocentrotus purpuratus
aaaaaaabyd;Theileria parva
aaaaaaaaaf;Plasmodium vivax
I have tried numerous things but this is the closest I got. The problem is it does it for one and doesn't print out the rest of the phylip file. I need to get to ((Theileria parva:0.23400159127856412500, etc.
open(my $tree, "$ARGV[0]") or die "Failed to open file: $!\n";
open(my $csv, "$ARGV[0]") or die "Failed to open file: $!\n";
open(my $new_tree, "> raxml_tree.phy");
# Declare variables
my $find;
my $replace;
my $digest;
# put the file of the tree into string variable
my $string = <$tree>;
# open csv file
while (my $line = <$csv>) {
# aaaaaaaaaa;Ciona savignyi
if ($line =~ m/(\w+)\;+(\w+\s+\w*)/) {
$find = $1;
$replace = $2;
$string =~ s/$find/$replace/g;
}
}
print $new_tree "$string";
close $tree;
close $csv;
close $new_tree;
Some guidelines on your own code
The problem is almost certainly that you are opening the same file $ARGV[0] twice. Presumably one should be `$ARGV[1]
You must always use strict and use warnings at the top of every Perl program you write (there is very little point in declaring your variables unless use strict is in place) and declare all your variables with my as close as possible to their first point of use. It is bad form to declare all your variables in a block at the start, because it makes them all effectively global, and you lose most of the advantages of declaring lexical variables
You should use the three-parameter form of open, and it is a good idea to put the name of the file in the die string so that you can see which one failed. So
open(my $tree, "$ARGV[0]") or die "Failed to open file: $!\n";
becomes
open my $tree, '<', $ARGV[0] or die qq{Failed to open "$ARGV[0]" for input: $!\n};
You should look for simpler solutions rather than apply regex methods every time. $line =~ m/(\w+)\;+(\w+\s+\w*)/ is much tidier as chomp, split /;/
You shouldn't use double-quotes around variables when you want just the value of the variable, so print $new_tree "$string" should be print $new_tree $string
Rather than trying to use the data from the other file (please try to use useful names for items in your question, as it's tough to know what to call them when writing a solution) it is best to build a hash that contains all the translations
This program will do as you ask. It builds a regex consisting of an alternation of all the hash keys, and then converts all ocurrences of that pattern into its corresponding name. Only those names that are in your sample other file are translated: the others are left as they are
use strict;
use warnings;
use 5.014; # For non-destructive substitution
use autodie;
my %names;
open my $fh, '<', 'other_file.txt';
while ( <$fh> ) {
my ($k, $v) = split /;/, s/\s+\z//r;
$names{$k} = $v;
}
open $fh, '<', 'phylip.txt';
my $data = <$fh>;
close $fh;
my $re = join '|', sort { length $b <=> length $a } keys %names;
$re = qr/(?:$re)/;
$data =~ s/\b($re)\b/$names{$1}/g;
print $data;
output
((Theileria parva:0.23400159127856412500,(((aaaaaaaaxv:0.44910864993667892753,aaaaaaaagf:0.51328033054009691849):0.06090419044604544752,((aaaaaaabyc:0.11709094683204501752,aaaaaaafzz:0.04488198976629347720):0.09529995111708353117,((aaaaaaadbn:0.34408087090010841536,Cryptosporidium hominis:0.47991503739434709930):0.06859184769990583908,((Ciona savignyi:0.09244297511609228524,Homo sapiens:0.12568841555837687030):0.28431
Update
Here is a revised version of your own program with the above points accounted for and the bugs fixed
use strict;
use warnings;
open my $tree_fh, '<', $ARGV[0] or die qq{Failed to open "$ARGV[0]" for input: $!\n};
my $string = <$tree_fh>;
close $tree_fh;
open my $csv_fh, '<', $ARGV[1] or die qq{Failed to open "$ARGV[1]" for input: $!\n};
while ( <$csv_fh> ) {
chomp;
my ($find, $replace) = split /;/;
$string =~ s/$find/$replace/g;
}
close $csv_fh;
open my $new_tree_fh, '>', 'raxml_tree.phy' or die qq{Failed to open "raxml_tree.phy" for output: $!\n};
print $new_tree_fh $string;
close $new_tree_fh;
I have info contained in a variable that I need to have written to a file. My script needs to be create the file and then write to it.
Here's my current script:
my $file_location = '/network/$custom_directory/$custom_filename';
open(my $file ">", $file_location) or die $!;
print $file "$variable_data";
close $file;
I'm getting the feeling that my script is getting hung up on the actual file creation, rather than the variable-writing process.
The error I get when I run the script is: 'No such file or directory' at the line where I try to open the file.
You have a syntax error in your programme. All three arguments of open must be separated by commas.
open my $file, '>', $file_location or die $!;
Single quotes do not interpolate, unlike double quotes, so you probably need them in the file path:
my $file_location = "/network/$custom_directory/$custom_filename";
BTW: Including a sole variable into double quotes server no purpose for string contents. You can equivalently
print $file $variable_data;
You didn’t say what your error is.
But you’re missing a comma.
You also have the wrong quotes.
You also (probably) forgot the newline at the end.
And you forgot to check that the close succeeded lest your filesystem should have filled up.
You may have forgotten the binmode or the encoding.
Which gives you something like this, with obligatory preamble:
#!/usr/bin/perl
use strict;
use warnings;
my $custom_directory = "something old";
my $custom_filename = "something new";
my $data = "something borrowed";
my $path = "/network/$custom_directory/$custom_filename";
open(my $handle, ">", $path) || die "can't open $path: $!";
binmode($handle); # for raw; else set the encoding
print $handle "$data\n";
close($handle) || die "can't close $path: $!";
Two things: First the file location is in single-quotes, so the $ variables won't be interpolated. Second, you're missing a comma in the call to open. The code should read:
my $file_location = "/network/$custom_directory/$custom_filename";
open(my $file, ">", $file_location) or die $!;
First,
use strict;
use warnings;
may help. Second, variable interpolation requires double quoted strings:
my $file_location = "/network/$custom_directory/$custom_filename";
Third, you may probably need a \n at the print statement:
print $file "$variable_data\n";
And finally, your open statement should be:
open my $file, ">", $file_location or die $!;
I have two scripts in which I'm experimenting with CSV_XS. In the first, I hard-coded everything: source directory, filename, and the csv delimiter I wanted to look for. The script works great. In the second, however, I try to dynamically discover as much as possible. That script seems to run, but it outputs nothing.
I'm having trouble figuring out why, and I was hoping you fine Perl folks wouldn't mind lending a second set of eyes to the problem:
First, the successful script:
#!/usr/bin/perl -w
use Text::CSV_XS;
my #records;
my $file = 'Data/space.txt';
my $csv=Text::CSV_XS->new({ sep_char => " " });
open(FILE,$file) || die "Couldn't open $file: $!\n";
while (<FILE>){
$csv->parse($_);
push(#records,[$csv->fields]);
}
close FILE;
foreach (#records){
print $_->[0], ",", $_->[1], ",", $_->[2], ",", $_->[3], ",", $_->[4], "\n";
}
And second, the "failing" script:
#!/usr/bin/perl -w
use Text::CSV_XS;
$input_dir = $ARGV[0]; #I pass "Data" on the command line
my #records;
opendir(DIR, $input_dir) || die "cannot open dir $input_dir: $!";
my #filelist = grep {$_ ne '.' && $_ ne '..'} readdir DIR;
closedir DIR;
foreach $file (#filelist){
print "Input file='",$input_dir,"/",$file,"'\n";
if ($file =~ /comma/) {$sep=','}
elsif ($file =~ /pipe/) {$sep='|'}
elsif ($file =~ /space/) {$sep=' '}
else {die "Cannot identify separator in $file: $!";}
print "Delimiter='",$sep,"'\n";
open(FILE,$input_dir||"/"||$file) || die "Couldn't open $file: $!\n";
my $csv=Text::CSV_XS->new({ sep_char => $sep });
while (<FILE>){
$csv->parse( $_ );
push(#records,[$csv->fields]);
print "File Input Line:'", $_ ,$csv->fields,"'\n";
};
close FILE;
}
foreach $record (#records){
print $record->[0], ",", $record->[1], ",", $record->[2], ",", $record->[3], ",", $record->[4], "\n";
}
This line looks kind of suspect:
open(FILE,$input_dir||"/"||$file) || die "Couldn't open $file: $!\n";
I don't think you want to put those || in there. What that does is check to see if $input_dir is true, then if it isn't, it check to see if "/" is true (which it always is). Your $input_dir is likely always true, so you're just opening the $input_dir.
You should be using File::Spec to create your fully-qualified files:
my $fullfile = File::Spec->catfile( $input_dir, $file );
open( FILE, $fullfile ) || die "Couldn't open $fullfile: $!\n";
This will "do the right thing" in putting a / where appropriate (or, if you're on Windows, \). Then pass that in to your open() command.
Further, you should be using lexical filehandles and directory handles, along with the three-option open():
open my $fh, '<', $fullfile or die "Could not open file $fullfile: $!\n";
Lexical filehandles are much safer, as they can't get overridden by some other module defining a FILE filehandle. Three-option open() is easier to understand and isn't prone to error when you have a filename that has a > or < or | in it.
If you want to get really crazy, put use autodie; at the top, so you don't even have to check for the return value of open() or opendir():
use autodie;
open my $fh, '<', $fullfile;