I have this script to read a devices list and send a command. but currently it reads only the first device and sends it the command, ignoring the rest. What have I missed?
#!\usr\bin\Perl\bin\perl
use warnings;
use strict;
use NET::SSH2;
use MIME::Base64;
my $host = "C:/temp/devices.txt"; # input file
my $user = "XXX"; # your account
my $pass = "XXXXXX"; # your password 64 bit mime
my $ssh2 = Net::SSH2->new();
my $result = "C:/temp/result.txt"; # output file
$ssh2->debug(1); # debug on/off
open(List, '<', "$host") or die "$!";
while(<List>) {
chomp $_;
$ssh2->connect("$_") or die "Unable to connect host $# \n";
my $dp=decode_base64("$pass");
$ssh2->auth_password("$user","$dp");
my $chan = $ssh2->channel();
$chan->exec('sh run');
my $buflen =100000;
my $buf = '0' x $buflen;
my $read = $chan->read($buf, $buflen );
warn 'More than ', $buflen, ' characters in listing' if $read >= $buflen;
open OUTPUT, ">", "$result";
print OUTPUT "HOST: $_\n\n";
print OUTPUT "$buf\n";
print OUTPUT "\n\n\n";
print OUTPUT
close (List);
$chan->close();
}
You shouldn't be closing your List filehandle inside of your while loop. Move the close (List); line to after the close brace:
open(List, '<', "$host") or die "$!";
while(<List>) {
# ⋮
}
close (List);
close(List);
should be after the closing bracket.
You're closing your filehandle inside the while() loop. Move close(List) so it's outside of the while():
while(<List>) {
...
}
close(List);
Edit: I just noticed that you're also doing this within your while() loop:
open OUTPUT, ">", "$result";
This will cause your output file to be overwritten each time through the loop, so it will only have the last command's results in it. You could either move the open() / close() outside of the loop, or open the file in append mode:
open OUTPUT, '>>', $result;
You're also not checking to see if the open() succeeds; you should put or die $! at the end of your open() statement.
Related
Limiting the scope of a variable $x to a particular code chunk or subroutine, by means of my $x, saves a coder from a world of "global variable"-caused confusion.
But when it comes to the input record separator, $/, apparently its scope cannot be limited.
Am I correct in this?
As a consequence, if I forget to reset the input record separator at the end of a loop, or inside a subroutine, the code below my call to the subroutine can give unexpected results.
The following example demonstrates this.
#!/usr/bin/perl
use strict; use warnings;
my $count_records; my $infile = $ARGV[0]; my $HANDLEinfile;
open $HANDLEinfile, '<', $infile or die "cannot open $infile for reading";
$count_records = 0;
while(<$HANDLEinfile>)
{
$count_records++;
print "$count_records:\n";
print;
}
close $HANDLEinfile;
look_through_other_file();
print "\nNOW, after invoking look_through_other_file:\n";
open $HANDLEinfile, '<', $infile or die "cannot open $infile for reading";
$count_records = 0;
while(<$HANDLEinfile>)
{
$count_records++;
print "$count_records:\n";
print;
}
close $HANDLEinfile;
sub look_through_other_file
{
$/ = undef;
# here, look through some other file with a while loop
return;
}
Here is how it behaves on an input file:
> z.pl junk
1:
All work
2:
and
3:
no play
4:
makes Jack a dull boy.
NOW, after invoking look_through_other_file:
1:
All work
and
no play
makes Jack a dull boy.
>
Note that if one tries to change to
my $/ = undef;
inside the subroutine, this generates an error.
Incidentally, among the stackoverflow tags, why is there no tag for "input record separator"?
The answer for the my $/ = undef; question is to change it to local $/ = undef;. Then the revised code is as follows.
#!/usr/bin/perl
use strict; use warnings;
my $count_records; my $infile = $ARGV[0]; my $HANDLEinfile;
open $HANDLEinfile, '<', $infile or die "cannot open $infile for reading";
$count_records = 0;
while(<$HANDLEinfile>)
{
$count_records++;
print "$count_records:\n";
print;
}
close $HANDLEinfile;
look_through_other_file();
print "\nNOW, after invoking look_through_other_file:\n";
open $HANDLEinfile, '<', $infile or die "cannot open $infile for reading";
$count_records = 0;
while(<$HANDLEinfile>)
{
$count_records++;
print "$count_records:\n";
print;
}
close $HANDLEinfile;
sub look_through_other_file
{
local $/ = undef;
# here, look through some other file with a while loop
return;
}
Then there is no need to return the input record separator to another value, or to the default, $/ = "\n";, by hand.
You can use local to temporarily update the value of a global variable, including $/.
sub look_through_other_file {
local $/ = undef;
# here, look through some other file with a while loop
return;
}
will use an undefined $/ as long as the look_through_other_file subroutine is in the call stack.
You may encounter this construction in this common idiom, to slurp the entire contents of a file into a variable without altering the value of $/ for the rest of the program:
open my $fh, "<", "/some/file";
my $o = do { local $/; <$fh> };
I am trying to improve the warning message issued by Encode::decode(). Instead of printing the name of the module and the line number in the module, I would like it to print the name of the file being read and the line number in that file where the malformed data was found. To a developer, the origial message can be useful, but to an end user not familiar with Perl, it is probably quite meaningless. The end user would probably rather like to know which file is giving the problem.
I first tried to solve this using a $SIG{__WARN__} handler (which is probably not a good idea), but I get a segfault. Probably a silly mistake, but I could not figure it out:
#! /usr/bin/env perl
use feature qw(say);
use strict;
use warnings;
use Encode ();
binmode STDOUT, ':utf8';
binmode STDERR, ':utf8';
my $fn = 'test.txt';
write_test_file( $fn );
# Try to improve the Encode::FB_WARN fallback warning message :
#
# utf8 "\xE5" does not map to Unicode at <module_name> line xx
#
# Rather we would like the warning to print the filename and the line number:
#
# utf8 "\xE5" does not map to Unicode at line xx of file <filename>.
my $str = '';
open ( my $fh, "<:encoding(utf-8)", $fn ) or die "Could not open file '$fn': $!";
{
local $SIG{__WARN__} = sub { my_warn_handler( $fn, $_[0] ) };
$str = do { local $/; <$fh> };
}
close $fh;
say "Read string: '$str'";
sub my_warn_handler {
my ( $fn, $msg ) = #_;
if ( $msg =~ /\Qdoes not map to Unicode\E/ ) {
recover_line_number_and_char_pos( $fn, $msg );
}
else {
warn $msg;
}
}
sub recover_line_number_and_char_pos {
my ( $fn, $err_msg ) = #_;
chomp $err_msg;
$err_msg =~ s/(line \d+)\.$/$1/; # Remove period at end of sentence.
open ( $fh, "<:raw", $fn ) or die "Could not open file '$fn': $!";
my $raw_data = do { local $/; <$fh> };
close $fh;
my $str = Encode::decode( 'utf-8', $raw_data, Encode::FB_QUIET );
my ($header, $last_line) = $str =~ /^(.*\n)([^\n]*)$/s;
my $line_no = $str =~ tr/\n//;
++$line_no;
my $pos = ( length $last_line ) + 1;
warn "$err_msg, in file '$fn' (line: $line_no, pos: $pos)\n";
}
sub write_test_file {
my ( $fn ) = #_;
my $bytes = "Hello\nA\x{E5}\x{61}"; # 2 lines ending in iso 8859-1: åa
open ( my $fh, '>:raw', $fn ) or die "Could not open file '$fn': $!";
print $fh $bytes;
close $fh;
}
Output:
utf8 "\xE5" does not map to Unicode at ./p.pl line 27
, in file 'test.txt' (line: 2, pos: 2)
Segmentation fault (core dumped)
Here is another way to locate where the warning fires, with un-buffered sysread
use warnings;
use strict;
binmode STDOUT, ':utf8';
binmode STDERR, ':utf8';
my $file = 'test.txt';
open my $fh, "<:encoding(UTF-8)", $file or die "Can't open $file: $!";
$SIG{__WARN__} = sub { print "\t==> WARN: #_" };
my $char_cnt = 0;
my $char;
while (sysread($fh, $char, 1)) {
++$char_cnt;
print "$char ($char_cnt)\n";
}
The file test.txt was written by the posted program, except that I had to add to it to reproduce the behavior -- it runs without warnings on v5.10 and v5.16. I added \x{234234} to the end. The line number can be tracked with $char =~ /\n/.
The sysread returns undef on error. It can be moved into the body of while (1) to allow reads to continue and catch all warnings, breaking out on 0 (returned on EOF).
This prints
H (1)
e (2)
l (3)
l (4)
o (5)
(6)
A (7)
å (8)
a (9)
==> WARN: Code point 0x234234 is not Unicode, may not be portable at ...
(10)
While this does catch the character warned about, re-reading the file using Encode may well be better than reaching for sysread, in particular if sysread uses Encode.
However, Perl is utf8 internally and I am not sure that sysread needs Encode.
Note. The page for sysread supports its use on data with encoding layers
Note that if the filehandle has been marked as :utf8 Unicode
characters are read instead of bytes (the LENGTH, OFFSET, and the
return value of sysread are in Unicode characters). The
:encoding(...) layer implicitly introduces the :utf8 layer.
See binmode, open, and the open pragma.
Note Apparently, things have moved on and after a certain version sysread does not support encoding layers. The link above, while for an older version (v5.10 for one) indeed shows what is quoted, with a newer version tells us that there'll be an exception.
Can't call method print on an undefined value in line 40 line 2.
Here is the code. I use FileHandle to settle files:
#!/usr/bin/perl
use strict;
use warnings;
use FileHandle;
die unless (#ARGV ==4|| #ARGV ==5);
my #input =();
$input[0]=$ARGV[3];
$input[1]=$ARGV[4] if ($#ARGV==4);
chomp #input;
$input[0] =~ /([^\/]+)$/;
my $out = "$1.insert";
my $lane= "$1";
my %fh=();
open (Info,">$ARGV[1]") || die "$!";
open (AA,"<$ARGV[0]") || die "$!";
while(<AA>){
chomp;
my #inf=split;
my $iden=$inf[0];
my $outputfile="$ARGV[2]/$iden";
$fh{$iden}=FileHandle->new(">$outputfile");
}
close AA;
foreach my $input (#input) {
open (IN, "<$input" ) or die "$!" ;
my #path=split (/\//,$input);
print Info "#$path[-1]\n";
while (<IN>) {
my $line1 = $_;
my ($id1,$iden1) = (split "\t", $line1)[6,7];
my $line2 = <IN> ;
my ($id2,$iden2) = (split "\t", $line2)[6,7];
if ($id1 eq '+' && $id2 eq '-') {
my #inf=split(/\t/,$line1);
$fh{$iden1}->print($line1);
$fh{$iden2}->print($line2);
}
}
close IN;
}
I’ve tried multiple variations of this, but none of them seem to work. Any ideas?
Please remember that the primary worth of a Stack Overflow post is not to fix your particular problem, but to help the thousands of others who may be stuck in the same way. With that in mind, "I fixed it, thanks, bye" is more than a little selfish
As I said in my comment, using open directly on a hash element is much preferable to involving FileHandle. Perl will autovivify the hash element and create a file handle for you, and most people at all familiar with Perl will thank you for not making them read up again on the FileHandle documentation
I rewrote your code like this, which is much more Perlish and relies less on "magic numbers" to access #ARGV. You should really assign #ARGV to a list of named scalars, or - better still - use Getopt::Long so that they are named anyway
You should open your file handles as late as possible, and close the output handles early. This is effected most easily by using lexical file handles and limiting their scope to a block. Perl will implicitly close lexical handles for you when they go out of scope
There is no need to chomp the contents of #ARGVunless you could be be called under strange and errant circumstances, in which case you need to do a hell of a lot more to verify the input
You never use the result of $input[0] =~ /([^\/]+)$/ or the variables $out and $lane, so I removed them
#!/usr/bin/perl
use strict;
use warnings 'all';
# $ARGV[0] -- input file
# $ARGV[1] -- output log file
# $ARGV[2] -- directory for outputs per ident
# $ARGV[3] -- 1, $input[0]
# $ARGV[4] -- 2, $input[1] or undef
die "Fix the parameters" unless #ARGV == 4 or #ARGV == 5;
my #input = #ARGV[3,4];
my %fh;
{
open my $fh, '<', $ARGV[0] or die $!;
while ( <$fh> ) {
my $id = ( split )[0];
my $outputfile = "$ARGV[2]/$id";
open $fh{$id}, '>', $outputfile or die qq{Unable to open "$outputfile" for output: $!};
}
}
open my $log_fh, '>', $ARGV[1] or die qq{Unable to open "$ARGV[1]" for output: $!};
for my $input ( #input ) {
next unless $input; # skip unspecified parameters
my #path = split qr|/|, $input; # Really should be done by File::Spec
print $log_fh "#$path[-1]\n"; # Or File::Basename
open my $fh, '<', $input or die qq{Unable to open "$input" for input: $!};
while ( my $line0 = <$fh> ) {
chomp $line0;
my $line1 = <$fh>;
chomp $line1;
my ($id0, $iden0) = (split /\t/, $line0)[6,7];
my ($id1, $iden1) = (split /\t/, $line1)[6,7];
if ( $id0 eq '+' and $id1 eq '-' ) {
$fh{$_} or die qq{No output file for "$_"} for $iden0, $iden1;
print { $fh{$iden0} } $line0;
print { $fh{$iden1} } $line1;
}
}
}
while ( my ($iden, $fh) = each %fh ) {
close $fh or die qq{Unable to close file handle for "$iden": $!};
}
You don't have any error handling on this line:
$fh{$iden}=FileHandle->new(">$outputfile");
It's possible that opening a filehandle is silently failing, and only producing an error when you try to print to it. For example, if you have specified an invalid filename.
Also, you never check if $iden1 and $iden2 are names of open filehandles that actually exist. It's possible one of them does not exist.
In particular, you aren't removing a newline from $line1, so if $iden1 and $iden2 happen to be the last values on the line, this will be included in the name you are trying to use, and it will fail.
In your first while loop, you set up a hash of filehandles that you will write to later. The keys in this hash are the "iden" strings from the first file passed to the program.
Later, you parse another file and use the "iden" values in that file to choose which filehandle to write data to. But one (or more) of the "iden" values in the second file is missing from the first file. So that filehandle can't be found in the %fh hash. Because you don't check for that, you get `undef back from the hash and you can't print to an undefined filehandle.
To fix it, put a check before trying to use one of the filehandles from the %fh hash.
die "Unknown fh identifier '$iden1'" unless exists $fh{$iden1};
die "Unknown fh identifier '$iden2'" unless exists $fh{$iden2};
$fh{$iden1}->print($line1);
$fh{$iden2}->print($line2);
I dont know what exactly is wrong but everytime I execute this script i keep getting "No such file or directory at ./reprioritize line 35, line 1".
here is my script that is having an issue:
my $newresult = "home/user/newresults_percengtage_vs_pn";
sub pushval
{
my #fields = #_;
open OUTFILE, ">$newresult/fixedhomdata_030716-031316.csv" or die $!; #line 35
while(<OUTFILE>)
{
if($fields[5] >= 13)
{
print OUTFILE "$fields[0]", "$fields[1]","$fields[2]","$fields[3]","$fields[4]","$fields[5]", "0";
}
elsif($fields[5] < 13 && $fields[5] > 1)
{
print OUTFILE "$fields[0]", "$fields[1]","$fields[2]","$fields[3]","$fields[4]","$fields[5]", "1";
}
elsif($fields[5] <= 1)
{
print OUTFILE "$fields[0]", "$fields[1]","$fields[2]","$fields[3]","$fields[4]","$fields[5]", "2";
}
}
close (OUTFILE);
You may want to have a look at Perl's tutorial on opening files.
I simplify it a bit. There are basically three modes: open for reading, open for writing, and open for appending.
Reading
Opening for reading is indicated by either a < preceeding the filename or on its own, as a separate parameter to the open() call (preferred), i.e.:
my $fh = undef;
my $filename = 'fixedhomdata_030716-031316.csv';
open($fh, "<$filename") or die $!; # bad
open($fh, '<', $filename) or die $!; # good
while( my $line = <$fh> ) { # read one line from filehandle $fh
...
}
close($fh);
When you open the file this way, it must exist, else you get your error (No such file or directory at ...).
Writing
Opening for writing is indicated by a >, i.e.:
open($fh, ">$filename") or die $!; # bad
open($fh, '>', $filename) or die $!; # good
print $fh "some text\n"; # write to filehandle $fh
print $fh "more text\n"; # write to filehandle $fh
...
close($fh);
When you open the file this way, it is truncated (cleared) and overwritten if it existed. If it did not exist, it will get created.
Appending
Opening for appending is indicated by a >>, i.e.:
open($fh, ">>$filename") or die $!; # bad
open($fh, '>>', $filename) or die $!; # good
print $fh "some text\n"; # append to filehandle $fh
print $fh "more text\n"; # append to filehandle $fh
...
close($fh);
When you open the file this way and it existed, then the new lines will be appended to the file, i.e. nothing is lost. If the file did not
exist, it will be created (as if only > had been given).
Your error message doesn't match your code. You opened the file for writing (>) but got doesn't exist, which indicates that you actually opened it for reading.
This might have happened because you use OUTPUT as a filehandle instead of a scoped variable, e.g. $fh. OUTPUT is a global filehandle, i.e. if you open a file this way, then all of your code (no matter which function in) can use OUTPUT. Don't do that. From the docs:
An older style is to use a bareword as the filehandle, as
open(FH, "<", "input.txt")
or die "cannot open < input.txt: $!";
Then you can use FH as the filehandle, in close FH and and so on.
Note that it's a global variable, so this form is not recommended
in new code.
To summarize:
use scoped variables as filehandles ($fh instead of OUTPUT)
open your file in the right mode (> vs. <)
always use three-argument open (open($fh, $mode, $filename) vs. open($fh, "$mode$filename")
The comments explain that your two issues with the snippet are
The missing leading '/' in the $newresult declaration
You are treating your filehandle as both a read and a write.
The first is easy to fix. The second is not as easy to fix properly with knowing the rest of the script. I am making an assumption that pushval is called once per record in a Array of Arrays(?). This snippet below should get the result you want, but there is likely a better way of doing it.
my $newresult = "/home/user/newresults_percengtage_vs_pn";
sub pushval{
my #fields = #_;
open OUTFILE, ">>$newresult/fixedhomdata_030716-031316.csv" or die $!; #line 35
print OUTFILE "$fields[0]", "$fields[1]","$fields[2]","$fields[3]","$fields[4]","$fields[5]"
if($fields[5] >= 13) {
print OUTFILE "0\n";
} elsif($fields[5] < 13 && $fields[5] > 1) {
print OUTFILE "1\n";
} elsif($fields[5] <= 1) {
print OUTFILE "2\n";
}
close (OUTFILE);
I am trying to both learn perl and use it in my research. I need to do a simple task which is counting the number of sequences and their lengths in a file such as follow:
>sequence1
ATCGATCGATCG
>sequence2
AAAATTTT
>sequence3
CCCCGGGG
The output should look like this:
sequence1 12
sequence2 8
sequence3 8
Total number of sequences = 3
This is the code I have written which is very crude and simple:
#!/usr/bin/perl
use strict;
use warnings;
my ($input, $output) = #ARGV;
open(INFILE, '<', $input) or die "Can't open $input, $!\n"; # Open a file for reading.
open(OUTFILE, '>', $output) or die "Can't open $output, $!"; # Open a file for writing.
while (<INFILE>) {
chomp;
if (/^>/)
{
my $number_of_sequences++;
}else{
my length = length ($input);
}
}
print length, number_of_sequences;
close (INFILE);
I'd be grateful if you could give me some hints, for example, in the else block, when I use the length function, I am not sure what argument I should pass into it.
Thanks in advance
You're printing out just the last length, not each sequence length, and you want to catch the sequence names as you go:
#!/usr/bin/perl
use strict;
use warnings;
my ($input, $output) = #ARGV;
my ($lastSeq, $number_of_sequences) = ('', 0);
open(INFILE, '<', $input) or die "Can't open $input, $!\n"; # Open a file for reading.
# You never use OUTFILE
# open(OUTFILE, '>', $output) or die "Can't open $output, $!"; # Open a file for writing.
while (<INFILE>) {
chomp;
if (/^>(.+)/)
{
$lastSeq = $1;
$number_of_sequences++;
}
else
{
my $length = length($_);
print "$lastSeq $length\n";
}
}
print "Total number of sequences = $number_of_sequences\n";
close (INFILE);
Since you have indicated that you want feedback on your program, here goes:
my ($input, $output) = #ARGV;
open(INFILE, '<', $input) or die "Can't open $input, $!\n"; # Open a file for reading.
open(OUTFILE, '>', $output) or die "Can't open $output, $!"; # Open a file for writing.
Personally, I think when dealing with a simple input/output file relation, it is best to just use the diamond operator and standard output. That means that you read from the special file handle <>, commonly referred to as "the diamond operator", and you print to STDOUT, which is the default output. If you want to save the output in a file, just use shell redirection:
perl program.pl input.txt > output.txt
In this part:
my $number_of_sequences++;
you are creating a new variable. This variable will go out of scope as soon as you leave the block { .... }, in this case: the if-block.
In this part:
my length = length ($input);
you forgot the $ sigil. You are also using length on the file name, not the line you read. If you want to read a line from your input, you must use the file handle:
my $length = length(<INFILE>);
Although this will also include the newline in the length.
Here you have forgotten the sigils again:
print length, number_of_sequences;
And of course, this will not create the expected output. It will print something like sequence112.
Recommendations:
Use a while (<>) loop to read your input. This is the idiomatic method to use.
You do not need to keep a count of your input lines, there is a line count variable: $.. Though keep in mind that it will also count "bad" lines, like blank lines or headers. Using your own variable will allow you to account for such things.
Remember to chomp the line before finding out its length. Or use an alternative method that only counts the characters you want: my $length = ( <> =~ tr/ATCG// ) This will read a line, count the letters ATGC, return the count and discard the read line.
Summary:
use strict;
use warnings; # always use these two pragmas
my $count;
while (<>) {
next unless /^>/; # ignore non-header lines
$count++; # increment counter
chomp;
my $length = (<> =~ tr/ATCG//); # get length of next line
s/^>(\S+)/$1 $length\n/; # remove > and insert length
} continue {
print; # print to STDOUT
}
print "Total number is sequences = $count\n";
Note the use of continue here, which will allow us to skip a line that we do not want to process, but that will still get printed.
And as I said above, you can redirect this to a file if you want.
For starters, you need to change your inner loop to this:
...
chomp;
if (/^>/)
{
$number_of_sequences++;
$sequence_name = $_;
}else{
print "$sequence_name ", length($input), "\n";
}
...
Note the following:
The my declaration has been removed from $number_of_sequences
The sequence name is captured in the variable $sequence_name. It is used later when the next line is read.
To make the script run under strict mode, you can add my declarations for $number_of_sequences and $sequence_name outside of the loop:
my $sequence_name;
my $number_of_sequences = 0;
while (<INFILE>) {
...(as above)...
}
print "Total number of sequences: $number_of_sequences\n";
The my keyword declares a new lexically scoped variable - i.e. a variable which only exists within a certain block of code, and every time that block of code is entered, a new version of that variable is created. Since you want to have the value of $sequence_name carry over from one loop iteration to the next you need to place the my outside of the loop.
#!/usr/bin/perl
use strict;
use warnings;
my ($file, $line, $length, $tag, $count);
$file = $ARGV[0];
open (FILE, "$file") or print"can't open file $file\n";
while (<FILE>){
$line=$_;
chomp $line;
if ($line=~/^>/){
$tag = $line;
}
else{
$length = length ($line);
$count=1;
}
if ($count==1){
print "$tag\t$length\n";
$count=0
}
}
close FILE;