The problem I am having is when I have a Perl script reading data (PE Executable) via STDIN and the stream contains a line terminator "0A" the conversion to hex misses it. Then when I convert the hex data back it is corrupted (missing 0A in the hex format). So how can I detect the "windows" version of line feed "0A" in Perl?
Note: Linux OS (Perl) is reading a Windows PE
!usr/bin/perl
while($line = <STDIN>)
{
chomp($line);
#bytes = split //, $line;
foreach (#bytes)
{
printf "%02lx", ord $_;
}
}
Usage example:
[root#mybox test]# cat test.exe | perl encoder.pl > output
In your loop, you are running chomp on each input line. This is removing whatever value is currently in $/ from the end of your line. Chances are this is 0x0a, and that's where the value is going. Try removing chomp($line) from your loop.
In general, using line oriented reading doesn't make sense for binary files that are themselves not line oriented. You should take a look at the lower level read function which allows you to read a block of bytes from the file without caring what those bytes are. You can then process your data in blocks instead of lines.
#With split
cat magic.exe | perl -e 'print join("", map { sprintf("\\x%02x", ord($_)) } split(//, join("", <STDIN>)))' > hex_encoded_binary
#With pack
cat magic.exe| perl -e 'print join("", map { "\\x" . $_ } unpack("H*", join("", <STDIN>)) =~ /.{2}/gs)' > hex_encoded_binary
Related
I have a large string file seq.txt of letters, unwrapped, with over 200,000 characters. No spaces, numbers etc, just a-z.
I have a second file search.txt which has lines of 50 unique letters which will match once in seq.txt. There are 4000 patterns to match.
I want to be able to find each of the patterns (lines in file search.txt), and then get the 100 characters before and 100 characters after the pattern match.
I have a script which uses grep and works, but this runs very slowly, only does the first 100 characters, and is written out with echo. I am not knowledgeable enough in awk or perl to interpret scripts online that may be applicable, so I am hoping someone here is!
cat search.txt | while read p; do echo "grep -zoP '.{0,100}$p' seq.txt | sed G"; done > do.grep
Easier example with desired output:
>head seq.txt
abcdefghijklmnopqrstuvwxyz
>head search.txt
fgh
pqr
uvw
>head desiredoutput.txt
cdefghijk
mnopqrstu
rstuvwxyz
Best outcome would be a tab separated file of the 100 characters before \t matched pattern \t 100 characters after. Thank you in advance!
One way
use warnings;
use strict;
use feature 'say';
my $string;
# Read submitted files line by line (or STDIN if #ARGV is empty)
while (<>) {
chomp;
$string = $_;
last; # just in case, as we need ONE line
}
# $string = q(abcdefghijklmnopqrstuvwxyz); # test
my $padding = 3; # for the given test sample
my #patterns = do {
my $search_file = 'search.txt';
open my $fh, '<', $search_file or die "Can't open $search_file: $!";
<$fh>;
};
chomp #patterns;
# my #patterns = qw(bcd fgh pqr uvw); # test
foreach my $patt (#patterns) {
if ( $string =~ m/(.{0,$padding}) ($patt) (.{0,$padding})/x ) {
say "$1\t$2\t$3";
# or
# printf "%-3s\t%3s%3s\n", $1, $2, $3;
}
}
Run as program.pl seq.txt, or pipe the content of seq.txt to it.†
The pattern .{0,$padding} matches any character (.), up to $padding times (3 above), what I used in case the pattern $patt is found at a position closer to the beginning of the string than $padding (like the first one, bcd, that I added to the example provided in the question). The same goes for the padding after the $patt.
In your problem then replace $padding to 100. With the 100 wide "padding" before and after each pattern, when a pattern is found at a position closer to the beginning than the 100 then the desired \t alignment could break, if the position is lesser than 100 by more than the tab value (typically 8).
That's what the line with the formatted print (printf) is for, to ensure the width of each field regardless of the length of the string being printed. (It is commented out since we are told that no pattern ever gets into the first or last 100 chars.)
If there is indeed never a chance that a matched pattern breaches the first or the last 100 positions then the regex can be simplified to
/(.{$padding}) ($patt) (.{$padding})/x
Note that if a $patt is within the first/last $padding chars then this just won't match.
The program starts the regex engine for each of #patterns, what in principle may raise performance issues (not for one run with the tiny number of 4000 patterns, but such requirements tend to change and generally grow). But this is by far the simplest way to go since
we have no clue how the patterns may be distributed in the string, and
one match may be inside the 100-char buffer of another (we aren't told otherwise)
If there is a performance problem with this approach please update.
† The input (and output) of the program can be organized in a better way using named command-line arguments via Getopt::Long, for an invocation like
program.pl --sequence seq.txt --search search.txt --padding 100
where each argument may be optional here, with defaults set in the file, and argument names may be shortened and/or given additional names, etc. Let me know if that is of interest
One in awk. -v b=3 is the before context length -v a=3 is the after context length and -v n=3 is the match length which is always constant. It hashes all the substrings of seq.txt to memory so it uses it depending on the size of the seq.txt and you might want to follow the consumption with top, like: abcdefghij -> s["def"]="abcdefghi" , s["efg"]="bcdefghij" etc.
$ awk -v b=3 -v a=3 -v n=3 '
NR==FNR {
e=length()-(n+a-1)
for(i=1;i<=e;i++) {
k=substr($0,(i+b),n)
s[k]=s[k] (s[k]==""?"":ORS) substr($0,i,(b+n+a))
}
next
}
($0 in s) {
print s[$0]
}' seq.txt search.txt
Output:
cdefghijk
mnopqrstu
rstuvwxyz
You can tell grep to search for all the patterns in one go.
sed 's/.*/.{0,100}&.{0,100}/' search.txt |
grep -zoEf - seq.txt |
sed G >do.grep
4000 patterns should be easy peasy, though if you get to hundreds of thousands, maybe you will want to optimize.
There is no Perl regex here, so I switched from the nonstandard grep -P to the POSIX-compatible and probably more efficient grep -E.
The surrounding context will consume any text it prints, so any match within 100 characters from the previous one will not be printed.
You can try following approach to your problem:
load string input data
load into an array patterns
loop through each pattern and look for it in the string
form an array from found matches
loop through matches array and print result
NOTE: the code is not tested due absence of input data
use strict;
use warnings;
use feature 'say';
my $fname_s = 'seq.txt';
my $fname_p = 'search.txt';
open my $fh, '<', $fname_s
or die "Couldn't open $fname_s";
my $data = do { local $/; <$fh> };
close $fh;
open my $fh, '<', $fname_p
or die "Couln't open $fname_p";
my #patterns = <$fh>;
close $fh;
chomp #patterns;
for ( #patterns ) {
my #found = $data =~ s/(.{100}$_.{100})/g;
s/(.{100})(.{50})(.{100})/$1 $2 $3/ && say for #found;
}
Test code for provided test data (added latter)
use strict;
use warnings;
use feature 'say';
my #pat = qw/fgh pqr uvw/;
my $data = do { local $/; <DATA> };
for( #pat ) {
say $1 if $data =~ /(.{3}$_.{3})/;
}
__DATA__
abcdefghijklmnopqrstuvwxyz
Output
cdefghijk
mnopqrstu
rstuvwxyz
I am new to perl. I have a requirement, where I have to convert UTF-8 characters in a string to hyphen(-).
Input string - "IVM IST 20150324095652 31610150096 10ÑatÑ25ÑDisco 0000000091"
Expected output - "IVM IST 20150324095652 31610150096 10-at-25-Disco 0000000091".
But the below program which I have written, reads UTF-8 char as two separate bytes and getting the output as "10--at--25--Disco"
[root# cdr]# cat ../asciifilter.pl
#!/usr/bin/perl
use strict;
use Encode;
my #chars;
my $character;
my $num;
while(my $row = <>) {
#chars = split(//,$row);
foreach $character (#chars) {
$num = ord($character);
if($num < 127) {
print $character;
} else {
print "-";
}
}
}
Output:
[root#MAVBGL-351L cdr]# echo "IVM IST 20150324095652 31610150096 10ÑatÑ25ÑDisco 0000000091" | ../asciifilter.pl
IVM IST 20150324095652 31610150096 10--at--25--Disco 0000000091
But this particular 4th string column has a fixed length of 14 characters only.So that additional hyphens are creating problem.
Can someone give me some clue on how to read UTF-8 char as single character ?
The main thing you need is perl -CSD. With that, the script can be as simple as
perl -CSD -pe 's/[^\x00-\x7F]/-/g'
See man perlrun for a discussion of the options; but briefly, -CS means STDIN, STDOUT, and STDERR are in UTF-8; and -CD means UTF-8 is the default PerlIO layer for both input and output streams. (This script only uses STDIN and STDOUT so the D isn't strictly necessary; but if you only learn one magic incantation, learn -CSD.)
Ok, so I'm very new to Perl. I have a text file and in the file there are 4 columns of data(date, time, size of files, files). I need to create a small script that can open the file and get the average size of the files. I've read so much online, but I still can't figure out how to do it. This is what I have so far, but I'm not sure if I'm even close to doing this correctly.
#!/usr/bin/perl
open FILE, "files.txt";
##array = File;
while(FILE){
#chomp;
($date, $time, $numbers, $type) = split(/ /,<FILE>);
$total += $numbers;
}
print"the total is $total\n";
This is how the data looks in the file. These are just a few of them. I need to get the numbers in the third column.
12/02/2002 12:16 AM 86016 a2p.exe
10/10/2004 11:33 AM 393 avgfsznew.pl
11/01/2003 04:42 PM 38124 c2ph.bat
Your program is reasonably close to working. With these changes it will do exactly what you want
Always use use strict and use warnings at the start of your program, and declare all of your variables using my. That will help you by finding many simple errors that you may otherwise overlook
Use lexical file handles, the three-parameter form of open, and always check the return status of any open call
Declare the $total variable outside the loop. Declaring it inside the loop means it will be created and destroyed each time around the loop and it won't be able to accumulate a total
Declare a $count variable in the same way. You will need it to calculate the average
Using while (FILE) {...} just tests that FILE is true. You need to read from it instead, so you must use the readline operator like <FILE>
You want the default call to split (without any parameters) which will return all the non-space fields in $_ as a list
You need to add a variable in the assignment to allow for athe AM or PM field in each line
Here is a modification of your code that works fine
use strict;
use warnings;
open my $fh, '<', "files.txt" or die $!;
my $total = 0;
my $count = 0;
while (<$fh>) {
my ($date, $time, $ampm, $numbers, $type) = split;
$total += $numbers;
$count += 1;
}
print "The total is $total\n";
print "The count is $count\n";
print "The average is ", $total / $count, "\n";
output
The total is 124533
The count is 3
The average is 41511
It's tempting to use Perl's awk-like auto-split option. There are 5 columns; three containing date and time information, then the size and then the name.
The first version of the script that I wrote is also the most verbose:
perl -n -a -e '$total += $F[3]; $num++; END { printf "%12.2f\n", $total / ($num + 0.0); }'
The -a (auto-split) option splits a line up on white space into the array #F. Combined with the -n option (which makes Perl run in a loop that reads the file name arguments in turn, or standard input, without printing each line), the code adds $F[3] (the fourth column, counting from 0) to $total, which is automagically initialized to zero on first use. It also counts the lines in $num. The END block is executed when all the input is read; it uses printf() to format the value. The + 0.0 ensures that the arithmetic is done in floating point, not integer arithmetic. This is very similar to the awk script:
awk '{ total += $4 } END { print total / NR }'
First drafts of programs are seldom optimal — or, at least, I'm not that good a programmer. Revisions help.
Perl was designed, in part, as an awk killer. There is still a program a2p distributed with Perl for converting awk scripts to Perl (and there's also s2p for converting sed scripts to Perl). And Perl does have an automatic (built-in) variable that keeps track of the number of lines read. It has several names. The tersest is $.; the mnemonic name $NR is available if you use English; in the script; so is $INPUT_LINE_NUMBER. So, using $num is not necessary. It also turns out that Perl does a floating point division anyway, so the + 0.0 part was unnecessary. This leads to the next versions:
perl -MEnglish -n -a -e '$total += $F[3]; END { printf "%12.2f\n", $total / $NR; }'
or:
perl -n -a -e '$total += $F[3]; END { printf "%12.2f\n", $total / $.; }'
You can tune the print format to suit your whims and fancies. This is essentially the script I'd use in the long term; it is fairly clear without being long-winded in any way. The script could be split over multiple lines if you desired. It is a simple enough task that the legibility of the one-line is not a problem, IMNSHO. And the beauty of this is that you don't have to futz around with split and arrays and read loops on your own; Perl does most of that for you. (Granted, it does blow up on empty input; that fix is trivial; see below.)
Recommended version
perl -n -a -e '$total += $F[3]; END { printf "%12.2f\n", $total / $. if $.; }'
The if $. tests whether the number of lines read is zero or not; the printf and division are omitted if $. is zero so the script outputs nothing when given no input.
There is a noble (or ignoble) game called 'Code Golf' that was much played in the early days of Stack Overflow, but Code Golf questions are no longer considered good questions. The object of Code Golf is to write a program that does a particular task in as few characters as possible. You can play Code Golf with this and compress it still further if you're not too worried about the format of the output and you're using at least Perl 5.10:
perl -Mv5.10 -n -a -e '$total += $F[3]; END { say $total / $. if $.; }'
And, clearly, there are a lot of unnecessary spaces and letters in there:
perl -Mv5.10 -nae '$t+=$F[3];END{say$t/$.if$.}'
That is not, however, as clear as the recommended version.
#!/usr/bin/perl
use warnings;
use strict;
open my $file, "<", "files.txt";
my ($total, $cnt);
while(<$file>){
$total += (split(/\s+/, $_))[3];
$cnt++;
}
close $file;
print "number of files: $cnt\n";
print "total size: $total\n";
printf "avg: %.2f\n", $total/$cnt;
Or you can use awk:
awk '{t+=$4} END{print t/NR}' files.txt
Try doing this :
#!/usr/bin/perl -l
use strict; use warnings;
open my $file, '<', "my_file" or die "open error [$!]";
my ($total, $count);
while (<$file>){
chomp;
next if /^$/;
my ($date, $time, $x, $numbers, $type) = split;
$total += $numbers;
$count++;
}
print "the average is " . $total/$count . " and the total is $total";
close $file;
It is as simple as this:
perl -F -lane '$a+=$F[3];END{print "The average size is ".$a/$.}' your_file
tested below:
> cat temp
12/02/2002 12:16 AM 86016 a2p.exe
10/10/2004 11:33 AM 393 avgfsznew.pl
11/01/2003 04:42 PM 38124 c2ph.bat
Now the execution:
> perl -F -lane '$a+=$F[3];END{print "The average size is ".$a/$.}' temp
The average size is 41511
>
explanation:
-F -a says store the line in an array format.with the default separator as space or tab.
so nopw $F[3] has you size of the file.
sum up all the sizes in the 4th column untill all the lines are processed.
END will be executed after processing all the lines in the file.
so $. at the end will gives the number of lines.
so $a/$. will give the average.
This solution opens the file and loops through each line of the file. It then splits the file into the five variables in the line by splitting on 1 or more spaces.
open the file for reading, "<", and if it fails, raise an error or die "..."
my ($total, $cnt) are our column total and number of files added count
while(<FILE>) { ... } loops through each line of the file using the file handle and stores the line in $_
chomp removes the input record separator in $_. In unix, the default separator is a newline \n
split(/\s+/, $_) Splits the current line represented by$_, with the delimiter \s+. \s represents a space, the + afterward means "1 or more". So, we split the next line on 1 or more spaces.
Next we update $total and $cnt
#!/usr/bin/perl
open FILE, "<", "files.txt" or die "Error opening file: $!";
my ($total, $cnt);
while(<FILE>){
chomp;
my ($date, $time, $am_pm, $numbers, $type) = split(/\s+/, $_);
$total += $numbers;
$cnt++;
}
close FILE;
print"the total is $total and count of $cnt\n";`
My test file has "n" number of lines and between each line there is a ^M, which in turn makes it one big string. The code I am working with opens said file and should parse out a header and then the subsequent rows, then searches for the Directory Path and File name. But because the file just ends up as a big string it doesn't work correctly
#!/usr/bin/perl
#use strict;
#use warnings;
open (DATA, "<file.txt") or die ("Unable to open file");
my $search_string = "Directory Path";
my $column_search = "Filename";
my $header = <DATA>;
my #header_titles = split /\t/, $header;
my $extract_col = 0;
my $col_search = 0;
for my $header_line (#header_titles) {
last if $header_line =~ m/$search_string/;
$extract_col++;
}
for my $header_line (#header_titles) {
last if $header_line =~m/$column_search/;
$col_search++;
}
print "Extracting column $extract_col $search_string\n";
while ( my $row = <DATA> ) {
last unless $row =~ /\S/;
chomp $row;
my #cells = split /\t/, $row;
$cells[74]=~s/:/\//g;
$cells[$extract_col]= $cells[74] . $cells[$col_search];
print "$cells[$extract_col] \n";
}
When i open the test file in VI i have used
:%s/^M/\r/g
and that removes the ^M's but how do i do it inside this perl program? When i tried a test program and inserted that s\^M/\r/g and had it write to a different file it came up as a lot of Chinese characters.
If mac2unix isn't working for you, you can write your own mac2unix as a Perl one-liner:
perl -pi -e 'tr/\r/\n/' file.txt
That will likely fail if the size of the file is larger than virtual memory though, as it reads the whole file into memory.
For completeness, let's also have a dos2unix:
perl -pi -e 'tr/\r//d' file.txt
and a unix2dos:
perl -pi -e 's/\n/\r\n/g' file.txt
Before you start reading the file, set $/ to "\r". This is set to the linefeed character by default, which is fine for UNIX-style line endings, and almost OK for DOS-style line endings, but useless for the old Mac-style line endings you are seeing. You can also try mac2unix on your input file if you have it installed.
For more, look for "INPUT_RECORD_SEPARATOR" in the perlvar manpage.
Did this file originate on a windows system? If so, try running the dos2unix command on the file before reading it. You can do this before invoking the perl script or inside the script before you read it.
You might want to set $\ (input record separator) to ^M in the beginning of your script, such as:
$\ = "^M";
perl -MExtUtils::Command -e dos2unix file
I have a directory full of files containing records like:
FAKE ORGANIZATION
799 S FAKE AVE
Northern Blempglorff, RI 99xxx
01/26/2011
These items are being held for you at the location shown below each one.
IF YOU ASKED THAT MATERIAL BE MAILED TO YOU, PLEASE DISREGARD THIS NOTICE.
The Waltons. The complete DAXXXX12118198
Pickup at:CHUPACABRA LOCATION 02/02/2011
GRIMLY, WILFORD
29 FAKE LANE
S. BLEMPGLORFF RI 99XXX
I need to remove all entries with the expression Pickup at:CHUPACABRA LOCATION.
The "record separator" issue:
I can't touch the input file's formatting -- it must be retained as is. Each record
is separated by roughly 40+ new lines.
Here's some awk ( this works ):
BEGIN {
RS="\n\n\n\n\n\n\n\n\n+"
FS="\n"
}
!/CHUPACABRA/{print $0}
My stab with perl:
perl -a -F\n -ne '$/ = "\n\n\n\n\n\n\n\n\n+";$\ = "\n";chomp;$regex="CHUPACABRA";print $_ if $_ !~ m/$regex/i;' data/lib51.000
Nothing is returned. I'm not sure how to specify 'field separator' in perl except at the commandline. Tried the a2p utility -- no dice. For the curious, here's what it produces:
eval '$'.$1.'$2;' while $ARGV[0] =~ /^([A-Za-z
# process any FOO=bar switches
#$FS = ' '; # set field separator
$, = ' '; # set output field separator
$\ = "\n"; # set output record separator
$/ = "\n\n\n\n\n\n\n\n\n+";
$FS = "\n";
while (<>) {
chomp; # strip record separator
if (!/CHUPACABRA/) {
print $_;
}
}
This has to run under someone's Windows box otherwise I'd stick with awk.
Thanks!
Bubnoff
EDIT ( SOLVED ) **
Thanks mob!
Here's a ( working ) perl script version ( adjusted a2p output ):
eval '$'.$1.'$2;' while $ARGV[0] =~ /^([A-Za-z
# process any FOO=bar switches
#$FS = ' '; # set field separator
$, = ' '; # set output field separator
$\ = "\n"; # set output record separator
$/ = "\n"x10;
$FS = "\n";
while (<>) {
chomp; # strip record separator
if (!/CHUPACABRA/) {
print $_;
}
}
Feel free to post improvements or CPAN goodies that make this more idiomatic and/or perl-ish. Thanks!
In Perl, the record separator is a literal string, not a regular expression. As the perlvar doc famously says:
Remember: the value of $/ is a string, not a regex. awk has to be better for something. :-)
Still, it looks like you can get away with $/="\n" x 10 or something like that:
perl -a -F\n -ne '$/="\n"x10;$\="\n";chomp;$regex="CHUPACABRA";
print if /\S/ && !m/$regex/i;' data/lib51.000
Note the extra /\S/ &&, which will skip empty paragraphs from input that has more than 20 consecutive newlines.
Also, have you considered just installing Cygwin and having awk available on your Windows machine?
There is no need for (much)conversion if you can download gawk for windows
Did you know that Perl comes with a program called a2p that does exactly what you described you want to do in your title?
And, if you have Perl on your machine, the documentation for this program is already there:
C> perldoc a2p
My own suggestion is to get the Llama book and learn Perl anyway. Despite what the Python people say, Perl is a great and flexible language. If you know shell, awk and grep, you'll understand many of the Perl constructs without any problems.