How can I count the number of times a pattern appears - perl

I am trying to count the number of occurrences that a particular string appears in a text document so that the string can be deleted if it occurs less than 5 times. The text file has a list of dates that are formatted as 2015-06-16 07:40:00.
After processing the incoming data from 2015-06-16 07:40:00 to 2015061607, I want to count the number of times that this string appears. I have the processing of the incoming data correct but I don't know how to count the occurrences of the string.
This is what I have so far.
#!/usr/bin/perl
foreach $file (#ARGV) {
open (OUT, ">/d2/aschwa/scripts_and_programs/NST_Scripts/data_organizers/Filtered_$file") || die "Cannot open specified file\n";
open (RAW, "/d2/aschwa/scripts_and_programs/NST_Scripts/data_organizers/$file") || die "Cannot open specified file to be processed\n";
while(<RAW>) {
$event = $_;
chop($event);
#event = split (',', $event);
($date_time, $var1, $var2, $var3) = #event[(0,1,2,3)];
#date_time = split (' ', $date_time);
($date, $time) = #date_time[(0,1)];
#date_mod = split ('-', $date);
($year, $month, $day) = #date_mod[(0,1,2)];
#time = split (':', $time);
($hr, $mins, $sec) = #time[(0,1,2)];
$datehr = $year . $month . $day . $hr;
foreach ($event) {
$count{$datehr}++;
}
}
}

I think you should use a regular expression rather than repeated calls to split
This example reads through each file twice, counting the dates on the first pass and printing those lines whose dates appear more than five times on the second
It doesn't compress the date-time as you have done, but captures just up to the hour field, so the keys of the %count hash look like 2015-06-16 07. It is only extra code to remove the punctuation and isn't necessary to make the program work
I've also used autodie, which has been available since v5.10 of Perl and automatically checks the status of open and chdir calls for you. It is also best practice to use lexical file handles and the three-parameter form of open
#!/usr/bin/perl
use strict;
use warnings;
use 5.010;
use autodie;
use constant DIR => '/d2/aschwa/scripts_and_programs/NST_Scripts/data_organizers';
chdir DIR;
for my $file ( #ARGV ) {
open my $raw_fh, '<', $file;
my %count;
while ( <$raw_fh> ) {
++$count{$1} if /^(\d\d\d\d-\d\d-\d\d \d\d):\d\d:\d\d/;
}
seek $raw_fh, 0, 0; # Rewind input file
open my $out_fh, '>', "Filtered_$file";
while ( <$raw_fh> ) {
print unless /^(\d\d\d\d-\d\d-\d\d \d\d):\d\d:\d\d/ and $count{$1} < 5;
}
}

Related

Split my output into multiple files

I have the following list in a CSV file, and my goal is to split this list into directories named YYYY-Month based on the date in each row.
NAME99;2018/06/13;12:27:30
NAME01;2018/06/13;13:03:59
NAME00;2018/06/15;11:33:01
NAME98;2018/06/15;12:22:00
NAME34;2018/06/15;16:58:45
NAME17;2018/06/18;15:51:10
NAME72;2018/06/19;10:06:37
NAME70;2018/06/19;12:44:03
NAME77;2018/06/19;16:36:55
NAME25;2018/06/11;16:32:57
NAME24;2018/06/11;16:32:57
NAME23;2018/06/11;16:37:15
NAME01;2018/06/11;16:37:15
NAME02;2018/06/11;16:37:15
NAME01;2018/06/11;16:37:18
NAME02;2018/06/05;09:51:17
NAME00;2018/06/13;15:04:29
NAME07;2018/06/19;10:02:26
NAME08;2018/06/26;16:03:57
NAME09;2018/06/26;16:03:57
NAME02;2018/06/27;16:58:12
NAME03;2018/07/03;07:47:21
NAME21;2018/07/03;10:53:00
NAMEXX;2018/07/05;03:13:01
NAME21;2018/07/05;15:39:00
NAME01;2018/07/05;16:00:14
NAME00;2018/07/08;11:50:10
NAME07;2018/07/09;14:46:00
What is the smartest method to achieve this result without having to create a list of static routes, in which to carry out the append?
Currently my program writes this list to a directory called YYYY-Month only on the basis of localtime but does not do anything on each line.
Perl
#!/usr/bin/perl
use strict;
use warnings 'all';
use feature qw(say);
use File::Path qw<mkpath>;
use File::Spec;
use File::Copy;
use POSIX qw<strftime>;
my $OUTPUT_FILE = 'output.csv';
my $OUTFILE = 'splitted_output.csv';
# Output to file
open( GL_INPUT, $OUTPUT_FILE ) or die $!;
$/ = "\n\n"; # input record separator
while ( <GL_INPUT> ) {
chomp;
my #lines = split /\n/;
my $i = 0;
foreach my $lines ( #lines ) {
# Encapsulate Date/Time
my ( $name, $y, $m, $d, $time ) =
$lines[$i] =~ /\A(\w+);(\d+)\/(\d+)\/(\d+);(\d+:\d+:\d+)/;
# Generate Directory YYYY-Month - #2009-January
my $dir = File::Spec->catfile( $BASE_LOG_DIRECTORY, "$y-$m" ) ;
unless ( -e $dir ) {
mkpath $dir;
}
my $log_file_path = File::Spec->catfile( $dir, $OUTFILE );
open( OUTPUT, '>>', $log_file_path ) or die $!;
# Here I append value into files
print OUTPUT join ';', "$y/$m/$d", $time, "$name\n";
$i++;
}
}
close( GL_INPUT );
close( OUTPUT );
There is no reason to care about the actual date, or to use date functions at all here. You want to split up your data based on a partial value of one of the columns in the data. That just happens to be the date.
NAME08;2018/06/26;16:03:57 # This goes to 2018-06/
NAME09;2018/06/26;16:03:57 #
NAME02;2018/06/27;16:58:12 #
NAME03;2018/07/03;07:47:21 # This goes to 2018-07/
NAME21;2018/07/03;10:53:00 #
NAMEXX;2018/07/05;03:13:01 #
NAME21;2018/07/05;15:39:00 #
The easiest way to do this is to iterate your input data, then stick it into a hash with keys for each year-month combination. But you're talking about log files, and they might be large, so that's inefficient.
We should work with different file handles instead.
use strict;
use warnings;
my %months = ( 6 => 'June', 7 => 'July' );
my %handles;
while (my $row = <DATA>) {
# no chomp, we don't actually care about reading the whole row
my (undef, $dir) = split /;/, $row; # discard name and everything after date
# create the YYYY-MM key
$dir =~ s[^(....)/(..)][$1-$months{$2}];
# open a new handle for this year/month if we don't have it yet
unless (exists $handles{$dir}) {
# create the directory (skipped here) ...
open my $fh, '>', "$dir/filename.csv" or die $!;
$handles{$dir} = $fh;
}
# write out the line to the correct directory
print { $handles{$dir} } $row;
}
__DATA__
NAME08;2018/06/26;16:03:57
NAME09;2018/06/26;16:03:57
NAME02;2018/06/27;16:58:12
NAME03;2018/07/03;07:47:21
NAME21;2018/07/03;10:53:00
NAMEXX;2018/07/05;03:13:01
NAME21;2018/07/05;15:39:00
I've skipped the part about creating the directory as you already know how to do this.
This code will also work if your rows of data are not sequential. It's not the most efficient as the number of handles will grow the more data you have, but as long you don't have 100s of them at the same time that does not really matter.
Things of note:
You don't need chomp because you don't care about working with the last field.
You don't need to assign all of the values after split because you don't care about them.
You can discard values by assigning them to undef.
Always use three-argument open and lexical file handles.
the {} in print { ... } $roware needed to tell Perl that this is the handle we are printing too. See http://perldoc.perl.org/functions/print.html.

How to print lines from log file which occurs after some particular time

I want to print all the lines which lets say occur after a time whose value is returned by localtime function of perl inside a perl script. I tried something like below:
my $timestamp = localtime();
open(CMD,'-|','cat xyz.log | grep -A1000 \$timestamp' || die ('Could not open');
while (defined(my $line=<CMD>)){
print $line;
}
If I replace the $timestamp in cat command with actaul time component from xyz.log then it print lines but its not printing with $timestamp variable.
Is there any alternative way I can print lines that occurs after current time in log files or how i can improve above command?
Your $timestamp is never evaluated in Perl as it appears only in single quotes. But why go out to shell in order to match a string and process a file? Perl is far better for that.
Here is a direct way first, then a basic approach. A full script is shown in the second example.
Read the file until you get to the line with the pattern, and exit the loop at that point. The next time you access that filehandle you'll be on the next line and can start printing, in another loop.
while (<$fh>) { last if /$timestamp/ }
print while <$fh>;
This prints out the part of the file starting with the line following the one which has the $timestamp anywhere in it. Adjust how exactly to match the timestamp if it is more specific.
Or -- set a flag when a line matches the timestamp, print if flag is set.
use warnings 'all';
use strict;
my $timestamp = localtime();
my $logile = 'xyz.log';
open my $fh, '<', $logfile or die "Can't open $logfile: $!";
my $mark = 0;
while (<$fh>)
{
if (not $mark) {
$mark = 1 if /$timestamp/;
}
else { print }
}
close $fh;
If you're doing the grepping in Shell anyway you might as well do it the other way round and call perl only to give you the result of localtime:
sed <xyz.log -ne"/^$(perl -E'say scalar localtime')/,\$p"
This uses sed's range addressing: first keep it from printing lines unless explicitly told so using -n, the select everything between the first occurrence of the timestamp (I added a ^ for good measure, just in case log lines could contain time stamps in plain text) and the end of file ($) and print it (p).
A pure Perl solution could look like this:
my $timestamp = localtime();
my $found;
open(my $fh, '<', 'xyz.log') or die ('Could not open xyz.log: $!');
while (<$fh>) {
if($found) {
print;
} else {
$found = 1 if /^$timestamp/;
}
}
I would suggest a Perlish approach like below:
open (my $cmd, "<", "xyz.log") or die $!;
#get all lines in an array with each index containing each line
my #log_lines = <$cmd>;
my $index = 0;
foreach my $line (#log_lines){
#write regex to capture time from line
my $rex = qr/regex_for_time_as_per_logline/is;
if ($line =~ /$rex/){
#found the line with expected time
last;
}
$index++;
}
#At this point we have got the index of array from where our expected time starts.
#So all indexes after that have desired lines, which you can write as below
foreach ($index..$#log_lines){
print $log_lines[$_];
}
If you share one of your logline, I could help with the regex.
You may also try this approach:
In this case, I tried to open /var/log/messages then convert each line timestamp to epoch and finding all the lines which has occurred after time()
use Date::Parse;
my $epoch_now = time(); # print epoch current time.
open (my $fh, "</var/log/messages") || die "error: $!\n";
while (<$fh>) {
chomp;
# one log line - looks like this
# Sep 9 08:17:01 localhost rsyslogd: rsyslogd was HUPed
my ($mon, $day, $hour, $min, $sec) = ($_ =~ /(\S+)\s*(\d+)\s*(\d+):(\d+):(\d+)/);
# date string part shouldn't be empty
if (defined($mon) && defined($day)
&& defined($hour) && defined($min)
&& defined($sec)) {
my $epoch_log = str2time("$mon $day $hour:$min:$sec");
if ($epoch_log > $epoch_now) {
print, "\n";
}
}
}

Parsing file based on column ID: perl

I have a tab delineated file with repeated values in the first column. The single, but repeated values in the first column correspond to multiple values in the second column. It looks something like this:
AAAAAAAAAA1 m081216|101|123
AAAAAAAAAA1 m081216|100|1987
AAAAAAAAAA1 m081216|927|463729
BBBBBBBBBB2 m081216|254|260489
BBBBBBBBBB2 m081216|475|1234
BBBBBBBBBB2 m081216|987|240
CCCCCCCCCC3 m081216|433|1000
CCCCCCCCCC3 m081216|902|366
CCCCCCCCCC3 m081216|724|193
For every type of sequence in the first column, I am trying to print to a file with just the sequences that correspond to it. The name of the file should include the repeated sequence in the first column and the number of sequences that correspond to it in the second column. In the above example I would therefore have 3 files of 3 sequences each. The first file would be named something like "AAAAAAAAAA1.3.txt" and look like the following when opened:
m081216|101|123
m081216|100|1987
m081216|927|463729
I have seen other similar questions, but they have been answered with using a hash. I don't think I can't use a hash because I need to keep the number of relationships between columns. Maybe there is a way to use a hash of hashes? I am not sure.
Here is my code so far.
use warnings;
use strict;
use List::MoreUtils 'true';
open(IN, "<", "/path/to/in_file") or die $!;
my #array;
my $queryID;
while(<IN>){
chomp;
my $OutputLine = $_;
processOutputLine($OutputLine);
}
sub processOutputLine {
my ($OutputLine) = #_;
my #Columns = split("\t", $OutputLine);
my ($queryID, $target) = #Columns;
push(#array, $target, "\n") unless grep{$queryID eq $_} #array;
my $delineator = "\n";
my $count = true { /$delineator/g } #array;
open(OUT, ">", "/path/to/out_$..$queryID.$count.txt") or die $!;
foreach(#array){
print OUT #array;
}
}
I would still recommend a hash. However, you store all sequences related to the same id in an anonymous array which is the value for that ID key. It's really two lines of code.
use warnings;
use strict;
use feature qw(say);
my $filename = 'rep_seqs.txt'; # input file name
open my $in_fh, '<', $filename or die "Can't open $filename: $!";
my %seqs;
foreach my $line (<$in_fh>) {
chomp $line;
my ($id, $seq) = split /\t/, $line;
push #{$seqs{$id}}, $seq;
}
close $in_fh;
my $out_fh;
for (sort keys %seqs) {
my $outfile = $_ . '_' . scalar #{$seqs{$_}} . '.txt';
open $out_fh, '>', $outfile or do {
warn "Can't open $outfile: $!";
next;
};
say $out_fh $_ for #{$seqs{$_}};
}
close $out_fh;
With your input I get the desired files, named AA..._count.txt, with their corresponding three lines each. If items separated by | should be split you can do that while writing it out, for example.
Comments
The anonymous array for a key $seqs{$id} is created once we push, if not there already
If there are issues with tabs (converted to spaces?), use ' '. See the comment.
A filehandle is closed and re-opened on every open, so no need to close every time
The default pattern for split is ' ', also triggering specific behavior -- it matches "any contiguous whitespace", and also omits leading whitespace. (The pattern / / matches a single space, turning off this special behavior of ' '.) See a more precise description on the split page. Thus it is advisable to use ' ' when splitting on unspecified number of spaces, since in the case of split this is a bit idiomatic, is perhaps the most common use, and is its default. Thanks to Borodin for prompting this comment and update (the original post had the equivalent /\s+/).
Note that in this case, since ' ' is the default along with $_, we can shorten it a little
for (<$in_fh>) {
chomp;
my ($id, $seq) = split;
push #{$seqs{$id}}, $seq;
}

Modifying CSV file and Preserving Order

The question that follows is a made up simplified example of a more complex problem that I'm trying to solve. I would like to preserve the structure of the code, especially the use of the %hash to store the outcomes for each patient but I do not need to read the data file into memory (but I cannot find a way of reading my csv data file line by line from the end.)
My sample data is made up of events that occur to patients. A patient can be added to the study (Event=B) or he can die (Event=D) or exit the study(Event=F.) Death and Exit are the only two possible outcomes for each patient.
For each event I have the date of occurrence (in hours from given point in time), the unique ID number of each patient, the event and the Outcome (a field set to 0 for every patient.)
I'm trying to write a code that will change the input file by putting next to each addition of a new patient, what is his eventual outcome (death or exit.)
In order to do so, I read the file from the end, and whenever I encounter a death or exit of a patient, I populate a hash that matches patient ID with outcome. When I encounter an event telling me that a new patient has been added to the study, I then match his ID with those in the hash and change the value of "Outcome" from 0 to either D or F.
I have been able to write a code that reads the file from bottom and then creates a new modified file with the updated value for Outcome. The problem is that since I read the input file from bottom to top and print each line after reading it, the output file is in reversed order and I do not know how to change this. Also, ideally I don't want to create a new file bu I would like to simply modify the input one. However, I have failed with every attempt to do so.
Sample data:
Data,PatientNumber,Event,Outcome
25201027,562962838335407,B,0
25201028,562962838335408,B,0
25201100,562962838335407,D,0
25201128,562962838335408,F,0
My code:
#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;
open (my $fh_input, "<", "mini_test2.csv")
or die "cannot open > mini_test2.csv: $!";
my #lines = <$fh_input>;
close $fh_input;
open (my $fh_output, ">>", "Revised_mini_test2.csv")
or die "cannot open > Revised_mini_test2.csv: $!";
my $length = scalar(#lines);
my %outcome;
my #input_variables;
for (my $i = 1; $i < #lines; $i++){
chomp($lines[$length-$i]);
#input_variables=split(/,/, $lines[$length - $i]);
if ($input_variables[2] eq "D" || $input_variables[2] eq "F"){
$outcome{$input_variables[1]} = $input_variables[2];
my $line = join(",", #input_variables);
print $fh_output $line . "\n";
}
elsif($input_variables[2] eq "B") {
$input_variables[3]=$outcome{$input_variables[1]};
my $line = join(",", #input_variables);
print $fh_output $line . "\n";
}
else{
# necessary since the actual data has many more possible "Events"
my $line = join(",", #input_variables);
print $fh_output $line . "\n";
}
}
close $fh_output;
EDIT: desired output should be
Data,PatientNumber,Event,Outcome
25201027,562962838335407,B,D
25201028,562962838335408,B,F
25201100,562962838335407,D,0
25201128,562962838335408,F,0
Also, an additional complication is that the unique patient ID after the exit of a patient gets re-used. This means that I cannot do a 1st pass and store the outcome for each patient and a 2nd one to update the values of Outcome.
EDIT 2: let me clarify that when I say that each patient has a "unique ID" I mean that there cannot be in the study, at the same time, two patients with the same ID. However, if a patient exits the study, his ID gets re-used.
Update
I have just read your additional information that patient numbers are re-used once they exit the study. Why you would design a system like that I don't know, but there it is
It becomes far harder to write something straightforward without reading the file into an array, so that's what I have done here
use strict;
use warnings;
use 5.010;
use autodie;
open my $fh, '<', 'mini_test2.csv';
my #data;
while ( <$fh> ) {
chomp;
push #data, [ split /,/ ];
}
my %outcome;
for ( my $i = $#data; $i > 0; --$i ) {
my ($patient_number, $event) = #{$data[$i]}[1,2];
if ( $event =~ /[DF]/ ) {
$outcome{$patient_number} = $event;
}
elsif ( $event =~ /[B]/ ) {
$data[$i][3] = delete $outcome{$patient_number} // 0;
}
}
print join(',', #$_), "\n" for #data;
output
Data,PatientNumber,Event,Outcome
25201027,562962838335407,B,D
25201028,562962838335408,B,F
25201100,562962838335407,D,0
25201128,562962838335408,F,0
There are a few ways to approach this. I have chosen to take two passes through the file, first accumulating the outcome for each patient in a hash, and then replacing all the outcome fields in the B records
use strict;
use warnings;
use 5.010;
use autodie;
use Fcntl ':seek';
my %outcome;
open my $fh, '<', 'mini_test2.csv';
<$fh>; # Drop header
while ( <$fh> ) {
chomp;
my #fields = split /,/;
my ($patient_number, $event) = #fields[1,2];
if ( $event =~ /[DF]/ ) {
$outcome{$patient_number} = $event;
}
}
seek $fh, 0, SEEK_SET; # Rewind
print scalar <$fh>; # Copy header
while ( <$fh> ) {
chomp;
my #fields = split /,/;
my ($patient_number, $event) = #fields[1,2];
if ( $event !~ /[DF]/ ) {
$fields[3] = $outcome{$patient_number} // 0;
}
print join(',', #fields), "\n";
}
output
Data,PatientNumber,Event,Outcome
25201027,562962838335407,B,D
25201028,562962838335408,B,F
25201100,562962838335407,D,0
25201128,562962838335408,F,0
What we can do is instead of printing out the line at each stage, we'll write it back to the array of lines. Then we can just print them out at the end.
for (my $i=$#lines; i>=0; i--)
{
chomp $lines[$i];
#input_variables = split /,/, $lines[$i];
if ($input_variables[2] eq "D" || $input_variables[2] eq "F")
{
$outcome{$input_variables[1]}=$input_variables[2];
}else
{
$input_variables[3]=$outcome{$input_variables[1]};
}
$line[$i] = join ",", #input_variables;
}
$, = "\n"; #Make list seperator for printing a newline.
print $fh_output #lines;
As for the second question of modifying the original file. It is possible to open a file for both reading and writing using modes "+<", "+>", or "+>>". Don't do this! It is error prone as you must replace data character by character.
The standard way to "modify" an existing file is to rename it, read from the renamed file, write to a new file with the original name, and delete the temp file.
my $file_name = "mini_test2.csv";
my $tmp_file_name = $file_name . ".tmp";
rename $file_name, $tmp_file_name;
open (my $fh_input, "<", $tmp_file_name)
or die "cannot open > $tmp_file_name: $!";
open (my $fh_output, ">>", $file_name)
or die "cannot open > $file_name: $!";
#Your code to process the data.
close $fh_input;
close $fh_output;
#delete the temp file
unlink $tmp_file_name;
But, in your case, you slurp all of the data into memory right away. Just open for writing that clobbers existing files
open (my $fh_output, ">", "mini_test2.csv")
or die "cannot open > mini_test2.csv: $!";

Perl merging columns in two text files

I am a beginner with Perl and I want to merge the content of two text files.
I have read some similar questions and answers on this forum, but I still cannot resolve my issues
The first file has the original ID and the recoded ID of each individual (in the first and fourth columns)
The second file has the recoded ID and some information on some of the individuals (in the first and second columns).
I want to create an output file with the original, recoded and information of these individuals.
This is the perl script I have created so far, which is not working.
If anyone could help it would be very much appreciated.
use warnings;
use strict;
use diagnostics;
use vars qw( #fields1 $recoded $original $IDF #fields2);
my %columns1;
open (FILE1, "<file1.txt") || die "$!\n Couldn't open file1.txt\n";
while ($_ = <FILE1>)
{
chomp;
#fields1=split /\s+/, $_;
my $recoded = $fields1[0];
my $original = $fields1[3];
my %columns1 = (
$recoded => $original
);
};
open (FILE2, "<file2.txt") || die "$!\n Couldnt open file2.txt \n";
for ($_ = <FILE2>)
{
chomp;
#fields2=split /\s+/, $_;
my $IDF= $fields2[0];
my $F=$fields2[1];
my %columns2 = (
$F => $IDF
);
};
close FILE1;
close FILE2;
open (FILE3, ">output.txt") ||die "output problem\n";
for (keys %columns1) {
if (exists ($columns2{$_}){
print FILE3 "$_ $columns1{$_}\n"
};
}
close FILE3;
One problem is with scoping. In your first loop, you have a my in front of $column1 which makes it local to the loop and will not be in scope when you next the loop. So the %columns1 (which is outside of the loop) does not have any values set (which is what I suspect you want to set). For the assignment, it would seem to be easier to have $columns1{$recorded} = $original; which assigns the value to the key for the hash.
In the second loop you need to declare %columns2 outside of the loop and possibly use the above assignment.
For the third loop, in the print you just need add $columns2{$_} in front part of the string to be printed to get the original ID to be printed before the recorded ID.
Scope:
The problem is with scope of the hash variables you have defined. The scope of the variable is limited to the loop inside which the variable has been defined.
In your code, since %columns1 and %columns2 are used outside the while loops. Hence, they should be defined outside the loops.
Compilation error : braces not closed properly
Also, in the "if exists" part, the open-and-closed braces symmetry is affected.
Here is your code with the required corrections made:
use warnings;
use strict;
use diagnostics;
use vars qw( #fields1 $recoded $original $IDF #fields2);
my (%columns1, %columns2);
open (FILE1, "<file1.txt") || die "$!\n Couldn't open CFC_recoded.txt\n";
while ($_ = <FILE1>)
{
chomp;
#fields1=split /\s+/, $_;
my $recoded = $fields1[0];
my $original = $fields1[3];
%columns1 = (
$recoded => $original
);
}
open (FILE2, "<file2.txt") || die "$!\n Couldnt open CFC_F.xlsx \n";
for ($_ = <FILE2>)
{
chomp;
#fields2=split /\s+/, $_;
my $IDF= $fields2[0];
my $F=$fields2[1];
%columns2 = (
$F => $IDF
);
}
close FILE1;
close FILE2;
open (FILE3, ">output.txt") ||die "output problem\n";
for (keys %columns1) {
print FILE3 "$_ $columns1{$_} \n" if exists $columns2{$_};
}
close FILE3;