I have ..tpl file with this line:
{$error|replace:"pno":"personal number error"}
I need to modify it so multiple values will be replaced, sort of:
{$error|replace:"pno_error":"personal number error", "error_1":"1", "error_2":"2"}
I need to make sure the code is correctly formed. How do I achieve this?
Like so
{assign "find" array('pno', 'error_1', 'error_2')}
{assign "repl" array('personal number error', 1, 2)}
{assign "text" 'error_1 and pno and error_2 are friends'}
{$text|replace:$find:$repl}
btw: dont'cha rather do it through a controller and in tpl files use final values?
EDIT
how to make it to replace the exact match only, for example if the $text is 'pno', then replace it, but if the $text is 'pnopno', then do nothing?
In that case, you can use regular expressions, however, it is not possible in an array (as far as I know) and you need to do it step by step, or rather a command after command.
Regarding of replacing pno and not pnopno, you need to figure out your own regular expression to suit your needs.
{assign "text" 'error_1 and pno and error_2 are friends'}
{$text|regex_replace:"/(\s)(pno)(\s)/":"personal number error"|regex_replace:"/(error_1)/":"1"|regex_replace:"/(error_2)/":"2"}
You can also use the short code:
{$text = "error_1 and pno and error_2 are friends"}
{$find = ['pno', 'error_1', 'error_2']}
{$repl = ['personal number error', 1, 2]}
{$text|replace:$find:$repl}
Related
I have a timestamp 2015-11-01 21:45:25,296 like I mentioned above. is it possible to extract the the day of the week(Mon, Tue,etc) using any regular expression or grok pattern.
Thanks in advance
this is quite easy if you want to use the ruby filter. I am lazy so I am only doing this.
Here is my filter:
filter {
ruby {
code => "
p = Time.parse(event['message']);
event['day-of-week'] = p.strftime('%A');
"
}
}
The 'message' variable is the field that contains your timestamp
With stdin and stdout and your string, you get:
artur#pandaadb:~/dev/logstash$ ./logstash-2.3.2/bin/logstash -f conf2/
Settings: Default pipeline workers: 8
Pipeline main started
2015-11-01 21:45:25,296
{
"message" => "2015-11-01 21:45:25,296",
"#version" => "1",
"#timestamp" => "2016-08-03T13:07:31.377Z",
"host" => "pandaadb",
"day-of-week" => "Sunday"
}
Hope that is what you need,
Artur
What you want is:
Assuming your string is 2015-11-01 21:45:25,296
mydate='2015-11-01'
date +%a -d ${mydate% *}
Will give you what you want.
Short answer is not, you can't.
A regex, according to Wikipedia:
...is a sequence of characters that define a search pattern, mainly for use in pattern matching with strings, or string matching, i.e. "find and replace"-like operations.
So, a regex allow you to parse a String, it searches for information within the String, but it doesn't make calculations over it.
If you want to make such calculations you need help from a programming language (java, c#, or Ruby[like #pandaadb suggested] etc) or some other tool that makes those calculations (Epoch Converter).
I have a variable $yearMonth := "2015-02"
I have to search this date on an element Date as xs:dateTime.
I want to use regex expression to find all files/documents having this date "2015-02-??"
I have path-range-index enabled on ModifiedInfo/Date
I am using following code but getting Invalid cast error
let $result := cts:value-match(cts:path-reference("ModifiedInfo/Date"), xs:dateTime("2015-02-??T??:??:??.????"))
I have also used following code and getting same error
let $result := cts:value-match(cts:path-reference("ModifiedInfo/Date"), xs:dateTime(xs:date("2015-02-??"),xs:time("??:??:??.????")))
Kindly help :)
It seems you are trying to use wild card search on Path Range index which has data type xs:dateTime().
But, currently MarkLogic don't support this functionality. There are multiple ways to handle this scenario:
You may create Field index.
You may change it to string index which supports wildcard search.
You may run this workaround to support your existing system:
for $x in cts:values(cts:path-reference("ModifiedInfo/Date"))
return if(starts-with(xs:string($x), '2015-02')) then $x else ()
This query will fetch out values from lexicon and then you may filter your desired date.
You can solve this by combining a couple cts:element-range-querys inside of an and-query:
let $target := "2015-02"
let $low := xs:date($target || "-01")
let $high := $low + xs:yearMonthDuration("P1M")
return
cts:search(
fn:doc(),
cts:and-query((
cts:element-range-query("country", ">=", $low),
cts:element-range-query("country", "<", $high)
))
)
From the cts:element-range-query documentation:
If you want to constrain on a range of values, you can combine multiple cts:element-range-query constructors together with cts:and-query or any of the other composable cts:query constructors, as in the last part of the example below.
You could also consider doing a cts:values with a cts:query param that searches for values between for instance 2015-02-01 and 2015-03-01. Mind though, if multiple dates occur within one document, you will need to post filter manually after all (like in option 3 of Navin), but it could potentially speed up post-filtering a lot..
HTH!
I would like to retrieve the coding amino-acid when there is certain pattern in a DNA sequence. For example, the pattern could be: ATAGTA. So, when having:
Input file:
>sequence1
ATGGCGCATAGTAATGC
>sequence2
ATGATAGTAATGCGCGC
The ideal output would be a table having for each amino-acid the number of times is coded by the pattern. Here in sequence1, pattern codes only for one amino-acid, but in sequence2 it codes for two. I would like to have this tool working to scale to thousands of sequences. I've been thinking about how to get this done, but I only thought to: replace all nucleotides different than the pattern, translate what remains and get summary of the coded amino-acids.
Please let me know if this task can be performed by an already available tool.
Thanks for your help. All the best, Bernardo
Edit (due to the confusion generated with my post):
Please forget the original post and sequence1 and sequence2 too.
Hi all, and sorry for the confusion. The input fasta file is a *.ffn file derived from a GenBank file using 'FeatureExtract' tool (http://www.cbs.dtu.dk/services/FeatureExtract/download.php), so a can imagine they are already in frame (+1) and there is no need to get amino-acids coded in a frame different than +1.
I would like to know for which amino-acid the following sequences are coding for:
AGAGAG
GAGAGA
CTCTCT
TCTCTC
The unique strings I want to get coding amino-acids are repeats of three AG, GA, CT or TC, that is (AG)3, (GA)3, (CT)3 and (TC)3, respectively. I don't want the program to retrieve coding amino-acids for repeats of four or more.
Thanks again, Bernardo
Here's some code that should at least get you started. For example, you can run like:
./retrieve_coding_aa.pl file.fa ATAGTA
Contents of retrieve_coding_aa.pl:
#!/usr/bin/perl
use strict;
use warnings;
use File::Basename;
use Bio::SeqIO;
use Bio::Tools::CodonTable;
use Data::Dumper;
my $pattern = $ARGV[1];
my $fasta = Bio::SeqIO->new ( -file => $ARGV[0], -format => 'fasta');
while (my $seq = $fasta->next_seq ) {
my $pos = 0;
my %counts;
for (split /($pattern)/ => $seq->seq) {
if ($_ eq $pattern) {
my $dist = $pos % 3;
unless ($dist == 0) {
my $num = 3 - $dist;
s/.{$num}//;
chop until length () % 3 == 0;
}
my $table = Bio::Tools::CodonTable->new();
$counts{$_}++ for split (//, $table->translate($_));
}
$pos += length;
}
print $seq->display_id() . ":\n";
map {
print "$_ => $counts{$_}\n"
}
sort {
$counts{$a} <=> $counts{$b}
}
keys %counts;
print "\n";
}
Here are the results using the sample input:
sequence1:
S => 1
sequence2:
V => 1
I => 1
The Bio::Tools::CodonTable class also supports non-standard codon usage tables. You can change the table using the id pointer. For example:
$table = Bio::Tools::CodonTable->new( -id => 5 );
or:
$table->id(5);
For more information, including how to examine these tables, please see the documentation here: http://metacpan.org/pod/Bio::Tools::CodonTable
I will stick to that first version of what you wanted cause the addendum only confused me even more. (frame?)
I only found ATAGTA once in sequence2 but I assume you want the mirror images/reverse sequence as well, which would be ATGATA in this case. Well my script doesn't do that so you would have to write it up twice in the input_sequences file but that should be no problem I would think.
I work with a file like yours which I call "dna.txt" and a input sequences file called "input_seq.txt". The result file is a listing of patterns and their occurences in the dna.txt file (including overlap-results but it can be set to non-overlap as explained in the awk).
input_seq.txt:
GC
ATA
ATAGTA
ATGATA
dna.txt:
>sequence1
ATGGCGCATAGTAATGC
>sequence2
ATGATAGTAATGCGCGC
results.txt:
GC,6
ATA,2
ATAGTA,2
ATGATA,1
Code is awk calling another awk (but one of them is simple). You have to run
"./match_patterns.awk input_seq.txt" to get the results file generated.:
*match_patterns.awk:*
#! /bin/awk -f
{return_value= system("awk -vsubval="$1" -f test.awk dna.txt")}
test.awk:
#! /bin/awk -f
{string=$0
do
{
where = match(string, subval)
# code is for overlapping matches (i.e ATA matches twice in ATATAC)
# for non-overlapping replace +1 by +RLENGTH in following line
if (RSTART!=0){count++; string=substr(string,RSTART+1)}
}
while (RSTART != 0)
}
END{print subval","count >> "results.txt"}
Files have to be all in the same directory.
Good luck!
For example we have a large database contains lots of oracle packages, and now we want to see where a specific table resists in the source code. The source code is stored in user_source table and our desired table is called 'company'.
Normally, I would like to use:
select * from user_source
where upper(text) like '%COMPANY%'
This will return all words containing 'company', like
121 company cmy
14 company_id, idx_name %% end of coding
453 ;companyname
1253 from db.company.company_id where
989 using company, idx, db_name,
So how to make this result more intelligent using regular expression to parse all the source lines matching a meaningful table name (means a table to the compiler)?
So normally we allow the matched word contains chars like . ; , '' "" but not _
Can anyone make this work?
To find company as a "whole word" with a regular expression:
SELECT * FROM user_source
WHERE REGEXP_LIKE(text, '(^|\s)company(\s|$)', 'i');
The third argument of i makes the REGEXP_LIKE search case-insensitive.
As far as ignoring the characters . ; , '' "", you can use REGEXP_REPLACE to suck them out of the string before doing the comparison:
SELECT * FROM user_source
WHERE REGEXP_LIKE(REGEXP_REPLACE(text, '[.;,''"]'), '(^|\s)company(\s|$)', 'i');
Addendum: The following query will also help locate table references. It won't give the source line, but it's a start:
SELECT *
FROM user_dependencies
WHERE referenced_name = 'COMPANY'
AND referenced_type = 'TABLE';
If you want to identify the objects that refer to your table, you can get that information from the data dictionary:
select *
from all_dependencies
where referenced_owner = 'DB'
and referenced_name = 'COMPANY'
and referenced_type = 'TABLE';
You can't get the individual line numbers from that, but you can then either look at user_source or use a regexp on the specific source code, which woudl at least reduce false positives.
SELECT * FROM user_source
WHERE REGEXP_LIKE(text,'([^_a-z0-9])company([^_a-z0-9])','i')
Thanks #Ed Gibbs, with a little trick this modified answer could be more intelligent.
I am attempting to write a script that collects user input using getopts. I need to be able to limit restrict the values the user can enter. I see how to set a default value but, I have been unable to find any way to set a list of allowed values... so,
I am attempting to use Config::Simple to create an array from values stored in a text file to use to validate against.
contents of values.txt
ChangeCategories resolution, storm
contents of main.pl
#---create array from values.txt ChangeCategories
my #chg_cats = $cfg->param("ChangeCategories");
unlink $_ for #chg_cats;
#----grab user input via getopts
my $change_categories = $opt_c || die "Please enter a valid change category; #chg_cats";
The issue occurs when I attempt to do the pattern match, it is matching only the first value listed on the ChangeCategories line in the values.txt file.
#---pattern mathching code
my $valid_category;
chomp(#chg_cats);
foreach (#chg_cats) {
##foreach my $line (#chg_cats) {
if(($_ =~ $change_categories) )
#if(($_ =~ m/$change_categories/) )
#if(($_ eq $change_categories) )
As you can see, I have tried numerous constructs to correct this and verify that I get correct matching results every time. I am not sure if this is somehow related to 'chomping' but, I have tried every pattern I can think of. I am a beginner to Perl and would very much appreciate any and all help.... and if anyone can tell me an easier/cleaner way to achieve this result, I would be very grateful