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Hi
I am very new to perl and struggling with simple things...
I am trying to check if an input DNA sequence only contains nucleotides. And if it doesn't I want to print out the position in the sequence where an invalid character was entered.
This is as far as I have come:
#!/usr/bin/perl -w
$DNA = <STDIN>;
chomp ($DNA);
@DNA = split ("", $DNA);
$lengthseq = scalar @DNA;
print "The length of the sequence is:\n", $lengthseq, "\n";
@nucleotideDNA = "";
#check if each element in array is nucleotide
foreach $nucleotide (@DNA){
if ($nucleotide =~ /^[ATCG]+$/){
push @nucleotideDNA, $nucleotide;
}
else {
push @nonvalid, $nucleotide;
}
}
every now and then I stumble upon the question of how to match something that doesn't match something else.
I.e. some expression in the sense of [^...]* for a general given regex $match.
The best I got so far is:
my $does_not_match = qr{((?:.*?(?=$match))|(?:(?:.(?!$match))*))};
The first branch matches a substring up to the given regex $match if there is a match and the second branch matches the whole string if there is no match.
Both fail in the opposite case. (The second branch by missing the last character.)
Does anybody know something simpler?
Or do you see any issues with the given regex?
Here is a small example:
#!/usr/bin/perl
use Test2::V0;
sub do_not_match {
my $pat = shift;
return qr{(?:.*?(?=$pat))|(?:(?:.(?!$pat))*)};
}
my $re = do_not_match(qr{\b[aeiou][a-z]*ion\b});
is [/($re)/], ['stimulated '], 'matches prefix'
for 'stimulated emission of radiation';
is [/($re)/], ['electron transition'],'no match'
for 'electron transition';
is [/($re)/], [''], 'matches empty prefix'
for 'absorbtion of photons';
is [/($re)/], ['light '], 'matches not greedy'
for 'light amplification by stimulated emission of radiation';
is [/($re)\bimpact/], ['electron '], 'gives characters back'
for 'electron impact ionization';
done_testing;
I might put this into an extension module for Regexp::Common, but I'm not sure if this makes sense at all.
And what would a proper naming be? Maybe something like:
use Regexp::Common 'do_not_match';
my $re = $RE{do_not}{-match => 'something'}
So I'm still having major issues with inconsistent/intermittent data fetch failures from my company's Oracle DB. I've been digging, a lot, and I may have narrowed down the issue further based on some earlier suggestions from the Monastery... but I still don't have a solid solution. I think this is an Oracle DB datatype issue, where there is a mismatch between what the DB has and DBD::Oracle is expecting, but being a newbie I'm not sure that's correct. Here is the relevant portion of the script I'm currently trying and using tracing options on to try and debug further.
use strict;
use warnings;
use DBI;
use DBD::Oracle qw(:ora_types);
print "Establishing DWASAS connection...\n";
# establish database connection and enable tracing option with dump to
+ 'tracelog.txt'.
my $dsn = 'dbi:Oracle:DWASAS';
my @connection = ($dsn, $user, $pass, {InactiveDestroy => 1, PrintErro
+r => 0, RaiseError => 1});
my $dbh = DBI->connect(@connection) or die;
open(my $tracelog_fh, '>', 'tracelog.txt') or die "Cannot open \"trace
+log.txt\": $!.";
$dbh->trace(4, $tracelog_fh);
# pepare and execute 'prepack_candidates.sql'
print "Preparing 'prepack_candidates.sql'...\n";
my $sth1 = $dbh->prepare($candidates_sql) or die;
print "Executing 'prepack_candidates.sql'...\n";
$sth1->execute() or die;
print "Fetching 'prepack_candidates.sql' returned data...\n";
print "\n----------\n";
my $print_format = '%7s '.
'%-50s '.
'%11s '.
'%12s'
;
printf("$print_format\n", 'ROW_NBR',
'REPORT_PART_NBR',
'SHIPPED_QYT',
'COUNT_AT_QTY'
);
my $row_counter = 1;
while(my $row = $sth1->fetchrow_hashref) {
foreach (keys(%$row)) {$row->{$_} = '' if (!defined($row->{$_}))};
+ # change all NULLs to empty strings
printf("$print_format\n", $row_counter,
$row->{'REPORT_PART_NBR'},
$row->{'SHIPPED_QTY'},
$row->{'COUNT_AT_QTY'}
);
$row_counter++;
}
print "----------\n";
And here is the basic SQL query it's running. And yes, it is successfully running, I can run this same query in 3 other tools: SQL Developer, Alation, and SAS (SAS modified for proc sql))
The failure happens during the $sth1->fetchrow_hashref loop. If I try various CASTs in the SQL it will tend to get hung up on different rows of data, but at this point rarely finishes successfully. But here's where things get interesting. The trace file, when it fails the fetch, just looks like this.
But, way back up at the top, when it's doing the prepare statement, the datatypes don't match what I would expect. When I look at them in the DB tables shown in Alation, Alation says one is a VARCHAR2(50) and the other is a NUMBER(10). I'm not sure what the COUNT I'm doing would become, but I was guessing NUMBER of some size as well.
Hello Friends,
I am new to perl program. Actually, I have an use case like, every hour we are running a script in Unix server to get some information from the server. So, every time we are sending a mail about that information. But, once the particular process has been completed, I don't want to send a mail for the day. This process will run on daily basis and every hour of the day. I am not sure, how can I do that. Anyone can guide me on this?
Thanks,
Arun Kumar Durairaj.
I get data correctly for the 17 fields with headers but then I see additional columns from R to AG with no data. Where is it picking the additional columns and how to prevent it?
I am messing around with libraries on macOS, and I am having the following problems: when you install a new module, their dependences, for example dylib, get installed in standard locations. The module then call the dynlib from there. I want to use at RUNTIME other locations where I want to put such dylib.
Let's say I want to use Image::PNG::QRCode; which requires "libpng". Let's say I put the "libpng16.16.dylib" library in a custom directory on my Desktop and I delete any other copy of this library from its standard location. I tried to add the path like following
use lib '/Users/xx/Desktop/lib/libpng16.16.dylib';
#or
use lib '/Users/xx/Desktop/lib';
I also tried to add the path to the env with in a begin block $ENV{'LD_LIBRARY_PATH'} = '/Users/xx/Desktop/lib'; with no success.
When I run my script, I get an error saying "Library not loaded: /usr/local/opt/libpng/lib/libpng16.16.dylib" which is the standard location (and I removed the dynlib!)
How can I force my script to look in another location for my libraries? I hope it makes sense.
