Re: REGEX help

Hello. Welcome.

I think you want to look at BioPerl.

This code is completely untested. I didn't want to install BioPerl on my system. But it might work if you can get BioPerl installed. (I know you're new to Perl, so installing BioPerl might be a stretch, but this might help: http://bioperl.org/INSTALL.html.)

#!/bin/perl
use strict;
use warnings;
use Bio::Seq;
use Data::Dumper::Simple;
use feature "say";

# Convert the sequence to lower case.  Upper Case might be ok,
# but the docs for Bio::Seq used lower case, so let's go with that.
my $letters = lc("TTCAGGTGTTTGCAACTGCGTTTTATTGCAAGAAAGAGTGGAGGGGTTTCCA
+TGGGGCCCACCTCACAACCCACTC TTCACCCCCAAAATCACGCAGGGATCGGACTCAGGAAAGGGAAG
+CATCTGTGTGTTGCATACGAGCCCTTCCTGTACTTACTTCTTTCACAGCAGGGAAGG AAGAGGGAAGA
+GGCAGCTGTGGAGAGGATCAGGTTGCGGGAGGTGGGTATCTCGCTGCTCTGACCTTACGTACAGTCCTC
+CACAGAAGCATCAAAGTGGACT GGCACATATCGGCTCCCTTCACAGGCCACAATCATCTGTCTCTCCT
+TCGGGCTGGTCCGGTATCCAC");

#Create a sequence object.
my $seq_object = Bio::Seq->new(-seq => $letters,
                         -alphabet => 'dna' );

#Look for the ORF.  I specified the start, but I didn't see how to 
#specify the stop.  Are the stop codons universal?  I'm way out of
#my league here.
$prot_object = $seq_object->translate( -orf => 1, -start => "atg" );

say Dumper $prot_object;
[download]

Cheers,

Brent

-- Yeah, I'm a Delt.

Comment on Re: REGEX help Download Code

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Re^2: REGEX help by karlgoethebier (Abbot) on Apr 21, 2018 at 16:21 UTC
One must be the volunteer. So i forced a `cpanm` install and only added a `my` you forgot. Unfortunately the script crashed the hard way: ------------- EXCEPTION ------------- MSG: Failed validation of sequence '[unidentified sequence]'. Invalid +characters were: STACK Bio::PrimarySeq::validate_seq /Users/karl/perl5/perlbrew/perls/p +erl-5.24.1threads/lib/site_perl/5.24.1/Bio/PrimarySeq.pm:338 STACK Bio::PrimarySeq::_set_seq_by_ref /Users/karl/perl5/perlbrew/perl +s/perl-5.24.1threads/lib/site_perl/5.24.1/Bio/PrimarySeq.pm:287 STACK Bio::PrimarySeq::seq /Users/karl/perl5/perlbrew/perls/perl-5.24. +1threads/lib/site_perl/5.24.1/Bio/PrimarySeq.pm:272 STACK Bio::PrimarySeq::new /Users/karl/perl5/perlbrew/perls/perl-5.24. +1threads/lib/site_perl/5.24.1/Bio/PrimarySeq.pm:229 STACK Bio::Seq::new /Users/karl/perl5/perlbrew/perls/perl-5.24.1thread +s/lib/site_perl/5.24.1/Bio/Seq.pm:496 STACK toplevel ./bio.pl:16 ------------------------------------- [download] Just for curiosity. Anyway - too bad. This stuff is PITA... Best regards, Karl ŤThe Crux of the Biscuit is the Apostropheť `perl -MCrypt::CBC -E 'say Crypt::CBC->new(-key=>'kgb',-cipher=>"Blowfish")->decrypt_hex($ENV{KARL});'`Help	[reply] [d/l] [select]
Re^3: REGEX help by poj (Abbot) on Apr 21, 2018 at 17:17 UTC
Take the spaces out of `$letters` and you should get `$prot_object = bless( { 'primary_seq' => bless( { 'length' => 63, '_root_verbose' => 0 +, '_nowarnonempty' => +undef, 'seq' => 'MGPTSQPTLH +PQNHAGIGLRKGKHLCVAYEPFLYLLLSQQGRKREEAAVERIRLREVGISLL*', 'alphabet' => 'prote +in' }, 'Bio::PrimarySeq' ) +, '_root_verbose' => 0 }, 'Bio::Seq' );` [download] whatever that means ! poj	[reply] [d/l] [select]
Re^4: REGEX help by dorko (Prior) on Apr 21, 2018 at 19:31 UTC
karlgoethebier and poj, Thank you for cleaning up my mess and throwing the code over the finish line. Cheers, Brent -- Yeah, I'm a Delt.	[reply]
Re^5: REGEX help by Your Mother (Archbishop) on Apr 21, 2018 at 20:04 UTC
Re^6: REGEX help by dorko (Prior) on Apr 21, 2018 at 20:36 UTC
Some notes below your chosen depth have not been shown here
Re^6: REGEX help by soonix (Canon) on Apr 21, 2018 at 20:35 UTC
Re^5: REGEX help by karlgoethebier (Abbot) on Apr 22, 2018 at 08:16 UTC
Re^4: REGEX help by karlgoethebier (Abbot) on Apr 21, 2018 at 19:22 UTC
"Take the spaces out...whatever..." D'oh! Thanks and best regards, Karl ŤThe Crux of the Biscuit is the Apostropheť `perl -MCrypt::CBC -E 'say Crypt::CBC->new(-key=>'kgb',-cipher=>"Blowfish")->decrypt_hex($ENV{KARL});'`Help	[reply] [d/l]


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