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Gmane
From: Joel Martin <j_martin <at> lbl.gov>
Subject: Re: codon usage
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 7th May 2012 19:15:46 UTC (over 4 years ago)
I think you're under-appreciating the perl regex engine, it operates
as a state machine not by matching all occurrences every time.  Here
is a nice excerpt from pro perl parsing
http://www.devshed.com/c/a/Perl/Parsing-and-Regular-Expression-Basics/2/

Joel

On Mon, May 7, 2012 at 8:28 AM, Jim Hu <[email protected]> wrote:
> I was looking at Bio::Tools::SeqStats.  It reminds me of the very first
bioinformatics program I worked on back when I was in grad school,
sequencing was done by Maxam-Gilbert chemistry on gels with radioactive DNA
(we were doing short reads, but we didn't call it that and the reads per
run was something like 8).  We were writing a program in Apple II basic to
find restriction sites.  Everyone in the group was doing this by putting
the target sequence in a string variable and looking for the site as a
substring match by whatever it was BASIC used.  Loop over all the sites
you are looking for.  This strikes me as the equivalent of how
Bio::Tools::SeqStats works, only with regexes.
>
> My roommate at the time, who was a math PhD student doing an MS in
CompSci, pointed out to me that this would be more efficient using a
discrete finite automaton algorithm, where each site we were looking for
would be a state automaton. This has the advantage of being able to process
the sequence as a stream.  Back when we were working with computers with
RAM measured in Kbytes, this was a big help.  I'm not sure if it would be
worth it today.  The slow interpreted implementation of the state machines
would likely lose to the fast internal implementation of the regex routines
for sequence lengths we are looking at these days.
>
> But it might be interesting to compare.
>
> Jim
>
> On May 6, 2012, at 3:52 PM, Smithies, Russell wrote:
>
>> Or use Bio::Tools::SeqStats
>> (this is straight from the perldocs http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Tools/SeqStats.pm
)
>>
>>         $seqobj = Bio::PrimarySeq->new(-seq      =>
'ACTGTGGCGTCAACTG',-alphabet => 'dna',-id       => 'test');
>>         $seq_stats  =  Bio::Tools::SeqStats->new(-seq => $seqobj);
>>
>>         $hash_ref = $seq_stats-> count_codons();  # for nucleic
acid sequence
>>         foreach $base (sort keys %$hash_ref) {
>>             print "Number of codons of type ", $base, "= ",
 %$hash_ref->{$base},"\n";
>>         }
>>
>>
>> --Russell
>>
>>
>> -----Original Message-----
>> From: [email protected]
[mailto:[email protected]] On Behalf Of subarna thakur
>> Sent: Saturday, 21 April 2012 3:00 p.m.
>> To: [email protected]
>> Subject: [Bioperl-l] codon usage
>>
>> I am writing a script for determining number of genes containing a
particular codon. The codons are mentioned in a separate file. The output
is coming all right for the first codon mentioned in the file but for the
other codons , the script is not working. Please suggest the error in the
script. The script is as follows ----
>>
>> #!/usr/bin/perl -w
>>
>> use Bio::SeqIO;
>>
>> $file2="table.txt";
>>
>> $codon=0;
>>
>> open OUT, ">out-test.txt" or die $!;
>>
>> $seqio_obj = Bio::SeqIO->new( -file => "gopi2.txt" , '-format'
=> 'Fasta');
>>
>> open( my $fh2, $file2 ) or die "$!";
>>
>> while( my $line = <$fh2> ){
>>
>> $acc=$line;
>>
>> chomp $acc;
>>
>> while ($seq1= $seqio_obj->next_seq){
>>
>> my @output = $seq1->id;
>>
>> my $string = $seq1->seq;
>>
>> $v=0;
>>
>> $l= length($string);
>>
>> $t=$l/3;
>>
>> $k=0;
>>
>> for ($i=1; $i <= $t; $i++){
>>
>> @array2 = substr($string, $k, 3);
>>
>> $k=$k+3;
>>
>> foreach $value (@array2)
>>
>> {
>>
>> if ($value eq "$acc")
>>
>> {
>>
>> print OUT " The sequence id is @output\n";
>>
>> print OUT "$acc codon found in position $i\n\n";
>>
>> $v=$v+1;
>>
>> }
>>
>> }
>>
>> }
>>
>> if ($v==0)
>>
>> {
>>
>> $h=0;
>>
>> }
>>
>> else
>>
>> {
>>
>> $h=1;
>>
>> }
>>
>> $codon=$codon+$h;
>>
>> }
>>
>> print OUT "Total number of sequences with $acc codon";
>>
>> print OUT "\t";
>>
>> print OUT $codon;
>>
>> }
>>
>> exit;
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>
> =====================================
> Jim Hu
> Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
>
>
>
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