[Bioperl-l] codon usage

[Jim Hu]

I wouldn't mind having a branch.  I could also use it to share the files for our class.  Not sure how soon I'd be able to get around to doing the alternative version of Bio::Tools::SeqStats... if I can find time to do some work on a BioPerl fork, I'd like to get the is_circular stuff working. 

Jim

On May 7, 2012, at 11:28 AM, Fields, Christopher J wrote:

> On May 7, 2012, at 10:28 AM, Jim Hu 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.
> 
> Yes, I'm sure that was the simplest way to implement it to get things working, I'm guessing.
> 
>> 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
> 
> Sure, we're always up for testing.  Would you like to run this on a fork on github?  Or we can probably set you up with commit access, as long as all this was confined to a branch.
> 
> chris
> 
>> 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: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of subarna thakur
>>> Sent: Saturday, 21 April 2012 3:00 p.m.
>>> To: bioperl-l at bioperl.org
>>> 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
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054