[Bioperl-l] no revcom method in Bio::Seq module?

chen li chen_li3 at yahoo.com
Sun May 14 13:14:30 EDT 2006


Hi all,

I need to get a reverse-complemenary sequence out of a
fasta sequence file. And the Synopsis of Bio::Seq
points out I can do like this way:

$revcom=$seqobj->revcom();

I use the following script trying to get the job done
but it doesn't work. Then I read documentation of
Bio::Seq and it looks like it doesn't contain revcom
method.

Any idea will be appreciated.

Li 


###############################
Here is the code:

#!c:/perl/bin/perl.exe
use strict;
use warnings;

use Bio::Seq; 
use Bio::SeqIO;     
       
my $file='c:/perl/local/primer3_1.0.0/src/est.txt';   
 
    
my $seqIO=Bio::SeqIO->new(-file=>"<$file",
                            -format=>'fasta' );
                            
    my $seqobj=$seqIO->next_seq();#create object  
    
  print "what attributes/keys are available:\n";    
  for my $key (sort keys %$seqobj){
           my $value=$seqobj->{$key};
	    print "$key\t=>\t$value\n"
	    }
# These are the output on the screen	    
#primary_id =>      gi|54093|emb|X61809.1|
#primary_seq =>     Bio::PrimarySeq=HASH(0x10492848)

#based on these results primary_id can get 
#access right away
# as to primary_seq it is an object in
#Bio::Primaryseq and it provides the following
#methods after reading the documentaion:
                #new   
		#seq 
		#validate_seq 
		#subseq 
		#length 
		#display_id
		#accession_number 
		#primary_id 
		#alphabet 
		#desc 
		#can_call_new
		#id 
		#is_circular 
		#object_id
		#version 
		#authority 
		#namespace 
		#display_name 
		#description 
    
print "primary_id=",$seqobj->primary_id, "\n\n";
print "id=",$seqobj->id, "\n\n"; 
print "revcom=",$seqobj->revcom,"\n\n";
                      
        my $now_time=localtime;
        print  $now_time, "\n\n";  
        exit;

 #These are the output on the screen 
	#primary_id=gi|54093|emb|X61809.1|
	#id=gi|54093|emb|X61809.1
	#revcom=Bio::Seq=HASH(0x10493304)
	#Sun May 14 12:45:20 2006

      

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


More information about the Bioperl-l mailing list