[Bioperl-l] The way to extract a segment of an EMBL record?

Chris Fields cjfields at uiuc.edu
Tue Jun 24 21:33:15 EDT 2008


The trunc() methods are not completely implemented; Bio::Seq::trunc()  
doesn't carry over either annotations or seqfeatures AFAIK.  I think  
Bio::SeqUtils::trunc_with_features does this though.

chris

On Jun 24, 2008, at 6:29 PM, Phillip San Miguel wrote:

>   When I use the trunc method to pull a segment of a sequence object  
> derived from large EMBL file, the annotations are not propagated. Do  
> I need to specify a heavy weight sequence object somehow for  
> annotation in the EMBL file to be carried along?
>
> Phillip
>
> PS The code I'm talking about is below. This produces what appears  
> to be a valid EMBL file, but only bare-bones annotation is carried  
> along, or generated on the fly:
>
> ID   NC_003070; SV 1; linear; unassigned DNA; STD; UNC; 70001 BP.
> XX
> AC   NC_003070;
> XX
> DE   Arabidopsis thaliana chromosome 1, complete sequence.
> XX
> XX
> FH   Key             Location/Qualifiers
> FH
> XX
> SQ   Sequence 70001 BP; 20783 A; 14173 C; 13896 G; 21149 T; 0 other;
>
>
> Here is the code:
>
> use Bio::SeqIO;
> use Bio::Seq;
>
> my $rh_opts =parseOptions();
>
> #create input sequence object
> my  $in  = Bio::SeqIO->new(-file => $rh_opts->{INFILE} , -format  
> =>   $rh_opts->{F_IN} );
>
> #pull in sequence. (Ignores all but first sequence)
> my $seq =   $in->next_seq()
>   ||  die "Hey, $rh_opts-{INFILE} contains no sequence of format  
> $rh_opts->{F_IN}!";
> $in->close();
>
> #xtract segment of sequence to output
> my $end     =(defined $rh_opts->{END})
>           ? $rh_opts->{END}
>           : $seq->length();
> my $begin   = $rh_opts->{BEGIN};
> my $segment =$seq->trunc($begin, $end);
>
> #create output object
> my $out = Bio::SeqIO->new(-file => ">$rh_opts->{OUTFILE}" , -format  
> => $rh_opts->{F_OUT});
> $out->write_seq($segment);
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






More information about the Bioperl-l mailing list