[Bioperl-guts-l] [Bug 1832] New: EMBL display ID not working correctly

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Jul 29 16:00:06 EDT 2005


http://bugzilla.open-bio.org/show_bug.cgi?id=1832

           Summary: EMBL display ID not working correctly
           Product: Bioperl
           Version: unspecified
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::SeqIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: wtclark at indiana.edu


Regards,

	I am having troubles with the Bio::SeqIO module when it comes to embl files.  I have a simple embl 
file from Repbase, that I am very sure is in correct format (see below), although the display_id function 
says it has no ID.  This is obviously not the case.  I wonder if this is a bug.  Below is my simple code and 
a snippet of one of the sequences.  If you could tell me what is wrong I would appreciate it.  I thought I 
was running Bio::Perl version 1.3, but that doesn't seem to be an option.

thanks,

Wyatt Clark

use Bio::SeqIO;
my $file = shift;

my $OH = Bio::SeqIO->new('-format' => 'EMBL', '-file' => "$file") || die "nope\n";



while( my $seq = $OH->next_seq){

	my $temp = $seq->display_id;
	print "$temp\n";
}




ID   BEL16-LTR_AG repbase; DNA   ; ANG   ; 287 BP.
XX
AC   .
XX
DT   03-APR-2003 (Rel. 8.03, Created)
DT   03-APR-2003 (Rel. 8.03, Last updated, Version 1)
XX
DE   BEL16-LTR_AG is a long terminal repeat of the BEL16_AG LTR
DE   retrotransposon - a consensus sequence.
XX
KW   5-bp TSD; BEL16-I_AG; BEL16-LTR_AG; BEL16_AG; Bel clade;
KW   LTR retrotransposon; reverse transcriptase.
XX
OS   Anopheles gambiae str. PEST
OC   Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera;
OC   Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Anophelinae;
OC   Anopheles; Anopheles gambiae.
XX
RN   [1]
RP   1-287
RA   Kapitonov V.V., Pavlicek A., Jurka J.;
RT   "BEL16_AG, a nonautonomous family of Bel/Pao-like LTR retrotransposons
RT   from African malaria mosquito.";
RL   Repbase Reports 3(3), 40-40 (2003).
XX
CC   [1] (Consensus)
XX
CC   BEL16-LTR_AG flank an internal portion of BEL16_AG (deposited as
CC   BEL16-I_AG).
XX
SQ   Sequence 287 BP; 85 A; 51 C; 75 G; 76 T; 0 others;
     tgttggaatg taagggttat gaaacggtca ttttgaattg tttgcggttg ttttgtcagt        60
     tgggaattaa aagttaaatg tattttctgg cagcactgcc gatcgacaat ttgtgattaa       120
     gtatgtgtgc gaataaagcg gcactagcgc atgaaactcg atacgagccg gacgtgttct       180
     ttactttgtc tcctttggcg atcgaagacg acacaacaaa acacaacgta gggcgtagag       240
     gcgtcaaggg ggaaaggaac caacaaacca tgttccagaa cgcaaca                     287
//



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