[Bioperl-l] Problem or Bug with Bio::LocatableSeq

[hyupaik at indiana.edu]

 Hello list,

 I am sorry for the pervious email. I sent it accidentally.

 I found out something strange when I used AlignIO.
 I was going to see a sequence through LocatableSeq.

 But I got extra characters than seq.

 I believe that those characters are from the index of the fasta result file.

 Here's my code and the result sequence.

 Is this a bug or did I something wrong?

 Thank you.

 - Henry.

 
----------------------------------------------------------------
 #! /local/bin/perl -w
 
use strict;
use lib '/home/hy1001/bin';
 
use Bio::SimpleAlign;
use Bio::AlignIO;
 
my $in = Bio::AlignIO->new('-file' => 'fastaResult',
                         '-format' => 'fasta');
my $aln = $in->next_aln();
print $aln->get_seq_by_pos(1)->seq(),"\n";



------------------------------------------------------------------

[hy1001 at biokdd fastaAlign]$ perl alignfasta.pl
initninitoptZ-score.bits.E.Smith-Watermanscore.identity.ungappedinaaoverlap--crabaMDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASPSLSPFLMRSPIFRMPSWL....crabcMDITIHNPLVRRPLFSWLTPSRIFDQIFGEHLQESELLPTSPSLSPFLMRSPFFRMPSWLcrabaETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDMVEIHGKHEERQDEHGFIAREFNRK..crabcETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDMIEIHGKHEERQDEHGFIAREFSRKcrabaYRIPADVDPLTITSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGAQRK.crabcYRIPADVDPLTITSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGSQRK