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

[hyupaik at indiana.edu]

#! /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();
 
my $out = new Bio::AlignIO('-file' => '>testout.fasta',
                         '-format' => 'fasta');
$out->write_aln($aln);






>>crab_chick/1-462
initninitoptZ-score.bits.E.Smith-Watermanscore.identity.unga
ppedinaaoverlap--crabaMDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELL
PASPSLSPFLMRSPIFRMPSWL....crabcMDITIHNPLVRRPLFSWLTPSRIFDQIFG
EHLQESELLPTSPSLSPFLMRSPFFRMPSWLcrabaETGLSEMRLEKDKFSVNLDVKHFS
PEELKVKVLGDMVEIHGKHEERQDEHGFIAREFNRK..crabcETGLSEMRLEKDKFSVN
LDVKHFSPEELKVKVLGDMIEIHGKHEERQDEHGFIAREFSRKcrabaYRIPADVDPLTI
TSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGAQRK.crabcYRIPADVDPLTI
TSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGSQRK
>>crab_bovin/1-628
initninitoptZ-score.bits.E.Smith-Watermanscore.identity.unga
ppedinaaoverlap--crabaMDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELL
PASPSLSPFLMRSPIF-RMPSW..........crabbMDIAIHHPWIRRPFFPFHSPSRL
FDQFFGEHLLESDLFPASTSLSPFYLRPPSFLRAPSWcrabaLETGLSEMRLEKDKFSVN
LDVKHFSPEELKVKVLGDMVEIHGKHEERQDEHGFIAREFNR........crabbIDTGL
SEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHRcraba
KYRIPADVDPLTITSSLSLDGVLTVSAPRKQSDVPERSIPITREEKPAIAGAQRK.....
....crabbKYRIPADVDPLAITSSLSSDGVLTVNGPRKQASGPERTIPITREEKPAVT
AAPKKresiduesinquerysequencesresiduesinlibrarysequencesScomp
libtstartFriNovdoneFriNovTotalScantime.TotalDisplaytime.Func
tionusedwasFASTAversion.tNov