[Bioperl-l] AlignIO problems

=?gb2312?B?va0gzsTi/Q==?= biology0046 at hotmail.com
Sun Feb 25 08:28:34 EST 2007


hi, all,
I use the AlignIO module to convert the alignment file.
my original file is :
CLUSTAL W(1.81) multiple sequence alignment


dana_GLEANR_11249      
MEAIAKHDFSATADDELSFRKTQTLKILNMEDDSNWYRAELDGKEGLIPSNYIEMKNHDW
dere_GLEANR_7213       
...V...................I....................................
dgri_GLEANR_6962       
.......................I....................................
FBgn0004638            
.......................I....................................
dmoj_GLEANR_6118       
...........N...........I....................................
dper_GLEANR_18885      
...V...................I....................................
dpse_GLEANR_14384      
...V...................I....................................
dsec_GLEANR_3096       
.................N.....I....................................
dsim_GLEANR_9744       
-----------------------------...............................
dvir_GLEANR_4811       
.......................I....................................
dwil_GLEANR_10869      
.......................I....................................
dyak_GLEANR_13576      
.......................I....................................



dana_GLEANR_11249      
YYGRITRADAEKLLSNKHEGAFLIRISESSPGDFSLSVKCPDGVQHFKVLRDAQSKFFLW
dere_GLEANR_7213       
............................................................
dgri_GLEANR_6962       
............................................................
FBgn0004638            
............................................................
dmoj_GLEANR_6118       
.................L..........................................
dper_GLEANR_18885      
............................................................
dpse_GLEANR_14384      
............................................................
dsec_GLEANR_3096       
............................................................
dsim_GLEANR_9744       
............................................................
dvir_GLEANR_4811       
............................................................
dwil_GLEANR_10869      
............................................................
dyak_GLEANR_13576      
............................................................



dana_GLEANR_11249      
VVKFNSLNELVEYHRTASVSRSQDVKLRDMIPEEMLVQALYDFVPQESGELDFRRGDVIT
dere_GLEANR_7213       
............................................................
dgri_GLEANR_6962       
............................................................
FBgn0004638            
............................................................
dmoj_GLEANR_6118       
..............................V.D...........................
dper_GLEANR_18885      
.......................E....................................
dpse_GLEANR_14384      
.......................E....................................
dsec_GLEANR_3096       
............................................................
dsim_GLEANR_9744       
............................................................
dvir_GLEANR_4811       
............................................................
dwil_GLEANR_10869      
............................................................
dyak_GLEANR_13576      
............................................................



dana_GLEANR_11249      VTDRSDENWWNGEIGNRKGIFPATYVTPYHS
dere_GLEANR_7213       ...............................
dgri_GLEANR_6962       ...............................
FBgn0004638            ...............................
dmoj_GLEANR_6118       ............Q..................
dper_GLEANR_18885      ...............................
dpse_GLEANR_14384      ...............................
dsec_GLEANR_3096       ...............................
dsim_GLEANR_9744       ...............................
dvir_GLEANR_4811       ...............................
dwil_GLEANR_10869      ...............................
dyak_GLEANR_13576      ...............................


I want to change those "." characters back to alphabetic expression, then i 
write the code like this:
use Bio::AlignIO;
my $in=Bio::AlignIO->new(-file =>"FBgn0000097.aln",
                      -format => 'clustalw');
my $out=Bio::AlignIO->new(-file=>">../clustalw/0097.aln",
                       -format =>'clustalw');
while (my $aln=$in->next_aln() ){
    $aln->unmatch();
    $aln->set_displayname_flat();
    $out->write_aln($aln);
}

but when i run the code, there are error message like:

-------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet []
---------------------------------------------------

------------- EXCEPTION  -------------
MSG: No sequence with name [dsim_GLEANR_9744/1-182]
STACK Bio::SimpleAlign::displayname 
/home/src/bioperl/bioperl-live/Bio/SimpleAlign.pm:2307
STACK Bio::SimpleAlign::set_displayname_flat 
/home/src/bioperl/bioperl-live/Bio/SimpleAlign.pm:2374
STACK toplevel aligntest.pl:11

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

I don't know where is the problem.

Jiang

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