[Bioperl-l] names/id in multi-alignment files

[martin]

Hi, 

In your code, you're treating $seq as a string; actually its a Bio::Seq
object.  Something like this should work:

$str = Bio::AlignIO->new('-file' => $filename);	
$aln = $str->next_aln;

foreach $seq ($aln->each_seq){
	print $seq->display_id, "\n";
}

calling the display_id method on a Bio::Seq object returns the name/

Hope this helps

Martin

On Thu, 2004-09-23 at 03:29, Marco Landwehr wrote:
> Hi,
> when reading in s multi alignment file of the fasta format:
> 
> #read in alignment
> $str = Bio::AlignIO->new('-file' => $filename);	
> $aln = $str->next_aln();
> 
> I cannot extract the "header" name or id with:
> 
> foreach $seq ($aln->id()){
> 	print $seq,"\n";
> }
> 
> Is there a way to do this?
> When using:
> 
> #alternative way to read all sequences from multi fasta file
> @seq_object_array = read_all_sequences($filename,'fasta');
> 
> I can get the name of a specific sequence with:
> $seq_object_array[$i]
> 
> but I dont want to read in the sequences both ways...
> 
> Thanks for you help...
> 
> Marco
> 
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-- 
Martin Jones
Blaxter Nematode Genomics Group  
School of Biological Sciences    
Ashworth Laboratories            
University of Edinburgh          
Edinburgh                        
EH9 3JT                          
UK                                   
tel: +44 131 650 7403
web: www.nematodes.org