[mira_talk] how to convert gap4 format to fasta multiple sequence alignment format

Hello,

i'm trying to find a way to convert several staden files (edited in gap4) 
into fasta multiple sequence alignment files.

I manage to use gap2caf to convert gap4 to caf format.

Then i can use Bastien's utilities to convert caf into several other 
formats like ace for instance.

Then i tried to use Bio::Assembly::IO bioperl package to print out each 
contig alignment in fasta format,
but with no success (code attached: the start and end of the LocatableSeq 
objects don't seem to be set).

Does anyone have any idea of some script which could do the work please ?
Or should i write a perl script to parse the caf format myself ?

Thanks for your help

jorge.

#!/usr/local/bin/perl

$input = shift || die
   "Usage: staden2fasta input_file > output_file";

use Bio::Assembly::IO;

$in = Bio::Assembly::IO->new(-file => $input, -format => 'ace');

my $assem = $in->next_assembly;

print STDERR "there are ", $assem->get_nof_contigs, " contigs in this 
assembly\n";

foreach my $contig ($assem->all_contigs){

  print STDERR "\tthere are ", $contig->no_sequences, " sequences in this 
contig\n";

  foreach my $seq ($contig->each_seq){

        print ">".$seq->id."\n";

        $i = 1;
        while ($i < $seq->start) {
                print "-";
                $i++;
        }
        print $seq->seq;
#       $i=$seq->end;
#       while ($i <= $contig->get_consensus_length) {
#               print "-";
#       }
        print "\n";
  }
}
--- 
Jorge Duarte
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Z.I. Du Brézet
8, Rue des Frères Lumière
63028 CLERMONT FERRAND Cedex 2
FRANCE
Tel : +33 (0)4 73 42 79 70 (Accueil)
Fax : +33 (0)4 73 42 79 81
E-mail : jorge.duarte@xxxxxxxxxxxx

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