[Bioperl-l] making msf file from the array of sequence string

[Nathan Haigh]

After creating your Bio::LocatableSeq object you need to add it to a Bio::SimpleAlign object not Bio::Align::AlignI.
Something along the lines of this should work:

my $aln = new Bio::SimpleAlign();

	# you will probably want to loop over this section for each of your seqs
	my $seq = new Bio::LocatableSeq(-seq => "CAGT-GGT",
				    -id  => "seq1",
				    -start => 1,
				    -end   => 7);
	$aln->add_seq($seq);


my $out_msf = Bio::AlignIO->new(-file   => ">out.aln.msf", -format => 'msf');
$out_msf->write_aln($aln);

Nathan

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Kwangbom Choi
> Sent: 29 October 2004 03:10
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] making msf file from the array of sequence string
> 
> 
> Given that the aligned sequences are available in the form of string
> array, how can I make it an msf file? My current idea is ...
> 
> (1) make each aligned sequence string to be an object of Bio::LocatableSeq
> (2) add_seq each LocatableSeq object to the Bio::Align::AlignI object
> (3) initiate msf format output filehandler using Bio::AlignIO
> (4) use write_aln in Bio::AlignIO::msf
> 
> But my problem in this scheme is that I do not know how to initiate
> an empty Bio::Align::AlignI object to which my aligned sequences are
> added (step 2 above). Thank you in advance.
> 
> --
> Sincerely,
> Kwangbom Choi
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