[Bioperl-l] assembling chromosomes from contigs and .agp file

[Smithies, Russell]

Was easier than I thought although I couldn't work out a way to "build" a Bio::Seq directly from bits.
Here's how I did it:
-------------------------------

use Bio::DB::Fasta;
use Bio::Seq;
use Bio::SeqIO;

open(AGP,"Mt2.0_pgp.agp") or die $!;
my @chr = ();

my $db = Bio::DB::Fasta->new("contigs.fa");

while(<AGP>){
	chomp;
	split /\s/;
	# extend temp string if it's too short
	do{$chr[$_[0]] .= ' ' x 1_000_000;}while length $chr[$_[0]] < $_[2] ;
	if($_[4] !~ m/N/){
		($start,$stop) = $_[8] eq '+'?($_[6], $_[7]):($_[7], $_[6]);
		$s = substr $chr[$_[0]], $_[1], $_[9], $db->seq($_[5],$start,$stop);
	}else{
		$s = substr $chr[$_[0]], $_[1], $_[5], "N" x $_[5] ;
	}
}

#remove any trailing whitespace
@chr = map{s/\s+//g;$_}@chr;

#print the sequence. chromosomes are chr0 -> chr8
foreach(0..$#chr){
    my $seqobj = Bio::Seq->new( -display_id => "chr$_", -seq => $chr[$_]);
    my $seq_out = Bio::SeqIO->new('-file' => ">chr$_.fa",'-format' => 'fasta');
    $seq_out->write_seq($seqobj);
}
-------------------------------

Please excuse my hacky use of substrings but this .agp file had overlapping runs of 'N' and this was the easiest way to deal with it
e.g. 
0	1	50000	1	N	50000	clone	yes
0	50001	167645	2	F	AC144644.3	1	117645	+	117645
0	167646	217645	3	N	50000	clone	yes		
0	217646	317645	4	N	100000	contig	no		
0	317646	367645	5	N	50000	clone	yes		
0	367646	411754	6	F	AC146805.17	1	44109	+	44109

--Russell



> -----Original Message-----
> From: Smithies, Russell
> Sent: Thursday, 8 January 2009 1:33 p.m.
> To: 'bioperl-l at lists.open-bio.org'
> Subject: assembling chromosomes from contigs and .agp file
> 
> Does anyone have a script for building chromosomes from an .agp file
> and a directory full of contigs?
> If not, I'll write something but I didn't want to re-invent the wheel
> if there's something "in the wild".
> 
> Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could
> an .agp file be regarded as a Bio::Assembly?
> 
> --Russell
> 

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