format puzzle

anyone1985 · 03-13-2009, 04:29 AM

Recently, I have finished Solexa assembly. I convert it to .ace by velvet's amos2ace. I want to transfer it to .phd file. But when I open it with Consed, it tell me that "BS line refers to a read that isn't in a AF line for this contig ". So I write a script like that :

#!/bin/perl -w
use Bio::SeqIO;
open TEMP, ">xp.phd" or die "can not create the file xp.phd";
close TEMP;
$in = Bio::SeqIO->new ( -file => "xp_4.ace", -format => 'ace');
$out = Bio::SeqIO->new (-file => ">xp.phd", -format => 'phd');
while( $seq = $in->next_seq())
{
print $seq->
$out->write_seq($seq);
}

But nothing happen. How should I do? or how .ace file transfer to .phd file without consed?

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03-13-2009, 04:29 AM	#1
anyone1985 Member Location: shanghai, chia Join Date: Mar 2009 Posts: 67	format puzzle Recently, I have finished Solexa assembly. I convert it to .ace by velvet's amos2ace. I want to transfer it to .phd file. But when I open it with Consed, it tell me that "BS line refers to a read that isn't in a AF line for this contig ". So I write a script like that : #!/bin/perl -w use Bio::SeqIO; open TEMP, ">xp.phd" or die "can not create the file xp.phd"; close TEMP; $in = Bio::SeqIO->new ( -file => "xp_4.ace", -format => 'ace'); $out = Bio::SeqIO->new (-file => ">xp.phd", -format => 'phd'); while( $seq = $in->next_seq()) { print $seq-> $out->write_seq($seq); } But nothing happen. How should I do? or how .ace file transfer to .phd file without consed?