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14:28 < balin> deafferret, I only posted about add_seq to bioperl-l. Should I start a new thread for write_aln or can I reuse this one? 14:28 <@deafferret> If it's a seperate issue I'd post a separate email 14:29 <@deafferret> ticket 2793 is definately add_seq only 14:29 < balin> I thought so too --irc.freenode.net #bioperl 20090319 http://bugzilla.open-bio.org/show_bug.cgi?id=2793 oh... maybe I can patch it before they do --jhannah 20090320 7 email discussion: http://thread.gmane.org/gmane.comp.lang.perl.bio.general/18973/focus=18980 --jhannah 20090320 12:26 < balin> deafferret, I found that add_seq function does not insert a new sequence into alignment, but replaces the old sequence. So this statement seems to work: 12:27 < balin> $aln->get_seq_by_pos($i)->display_id("new header"); 12:27 < balin> $aln->add_seq($aln->get_seq_by_pos($i),$i-1); 12:29 <@deafferret> ahh... congrats. :) 12:30 < balin> still, this looks awkward 12:38 < balin> It turns out I need $i-1 here because get_seq_by_pos counts from 1 and add_seq counts from 0. Would that be considered a bug? 13:01 <@deafferret> hmm... maybe a bug that can't be fixed because no one wants to break backwards-compatibility ... so a FEATURE? :) 13:01 <@deafferret> you should probably post that to bioperl-l and ask the long white beards 13:37 < balin> yes, I'll probably do that 13:37 < balin> white beards, haha 13:46 <@deafferret> :) --irc.freenode.net #bioperl 20090319 Possible bug report from #bioperl balin http://pastebin.com/m182fca5d --jhannah 20090318