[Bioperl-l] extending the PHYLIP format
weigang at GENECTR.HUNTER.CUNY.EDU
Wed May 28 14:01:55 EDT 2008
Let me summarize a few things I implemented during the 07 Nescent
Hackathon (with a lot of help from Sandu, Aaron, and Jason):
1. A "longname.aln" is included in the bioperl-live. Which turns out to
be the same file as "pep-266.aln" (one of them showed be removed). This
file is in clustalw format. Also, it doesn't contain the tough cases
like 50 chars long, with spaces and single quotes.
2. The solution to this ugly restriction that had been implemented
include the following pair of SimpleAlignI methods:
Title : set_displayname_safe
Usage : ($new_aln, $ref_name)=$ali->set_displayname_safe(4)
Function : Assign machine-generated serial names to sequences in
Designed to protect names during PHYLIP runs. Assign
in the form of "S000000001" to "S999999999". Restore
names using "restore_displayname".
Returns : 1. a new $aln with system names;
2. a hash ref for restoring names
Argument : Number for id length (default 10)
Title : restore_displayname
Usage : $aln_name_restored=$ali->restore_displayname($hash_ref)
Function : Restore original sequence names (after running
Returns : a new $aln with names restored.
Argument : a hash reference of names from "set_displayname_safe".
3. Added following tests in "SimpleAlign.t":
# test set_displayname_safe & restore_displayname:
$str = Bio::AlignIO->new(-file=>
is $aln->get_seq_by_pos(3)->display_id, 'Smik_Contig1103.1', 'initial
display id ok';
my ($new_aln, $ref)=$aln->set_displayname_safe();
is $new_aln->get_seq_by_pos(3)->display_id, 'S000000003', 'safe display
is $restored_aln->get_seq_by_pos(3)->display_id, 'Smik_Contig1103.1',
'restored display id ok';
I would be happy to contribute more if additional work or design is needed.
ps. We developed a module for graphic annotation of alignments using GD
(modeled after Bio::Graphics). This should be useful for people who are
annotating alignments manually (such as highlight alignment positions,
labeling domains, etc). Someone help me to deposit it in bioperl-live
through subversion would be great (my cvs developer's account was told
to be not useful any more).
Jason Stajich wrote:
> Should also ask Weigang what the status is, I think he implemented a
> lot of it.
> On May 28, 2008, at 6:51 AM, Chris Fields wrote:
>> Could you post a few example phylip sequences with long names to svn
>> and add a ticket to bugzilla? I would consider this a somewhat
>> high-priority enhancement.
>> I think keeping this in a single phylip module would be best, but
>> we'll to see how feasible it is. I think it is possible to do so,
>> however, and still retain some backwards compatibility (I may even
>> have an idea how, just need to test it out).
>> On May 28, 2008, at 3:23 AM, Heikki Lehvaslaiho wrote:
>>> I just learned that a number of phylogenetics packages (PAUP, PHYML,
>>> Mr Bayes
>>> at least ) now allow longer than 10 character IDs in PHYLIP format. The
>>> documentation is scarce but the rules seem to be:
>>> 1. There can be spaces before the ID.
>>> 2. The ID can be up to 50 characters long.
>>> 3. ID can contain any characters. If you are using spaces within the
>>> ID, you
>>> have to put the whole ID in single quotes ('). Single quotes can be
>>> used for
>>> all IDs and are removed when parsing in.
>>> 4. It is customary to have two spaces between the ID and the sequence.
>>> This custom seems to have come into PHYLIP format from Nexus.
>>> Note that this allows sequences in a file to start at different
>>> Can anyone shed more light into matter?
>>> I need to get this into bioperl as the names in HIV sequences that I
>>> work with
>>> are very long and can not be sensibly truncated.
>>> What would be the best way to do this?
>>> 1. Add more options to the already heavily
>>> hacked Bio::AlignIO::phylip.pm
>>> 2. Create a Bio::AlignIO::phyliplong.pm
>>> Do those ugly hacks for supporting fixed length long IDs really
>>> really belong
>>> in the vanilla phylip.pm file?
>>> --______ _/
>>> _/ _/
>>> _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
>>> _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho
>>> _/ _/ _/ SANBI, South African National Bioinformatics Institute
>>> _/ _/ _/ University of Western Cape, South Africa
>>> _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
>>> ___ _/_/_/_/_/________________________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Marie-Claude Hofmann
>> College of Veterinary Medicine
>> University of Illinois Urbana-Champaign
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
Weigang Qiu, Assist. Professor
Department of Biological Sciences
Hunter College, City University of New York
695 Park Ave, New York, NY 10021
1-212-772-5296 (Office, Room 839, Hunter North)
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