Aaron--
I wasn't sure if the bug tracker would send this to you automatically
(we don't use it too often), so I cc'ed you. Let me know if this
wasn't necessary.
With regard to the bug, I don't get this problem with your file. I
added it to the test suite so that you can test it. Please put a
copy of your file in t/data/compliant and replace the test file
corresponding to the attached file (matrix_charactersblock-
interleave.t ). This will pick the first OTU (Homo_sapiens) and
check that 124 characters are read from the file. I don't get any
errors with this:
camel12:~/Projects/Bio-NEXUS/NEXPL arlin$ perl t/
matrix_charactersblock-interleave.t
Testing interleaved file 't/data/compliant/characters-block-
interleave.nex' (expect 59 chars from OTU 'A')
ok 1 - Parsing nexus files
ok 2 - NEXUS object defined isa Bio::NEXUS
ok 3 - 2 blocks are present
ok 4 - Bio::NEXUS::CharactersBlock object present isa
Bio::NEXUS::CharactersBlock
ok 5 - 59 characters are present in 'A'
Testing interleaved file 't/data/compliant/
HCRT_all_orths_pep1_msfed1.aln.nxs' (expect 124 chars from OTU
'Homo_sapiens')
ok 6 - Parsing nexus files
ok 7 - NEXUS object defined isa Bio::NEXUS
ok 8 - 2 blocks are present
ok 9 - Bio::NEXUS::CharactersBlock object present isa
Bio::NEXUS::CharactersBlock
ok 10 - 124 characters are present in 'Homo_sapiens'
1..10
Arlin
On Aug 5, 2008, at 2:15 PM, Aaron J. Mackey via RT wrote:
Show quoted text> Tue Aug 05 14:15:32 2008: Request 38210 was acted upon.
> Transaction: Ticket created by AMACKEY
> Queue: Bio-NEXUS
> Subject: interleaved data matrix from Readseq2 not parsed
> properly
> Broken in: (no value)
> Severity: Important
> Owner: Nobody
> Requestors: ajmackey@gmail.com
> Status: new
> Ticket <URL:
http://rt.cpan.org/Ticket/Display.html?id=38210 >
>
>
> See the attached file generated using Readseq2. It repeats the taxa
> labels for each interleaved block. Bio::NEXUS will only report the
> last
> block of the alignment.
>
> Lines 451 and 456 of Bio/Nexus/CharactersBlock.pm should be:
>
> $taxa{$name} ||= [];
>
> instead of:
>
> $taxa{$name} = [];
>
> so that it won't overwrite the previously read
> sequence.<HCRT_all_orths_pep1_msfed1.aln.nxs>
------------
Arlin Stoltzfus (arlin.stoltzfus@nist.gov), Research Biologist, NIST
Fellow, CARB, 9600 Gudelsky Drive, Rockville, Maryland 20850
tel 240 314 6208, fax 240 314 6255, www.molevol.org/camel

