[Bioperl-l] Problem with Bio::TreeIO::nexus

[Donald G. Jackson]

Jason or another TreeIO wizard,

I'm having trouble reading in a nexus treefile created with Paup4b10.  
I've attached my code and an example treefile.  Briefly, when I call 
next_tree() I get no trees back.

It looks as though the comment-counting mechanism is getting thrown off 
(Bio::TreeIO::nexus lines 124ff).  Once the opening comment closes, the 
module stops reading any data ;(.   I'm using version 1.3 of 
Bio::TreeIO::nexus

I'd appreciate any suggestions or assistance.

Thanks,

Don Jackson
BMS Bioinformatics
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#NEXUS 

Begin trees;  [Treefile saved Wed Jul  7 16:13:25 2004]
[!
>Data file = /net/hox/home/jacksod/Kinase_Struc_Phylogeny/Phylogeny/v2/kinase_set_v3_run.nex
>Heuristic search settings:
>  Optimality criterion = distance (minimum evolution)
>    Negative branch lengths allowed, but set to zero for tree-score calculation
>    Distance measure = total character difference
>    138 characters are excluded
>  Starting tree(s) obtained via neighbor-joining
>  Branch-swapping algorithm: tree-bisection-reconnection (TBR)
>  Steepest descent option not in effect
>  Initial 'MaxTrees' setting = 100
>  Zero-length branches not collapsed
>  'MulTrees' option in effect
>  Topological constraints not enforced
>  Trees are unrooted
>
>NOTE: Random-addition-sequence option is ignored when starting trees are
>      obtained using neighbor-joining.
>
>Heuristic search completed
>   Total number of rearrangements tried = 13674
>   Score of best tree(s) found = 2445.54947
>   Number of trees retained = 1
>   Time used = 1 sec (CPU time = 0.75 sec)
]
	Translate
		1 ABL1,
		2 LCK,
		3 FYN,
		4 SRC,
		5 HCK,
		6 LYN,
		7 EMT,
		8 IR,
		9 'IGF-1R',
		10 MET,
		11 FLT3,
		12 CKIT,
		13 'PDGF-ALPHA',
		14 'PDGF-BETA',
		15 VEGFR2,
		16 FGFR1,
		17 FAK1,
		18 FAK2,
		19 SYK,
		20 ZAP70,
		21 HER1,
		22 HER2,
		23 LIMK2,
		24 LIMK1,
		25 TESK1,
		26 TESK2,
		27 MEK1,
		28 MEKK2,
		29 MINK,
		30 AURORA1,
		31 MK2,
		32 PKA,
		33 AKT1,
		34 'PKC-DELTA',
		35 'PCK-THETA',
		36 GSK3,
		37 CDK2,
		38 'P38-ALPHA'
		;
tree PAUP_1 = [&U] (((((1:62.006250,((2:28.407143,(5:22.986111,6:22.013889):6.092857):8.340260,(3:18.930556,4:19.069444):17.795455):27.952841):1.772984,7:70.397849):9.335071,((((8:21.027778,9:21.972222):53.928571,10:76.071429):3.947181,(((11:41.361111,12:42.638889):3.257353,(13:30.430556,14:29.569444):16.742647):10.640625,(15:51.736111,16:51.263889):4.484375):19.765864):4.506663,(((17:47.861111,18:49.138889):24.632353,(19:45.791667,20:45.208333):31.617647):1.031250,(21:23.736111,22:22.263889):54.468750):5.022192):0.043724):15.646889,((23:41.902778,24:33.097222):40.794118,(25:38.347222,26:37.652778):35.205882):24.266098):0,(((27:96.442857,(28:89.527778,29:93.472222):5.057143):2.725744,(36:94.842857,(37:79.750000,38:88.250000):10.657143):11.369494):0.867521,((30:81.763889,31:97.236111):0.992187,((32:68.777778,33:66.222222):6.801471,(34:32.069444,35:30.930556):36.198529):16.632813):8.518763):10.268624);
End;