1.4. Examining Data Objects

High-level summaries of the contents of DendroPy phylogenetic data objects are given by the description instance method of the Tree, TreeList, CharacterMatrix-derived, and DataSet classes. This method optionally takes a numeric value as its first argument that determines the level of detail (or depth) of the summary:

>>> import dendropy
>>> d = dendropy.DataSet.get_from_path('pythonidae.nex', 'nexus')
>>> print(d.description())
DataSet object at 0x79dd0: 1 Taxon Sets, 0 Tree Lists, 1 Character Matrices
>>> print(d.description(3))
DataSet object at 0x79dd0: 1 Taxon Sets, 0 Tree Lists, 1 Character Matrices
    [Taxon Sets]
        [0] TaxonSet object at 0x5a4a20 (TaxonSet5917216): 29 Taxa
            [0] Taxon object at 0x22c0fd0 (Taxon36442064): 'Python regius'
            [1] Taxon object at 0x22c0f10 (Taxon36441872): 'Python sebae'
            [2] Taxon object at 0x22c0ed0 (Taxon36441808): 'Python brongersmai'
            [3] Taxon object at 0x22c0f70 (Taxon36441968): 'Antaresia maculosa'
            [4] Taxon object at 0x22c0f30 (Taxon36441904): 'Python timoriensis'
            [5] Taxon object at 0x22c0f50 (Taxon36441936): 'Python molurus'
            [6] Taxon object at 0x22c0ff0 (Taxon36442096): 'Morelia carinata'
            [7] Taxon object at 0x23ae050 (Taxon37412944): 'Morelia boeleni'
            [8] Taxon object at 0x23ae030 (Taxon37412912): 'Antaresia perthensis'
            [9] Taxon object at 0x23ae070 (Taxon37412976): 'Morelia viridis'
            [10] Taxon object at 0x23ae090 (Taxon37413008): 'Aspidites ramsayi'
            [11] Taxon object at 0x23ae0b0 (Taxon37413040): 'Aspidites melanocephalus'
            [12] Taxon object at 0x22c0fb0 (Taxon36442032): 'Morelia oenpelliensis'
            [13] Taxon object at 0x23ae0d0 (Taxon37413072): 'Bothrochilus boa'
            [14] Taxon object at 0x23ae130 (Taxon37413168): 'Morelia bredli'
            [15] Taxon object at 0x23ae110 (Taxon37413136): 'Morelia spilota'
            [16] Taxon object at 0x23ae150 (Taxon37413200): 'Antaresia stimsoni'
            [17] Taxon object at 0x23ae0f0 (Taxon37413104): 'Antaresia childreni'
            [18] Taxon object at 0x23ae1b0 (Taxon37413296): 'Leiopython albertisii'
            [19] Taxon object at 0x23ae170 (Taxon37413232): 'Python reticulatus'
            [20] Taxon object at 0x23ae190 (Taxon37413264): 'Morelia tracyae'
            [21] Taxon object at 0x23ae1d0 (Taxon37413328): 'Morelia amethistina'
            [22] Taxon object at 0x23ae230 (Taxon37413424): 'Morelia nauta'
            [23] Taxon object at 0x23ae250 (Taxon37413456): 'Morelia kinghorni'
            [24] Taxon object at 0x23ae210 (Taxon37413392): 'Morelia clastolepis'
            [25] Taxon object at 0x23ae290 (Taxon37413520): 'Liasis fuscus'
            [26] Taxon object at 0x23ae2b0 (Taxon37413552): 'Liasis mackloti'
            [27] Taxon object at 0x23ae270 (Taxon37413488): 'Liasis olivaceus'
            [28] Taxon object at 0x23ae2f0 (Taxon37413616): 'Apodora papuana'
    [Character Matrices]
        [0] DnaCharacterMatrix object at 0x22c0f90 (DnaCharacterMatrix36442000):  29 Sequences
            [Taxon Set]
                TaxonSet object at 0x5a4a20 (TaxonSet5917216): 29 Taxa
            [Characters]
                [0] Python regius : 1114 characters
                [1] Python sebae : 1114 characters
                [2] Python brongersmai : 1114 characters
                [3] Antaresia maculosa : 1114 characters
                [4] Python timoriensis : 1114 characters
                [5] Python molurus : 1114 characters
                [6] Morelia carinata : 1114 characters
                [7] Morelia boeleni : 1114 characters
                [8] Antaresia perthensis : 1114 characters
                [9] Morelia viridis : 1114 characters
                [10] Aspidites ramsayi : 1114 characters
                [11] Aspidites melanocephalus : 1114 characters
                [12] Morelia oenpelliensis : 1114 characters
                [13] Bothrochilus boa : 1114 characters
                [14] Morelia bredli : 1114 characters
                [15] Morelia spilota : 1114 characters
                [16] Antaresia stimsoni : 1114 characters
                [17] Antaresia childreni : 1114 characters
                [18] Leiopython albertisii : 1114 characters
                [19] Python reticulatus : 1114 characters
                [20] Morelia tracyae : 1114 characters
                [21] Morelia amethistina : 1114 characters
                [22] Morelia nauta : 1114 characters
                [23] Morelia kinghorni : 1114 characters
                [24] Morelia clastolepis : 1114 characters
                [25] Liasis fuscus : 1114 characters
                [26] Liasis mackloti : 1114 characters
                [27] Liasis olivaceus : 1114 characters
                [28] Apodora papuana : 1114 characters

If you want to see the data in a particular schema, you can call the as_string method, passing it a schema-specification string (“nexus”, “newick”, “fasta”, “phylip”, etc.), as well as other optional arguments specific to varous formats:

>>> import dendropy
>>> d = dendropy.DataSet.get_from_path('pythonidae.nex', 'nexus')
>>> print(d.as_string("nexus"))
>>> print(d.as_string("fasta"))
>>> print(d.as_string("phylip"))

It is also possible to get an ASCII text plot of a tree object:

>>> import dendropy
>>> t = dendropy.Tree.get_from_path('pythonidae.mle.nex', 'nexus')
>>> print(t.as_ascii_plot())
                          /---------- Python regius
                          |
   /----------------------+      /--- Python sebae
   |                      |   /--+
   |                      \---+  \--- Python molurus
   |                          |
   |                          \------ Python curtus
   |
   |                             /--- Morelia bredli
   |            /----------------+
   |            |                \--- Morelia spilota
   |            |
   |            |      /------------- Morelia tracyae
   |         /--+      |
   |         |  |   /--+      /------ Morelia clastolepis
   |         |  |   |  |  /---+
   |         |  |   |  |  |   |  /--- Morelia kinghorni
   |         |  |   |  \--+   \--+
   |         |  \---+     |      \--- Morelia nauta
   |         |      |     |
   |         |      |     \---------- Morelia amethistina
   |      /--+      |
   |      |  |      \---------------- Morelia oenpelliensis
   |      |  |
/--+      |  |            /---------- Antaresia maculosa
|  |      |  |         /--+
|  |      |  |         |  |   /------ Antaresia perthensis
|  |      |  |         |  \---+
|  |      |  |         |      |  /--- Antaresia stimsoni
|  |      |  \---------+      \--+
|  |      |            |         \--- Antaresia childreni
|  |      |            |
|  |      |            |      /------ Morelia carinata
|  |      |            \------+
|  |      |                   |  /--- Morelia viridisN
|  |  /---+                   \--+
|  |  |   |                      \--- Morelia viridisS
|  |  |   |
|  |  |   |                      /--- Apodora papuana
|  |  |   |                   /--+
|  |  |   |                   |  \--- Liasis olivaceus
|  |  |   |               /---+
|  |  |   |               |   |  /--- Liasis fuscus
|  |  |   |               |   \--+
+  |  |   |            /--+      \--- Liasis mackloti
|  |  |   |            |  |
|  \--+   |            |  |      /--- Antaresia melanocephalus
|     |   |         /--+  \------+
|     |   |         |  |         \--- Antaresia ramsayi
|     |   |         |  |
|     |   \---------+  |         /--- Liasis albertisii
|     |             |  \---------+
|     |             |            \--- Bothrochilus boa
|     |             |
|     |             \---------------- Morelia boeleni
|     |
|     |                          /--- Python timoriensis
|     \--------------------------+
|                                \--- Python reticulatus
|
|                                /--- Xenopeltis unicolor
|--------------------------------+
|                                \--- Candola aspera
|
\------------------------------------ Loxocemus bicolor