UNDER DEVELOPMENT
Phython library to manipulate excel files from PhyloTree.org
Tested with Phyton V2.7
This library allows you to open an excel file containning the whole PhyloTree and ask questions:
import PhyloTree_lib
tree_17=PhyloTree_lib.PhyloTree("resources/PhyloTree_17.xlsx")
print("The root of the tree:")
print(tree_17.get_root())
print("")
print("From the Root to H1a1:")
print(tree_17.get_all_haplogroups_leaf_to_root("H1a1"))
print("")
print("From H1a1 to the leaves:")
print(tree_17.get_all_haplogroups_root_to_leaf("H1a1"))
print("")
print("From H1a1 to the leaves, only 1 level:")
print(tree_17.get_all_haplogroups_root_to_leaf("H1a1",1))
print("")
print("SNPs for haplogroup H1a1:")
print tree_17.get_snps_haplogroup("H1a1")Output:
The root of the tree:
mt-MRCA (RSRS)
From the Root to H1a1:
[u'mt-MRCA (RSRS)', u"L1'2'3'4'5'6", u"L2'3'4'5'6", u"L2'3'4'6", u"L3'4'6", u"L3'4", u'L3', u'N', u'R', u'R0', u'HV', u'HV1', u'HV5', u'H', u'H1', u'H1a', u'H1a1']
From H1a1 to the leaves:
['H1a1', u'H1a1a', u'H1a1a1', u'H1a1b', u'H1a1c']
From H1a1 to the leaves, only 1 level:
['H1a1', u'H1a1a', u'H1a1b', u'H1a1c']
SNPs for haplogroup H1a1:
[u'C146T', u'C182T', u'T4312C', u'T10664C', u'C10915T', u'A11914G', u'G13276A', u'G16230A', u'C152T', u'A2758G', u'C2885T', u'G7146A', u'T8468C', u'C195T', u'A247G', u'A825t', u'T8655C', u'A10688G', u'C10810T', u'G13105A', u'T13506C', u'G15301A', u'A16129G', u'T16187C', u'C16189T', u'G4104A', u'A7521G', u'T182C!', u'T3594C', u'T7256C', u'T13650C', u'T16278C', u'A769G', u'A1018G', u'C16311T', u'G8701A', u'C9540T', u'G10398A', u'C10873T', u'A15301G!', u'T12705C', u'T16223C', u'G73A', u'A11719G', u'T14766C', u'A8014t', u'C16067T', u'A13105G!', u'G2706A', u'T7028C', u'G3010A', u'A73G!', u'A16162G', u'T6365C', u'T16209C']
In the resources folder there are two excel files corresponging to PhyloTree V16 and V17. To generate one of these files, just download the PhyloTree in html format from http://www.phylotree.org/builds/mtDNA_tree_Build_17.zip, and open it with excel, then just save it with xlsx format.