mtoolbox_debug_haplogroups's People
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jeremy9959mtoolbox_debug_haplogroups's Issues
Mutation annotation style raises error when parsing csv to pickle
- is eg G263A
- must be 263 if transition; 263C if transversion
will correct it in the function in the notebook parse_phylotree_html
Mutation annotation style raises error when parsing csv to pickle (deletion)
C5899.d!
raises an error during the generation of pickle from tree csv
Assigning labels to NoLabel create issues in the tree structure
For some reason there is a bunch of NoLabel that are being converted in a bad way, eg:
phyotree csv with "NoLabel"
#bash
grep -A 4 A2an phylotree_17_190121.csv
,,,,,,,,,,,,A2an,8772
,,,,,,,,,,,,NoLabel,16189!
,,,,,,,,,,,,,A2ap,9809
,,,,,,,,,,,,A2aq,143,808,3421,6267,6374,16355
,,,,,,,,,,,A2r,6935
phyotree csv with names assigned to "NoLabel"
#bash
grep -A 4 A2an phylotree_17_190127.csv
,,,,,,,,,,,,A2an,8772
,,,,,,,,,,,,NoLabel
_16189!,16189!
,,,,,,,,,,,,,A2ap,9809
,,,,,,,,,,,,A2aq,143,808,3421,6267,6374,16355
This issue is also reported in the notebook file, together with a function that allows to get the parent nodes of a given tree.
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