alifedata-phyloinformatics-convert 0.14.2

alifedata-phyloinformatics-convert

alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data

• Free software: MIT license

• Documentation: https://alifedata-phyloinformatics-convert.readthedocs.io.

Built using the dendropy library.

Use it as a command line tool to convert to alife standard phylogenetics data

Usage: alifedata-phyloinformatics-convert toalifedata [OPTIONS]

  convert standard alife phylogeny data to phloinformatics format

Options:
  --input-file FILENAME           phyloinformatics data file path; default
                                  stdin
  --input-schema TEXT             phyloinformatics data format schema; options
                                  include newick, nexml, and nexus  [required]
  --output-file FILENAME          alife data file path; default stdout
  --output-format TEXT            alife data file format; default csv
  --suppress-unifurcations / --keep-unifurcations
                                  Compress sequences of nodes with single
                                  descendants
  --help                          Show this message and exit.

Use it as a command line tool to convert from alife standard phylogenetics data

Usage: alifedata-phyloinformatics-convert fromalifedata [OPTIONS]

  convert phloinformatics data to standard alife phylogeny format

Options:
  --input-file FILENAME           alife data file path; default stdin
  --input-format TEXT             alife data file format; default csv
  --output-file FILENAME          phyloinformatics data file path; default
                                  stdout
  --output-schema TEXT            phyloinformatics data format schema; options
                                  include newick, nexml, and nexus  [required]
  --suppress-unifurcations / --keep-unifurcations
                                  Compress sequences of nodes with single
                                  descendants
  --help                          Show this message and exit.

Use it as a Python module

import alifedata_phyloinformatics_convert as apc

alife_df = pd.read_csv('alifedata.csv')


# get a dendropy Tree from alife-standardized phylogeny pandas dataframe
dendropy_tree = apc.alife_dataframe_to_dendropy_tree(alife_df)

# get an alife-standardized phylogeny pandas dataframe from a dendropy Tree
reconverted_alife_df = apc.dendropy_tree_to_alife_dataframe(dendropy_tree)

# get an ete Tree from alife-standardized phylogeny pandas dataframe
ete_tree = apc.alife_dataframe_to_ete_tree(alife_df)

# get an alife-standardized phylogeny pandas dataframe from an ete Tree
reconverted_alife_df = apc.ete_tree_to_alife_dataframe(ete_tree)

# get a biopython Tree from alife-standardized phylogeny pandas dataframe
biopython_tree = apc.alife_dataframe_to_biopython_tree(alife_df)

# get an alife-standardized phylogeny pandas dataframe from a biopython Tree
reconverted_alife_df = apc.dendropy_tree_to_alife_dataframe(biopython_tree)

# get a networkx DiGraph from alife-standardized phylogeny pandas dataframe
networkx_digraph = apc.alife_dataframe_to_networkx_digraph(alife_df)

# get adjacency lists from alife-standardized phylogeny pandas dataframe
adjacency_lists = apc.alife_dataframe_to_dict_of_lists(alife_df)

Install from PyPi

pip3 install alifedata-phyloinformatics-convert

History

0.0.0 (2022-03-22)

• First release on PyPI.