mapping_df.to_csv(mapping_out, sep='\t')
# FEEDBACK
print("All your files have been written to the directory", output_dir)
print("Simply open the file index.html in a browser that has")
print("an internet connection to view the interactive phylogram.")
plugin = Plugin(
name='phylogram',
version=__version__,
website='https://github.com/ConstantinoSchillebeeckx/q2-phylogram',
package='q2_phylogram'
)
plugin.visualizers.register_function(
function=make_d3_phylogram,
inputs={'tree': Phylogeny},
parameters={'otu_metadata': qiime.plugin.Metadata},
name='Visualize phylogram',
description='Generate interactive visualization of your phylogenetic tree.'
)
def tree_to_biopython_tree(data_dir):
with open(os.path.join(data_dir, 'tree.nwk'), 'r') as fh:
return Bio.Phylo.read(fh, 'newick')
plugin.register_data_layout_reader('tree', 1, Bio.Phylo.Newick.Tree, tree_to_biopython_tree)
ROM_data_layout.register_file('game.gba', GBAFormat)
plugin.register_type_to_data_layout(Game[GBA], 'rom', 1)
def ROM_data_layout_to_buffered_reader(data_dir):
return open(os.path.join(data_dir, 'game.gba'), 'rb')
def buffered_reader_to_ROM_data_layout(view, data_dir):
with open(os.path.join(data_dir, 'game.gba'), 'wb') as fh:
fh.write(view.read())
plugin.register_data_layout(ROM_data_layout)
plugin.register_data_layout_reader('rom', 1, io.BufferedReader,
ROM_data_layout_to_buffered_reader)
plugin.register_data_layout_writer('rom', 1, io.BufferedReader,
buffered_reader_to_ROM_data_layout)
def play(output_dir : str, rom : io.BufferedReader) -> None:
with open(os.path.join(output_dir, 'gameloader.js'), 'wb') as fh:
fh.write(b"onDataLoad('" + base64.b64encode(rom.read()) + b"');")
copytree(os.path.join(os.path.dirname(__file__), 'assets'),
os.path.join(output_dir))
# From http://stackoverflow.com/a/12514470/579416
def copytree(src, dst, symlinks=False, ignore=None):
os.makedirs(dat_dir)
with open(os.path.join(output_dir,'index.html'), 'w') as fout:
fout.write(index)
tree_out = os.path.join(dat_dir,'tree.tre')
with open(tree_out, 'w') as fout:
fout.write("d3.jsonp.readNewick('%s');" %str(tree).strip()) # add callback around Newick string for use in cross-origin setting
plugin = Plugin(
name='phylogram',
version=__version__,
website='https://github.com/ConstantinoSchillebeeckx/q2-phylogram',
package='q2_phylogram'
)
plugin.visualizers.register_function(
function=make_d3_phylogram,
inputs={'tree': Phylogeny},
parameters={'otu_metadata': qiime.plugin.Metadata},
name='Visualize phylogram',
description='Generate interactive visualization of your phylogenetic tree.'
)
def tree_to_skbio_tree(data_dir):
with open(os.path.join(data_dir, 'tree.nwk'), 'r') as fh:
return read(fh, format="newick", into=TreeNode)
plugin.register_data_layout_reader('tree', 1, skbio.TreeNode, tree_to_skbio_tree)
