Metadata-Version: 1.1
Name: cytopast
Version: 0.5.1
Summary: Visualisation of PASTML trees.
Home-page: https://github.com/evolbioinfo/cytopast
Author: Anna Zhukova
Author-email: anna.zhukova@pasteur.fr
License: UNKNOWN
Description-Content-Type: UNKNOWN
Description: # cytopast
        
        __cytopast__ is a python3 module that creates zoomable HTML visualisation of phylogenetic trees with annotated nodes.
        
        Given a tree and its node annotations, it can either visualise them as-is, 
        or apply [PASTML](https://github.com/saishikawa/PASTML) to infer ancestral states based on the tip states. 
        
        The states are visualised as different colours of the tree nodes using [Cytoscape.js](http://js.cytoscape.org/)
        
        ## Installation
        ```bash
        pip3 install cytopast
        ```
        
        ## Basic usage in python3
        ```python
        from cytopast.pastml_analyser import pastml_pipeline
        
        # Path to the table containing tip/node annotations, in csv or tab format
        data = "/path/to/the/table/eg/data.csv"
        
        # Path to the tree in newick format
        tree = "/path/to/the/tree/eg/tree.nwk"
        
        # Columns present in the annotation table,
        # for which we want to reconstruct ancestral states
        columns = ['Location', 'Resistant_or_not']
        
        # Columns present in the annotation table,
        # for which we want to copy existing annotations from the annotation table,
        # without inferring ancestral states
        copy_columns = ['Sex']
        
        # Path to the output compressed map visualisation
        html_compressed = "/path/to/the/future/map/eg/map.html"
        
        # Path to the output tree visualisation
        html = "/path/to/the/future/tree/visualisation/eg/tree.html"
        
        pastml_pipeline(data=data, data_sep=',', columns=columns, name_column='Location',
                        tree=tree,
                        html_compressed=html_compressed, html=html, 
                        verbose=True)
        ```
        
        ## Basic usage from console
        ```bash
        cytopast --tree /path/to/the/tree.nwk --data /path/to/the/annotation/data.txt --data_sep , \
        --html /path/to/the/output/visualisation/of/the/tree.html \
        --html_compressed /path/to/the/output/visualisation/of/the/compressed/map.html \
        --columns Location Resistant_or_not --name_column Location --verbose
        ```
        
        ## Basic usage with [docker](https://hub.docker.com/)
        ```bash
        docker run -v /path/to/the/folder/containing/the_tree_and_annotations/:/data:rw -t evolbioinfo/pastml \
        --tree /data/tree.nwk --data /data/data.txt --data_sep , \
        --html /data/tree.html --html_compressed /data/map.html \
        --columns Location Resistant_or_not --name_column Location --verbose
        ```
        
        ## Options
        
        ```
        usage: cytopast [-h] -d DATA [-s DATA_SEP] [-i ID_INDEX]
                        [-c [COLUMNS [COLUMNS ...]]]
                        [--copy_columns [COPY_COLUMNS [COPY_COLUMNS ...]]] -t TREE
                        [-m MODEL] [--work_dir WORK_DIR] [--cache] [-n NAME_COLUMN]
                        [-a] [-o OUT_DATA] [-p HTML_COMPRESSED] [-l HTML] [-v]
        
        Visualisation of annotated phylogenetic trees (as html maps).
        
        optional arguments:
          -h, --help            show this help message and exit
          -v, --verbose         print information on the progress of the analysis
        
        annotation-related arguments:
          -d DATA, --data DATA  the annotation file in tab/csv format with the first
                                row containing the column names.
          -s DATA_SEP, --data_sep DATA_SEP
                                the column separator for the data table. By default is
                                set to tab, i.e. for tab file. Set it to ',' if your
                                file is csv.
          -i ID_INDEX, --id_index ID_INDEX
                                the index of the column in the data table that
                                contains the tree tip names, indices start from zero
                                (by default is set to 0).
          -c [COLUMNS [COLUMNS ...]], --columns [COLUMNS [COLUMNS ...]]
                                names of the data table columns that contain states to
                                be analysed with PASTML. If neither columns nor
                                copy_columns are specified, then all columns will be
                                considered for PASTMl analysis.
          --copy_columns [COPY_COLUMNS [COPY_COLUMNS ...]]
                                names of the data table columns that contain states to
                                be copied as-is, without applying PASTML (the missing
                                states will stay unresolved).
        
        tree-related arguments:
          -t TREE, --tree TREE  the input tree in newick format.
        
        ancestral-state inference-related arguments:
          -m MODEL, --model MODEL
                                the evolutionary model to be used by PASTML (can be JC
                                or F81).
          --work_dir WORK_DIR   the working dir for PASTML to put intermediate files
                                into (if not specified a temporary dir will be
                                created).
          --cache               if set, the results of previous PASTML runs on this
                                data will be reused when possible
        
        visualisation-related arguments:
          -n NAME_COLUMN, --name_column NAME_COLUMN
                                name of the data table column to be used for node
                                names in the compressed map visualisation(must be one
                                of those specified in columns or copy_columns if they
                                are specified).If the data table contains only one
                                column it will be used by default.
          -a, --all             Keep all the nodes in the compressed map
                                visualisation, even the minor ones.
        
        output-related arguments:
          -o OUT_DATA, --out_data OUT_DATA
                                the output annotation file with the states inferred by
                                PASTML.
          -p HTML_COMPRESSED, --html_compressed HTML_COMPRESSED
                                the output summary map visualisation file (html).
          -l HTML, --html HTML  the output tree visualisation file (html).
        ```
Keywords: PASTML,visualisation,phylogeny
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Libraries :: Python Modules
