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.. jupyter-execute::
:hide-code:
import set_working_directory
Loading tabular data
--------------------
How to load data from a tsv file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
We can load a file containing tab seperated values with the ``load_tabular`` app, providing it with the appropriate separator, ``sep="\t"``.
.. jupyter-execute::
:raises:
from cogent3 import get_app
load_tsv_app = get_app("load_tabular", sep="\t")
tsv_data = load_tsv_app("data/stats.tsv")
tsv_data
How to load data from a csv file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
We can load a file containing comma seperated values with the ``load_tabular`` app, providing it with the seperator, ``sep=","``.
In the above example, ``data`` is a ``cogent3.util.Table`` object, if we write it to disk in csv format, we can re-use it for this example too.
.. jupyter-execute::
:hide-code:
from tempfile import NamedTemporaryFile
tmpdir = NamedTemporaryFile(dir=".")
path_to_csv_file = tmpdir.name
.. tip:: If you are executing this code on your machine, replace ``path_to_csv_file`` with the path containing your csv file!
.. jupyter-execute::
:raises:
from cogent3 import get_app
tsv_data.write(path_to_csv_file, sep=",")
load_csv_app = get_app("load_tabular", sep=",")
csv_data = load_csv_app(path_to_csv_file)
csv_data
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