###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
# #
# Copyright © 2018-2022 Institut Pasteur, Paris and CNRS. #
# #
# bioconvert is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# bioconvert is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see <http://www.gnu.org/licenses/>. #
# #
# Repository: https://github.com/bioconvert/bioconvert #
# Documentation: http://bioconvert.readthedocs.io #
###########################################################################
"""Convert :term:`XLS` format to :term:`CSV` format"""
import csv
import colorlog
from bioconvert import ConvBase
from bioconvert.core.base import ConvArg
from bioconvert.core.decorators import compressor, requires
logger = colorlog.getLogger(__name__)
[docs]class XLS2CSV(ConvBase):
"""Convert :term:`XLS` file into :term:`CSV` file
Extra arguments when using **Bioconvert** executable.
=================== ============================================
name Description
=================== ============================================
--sheet-name The name or id of the sheet to convert
--out-sep The separator used in the output file
--line-terminator The line terminator used in the output file
=================== ============================================
Methods available are based on pandas [PANDAS]_ and pyexcel [PYEXCEL]_.
"""
_default_method = "pandas"
DEFAULT_OUT_SEP = ","
DEFAULT_LINE_TERMINATOR = "\n"
def __init__(self, infile, outfile):
""".. rubric:: Constructor
:param str infile:
:param str outfile:
"""
super(XLS2CSV, self).__init__(infile, outfile)
[docs] @requires(python_libraries=["pyexcel", "pyexcel-xls"])
@compressor
def _method_pyexcel(
self, out_sep=DEFAULT_OUT_SEP, line_terminator=DEFAULT_LINE_TERMINATOR, sheet_name=0, *args, **kwargs
):
"""Do the conversion :term:`XLS` -> :term:`CSV` using pyexcel library
`pyexcel documentation <http://docs.pyexcel.org/en/latest/>`_"""
import pyexcel
with open(self.outfile, "w") as out_stream:
writer = csv.writer(out_stream, delimiter=out_sep, lineterminator=line_terminator)
first_row = True
for row in pyexcel.get_records(file_name=self.infile):
if first_row:
writer.writerow([k for k, v in row.items()])
first_row = False
writer.writerow([v for k, v in row.items()])
[docs] @requires(python_libraries=["pandas", "xlrd"])
@compressor
def _method_pandas(
self, out_sep=DEFAULT_OUT_SEP, line_terminator=DEFAULT_LINE_TERMINATOR, sheet_name=0, *args, **kwargs
):
"""Do the conversion :term:`XLSX` -> :term:`CSV` using Pandas library.
`pandas documentation <https://pandas.pydata.org/docs/>`_"""
import pandas as pd
df = pd.read_excel(self.infile, sheet_name=sheet_name)
df.to_csv(
self.outfile,
sep=out_sep,
lineterminator=line_terminator,
index=False,
header="infer",
)
@classmethod
def get_additional_arguments(cls):
yield ConvArg(
names=[
"--sheet-name",
],
default=0,
help="The name or id of the sheet to convert",
)
yield ConvArg(
names=[
"--out-sep",
],
default=cls.DEFAULT_OUT_SEP,
help="The separator used in the output file",
)
yield ConvArg(
names=[
"--line-terminator",
],
default=cls.DEFAULT_LINE_TERMINATOR,
help="The line terminator used in the output file",
)