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def test_add_book1(self):
"""
test this scenario: book3 = book1 + book2
"""
b1 = pyexcel.get_book(file_name=self.testfile)
b2 = pyexcel.get_book(file_name=self.testfile2)
b3 = b1 + b2
content = b3.dict
sheet_names = content.keys()
assert len(sheet_names) == 6
for name in sheet_names:
if "Sheet3" in name:
assert content[name] == self.content["Sheet3"]
elif "Sheet2" in name:
assert content[name] == self.content["Sheet2"]
elif "Sheet1" in name:
assert content[name] == self.content["Sheet1"]
def test_get_book_auto_detect_int(self):
book = pe.get_book(file_name=self.test_file, library="pyexcel-ods")
expected = dedent(
"""
pyexcel_sheet1:
+---+---+-----+
| 1 | 2 | 3.1 |
+---+---+-----+"""
).strip()
eq_(str(book), expected)
def test_load_a_single_sheet(self):
b1 = pyexcel.get_book(file_name=self.testfile, sheet_name="Sheet1")
assert len(b1.sheet_names()) == 1
assert b1["Sheet1"].to_array() == self.content["Sheet1"]
def test_get_book_auto_detect_int_false(self):
book = pe.get_book(
file_name=self.test_file,
auto_detect_int=False,
library="pyexcel-ods",
)
expected = dedent(
"""
pyexcel_sheet1:
+-----+-----+-----+
| 1.0 | 2.0 | 3.1 |
+-----+-----+-----+"""
).strip()
eq_(str(book), expected)
def test_get_book_auto_detect_int(self):
book = pe.get_book(file_name=self.test_file)
expected = dedent(
"""
test_auto_detect_init.csv:
+---+---+-----+
| 1 | 2 | 3.1 |
+---+---+-----+"""
).strip()
self.assertEqual(str(book), expected)
def add_excel_file_to_bindings(excel_filepath: str, sheet_name: str) -> None:
"""
This function reads the excel file and add the pyexcel object to the bindings
:return: None
"""
try:
records = pyexcel.get_book(file_name=excel_filepath)
if not sheet_name:
bindings["excel_sheet"] = records[0]
else:
bindings["excel_sheet"] = records[sheet_name]
except IOError:
raise IOError('Excel File cannot be found or opened')
def sheet_file( sheet_file, verbose_level=2):
sheets = pe.get_book(file_name=sheet_file)
print_pref = "[sheet_file]:"
param_values = {}
configs = {}
metadata = {}
for sheet_idx, sheet in enumerate(sheets):
try:
param_values_tmp, configs_tmp, metadata_ = spread_sheet(sheet, verbose_level)
metadata.update(metadata_)
except AssertionError as e:
raise AssertionError( print_pref + "failed to read sheet \"" + str(sheet.name) + "\":" + str(e))
# merge with existing data, conflicting data not allowed:
if len(set(param_values_tmp.keys()).intersection(param_values.keys())) > 0:
raise AssertionError(print_pref + "E: conflicting parameter values, did you specify parameters muliple time?")
elif len(set(configs_tmp.keys()).intersection(configs.keys())) > 0:
if len(self.arguments) > 0:
fn = search_image_for_language(self.arguments[0], env)
relfn, excel_file = env.relfn2path(fn)
env.note_dependency(relfn)
if self.options:
width = self.options.get('width', 600)
height = self.options.get('height')
book = pyexcel.get_book(file_name=excel_file)
else:
content = '\n'.join(self.content)
if '---pyexcel' in content:
multiple_sheets = True
else:
multiple_sheets = False
book = pyexcel.get_book(file_content='\n'.join(self.content),
multiple_sheets=multiple_sheets,
lineterminator='\n',
file_type='csv')
html = self.render_html(book, width, height)
return [docutils.nodes.raw('', html,
format='html')]
from __future__ import print_function
import sys
import pyexcel as pe
path_book = pe.get_book(file_name=sys.argv[1])
benign_book = pe.get_book(file_name=sys.argv[2])
bfh = open('homsy.benign.vcf', 'w')
pfh = open('homsy.pathogenic.vcf', 'w')
header = """##fileformat=VCFv4.1
##source=pathoscore
##reference=GRCh37
#CHROM POS ID REF ALT QUAL FILTER INFO"""
print(header, file=bfh)
print(header, file=pfh)
sheet = path_book['Database S2']
for i, record in enumerate(sheet):
if i == 0:
continue