def make_spreadsheet_for_ena_download(self):
sheet = Spreadsheet()
sheet.supplier, sheet.organisation, sheet.contact, sheet.technology, sheet.name, sheet.accession, sheet.size, \
sheet.limit = ('Supplier', 'Org', 'Contact', 'Illumina', 'AStudyName1', None, 1.90, '01/01/2025')
sheet.reads = [RawRead(forward_read='PAIR1', reverse_read='T', sample_name='SAMPLE1',
taxon_id='1280', library_name='LIB1', sample_accession=None),
RawRead(forward_read='Pair2.fastq.gz', reverse_read='F', sample_name='SAMPLE2',
taxon_id='1280', library_name='LIB2', sample_accession=None)]
return sheet
def load_xlsx(self):
result = Spreadsheet()
data_row = 0
header_row = 0
for i in range(10):
if self._sheet.cell(row=i + 1, column=1).value == 'Study Name':
result.name = self._sheet.cell(row=i + 1, column=2).value
if self._sheet.cell(row=i + 1, column=1).value == 'Supplier Name':
result.supplier = self._sheet.cell(row=i + 1, column=2).value
if self._sheet.cell(row=i + 1, column=1).value == 'Supplier Organisation':
result.organisation = self._sheet.cell(row=i + 1, column=2).value
if self._sheet.cell(row=i + 1, column=1).value == 'Sanger Contact Name':
result.contact = self._sheet.cell(row=i + 1, column=2).value
if self._sheet.cell(row=i + 1, column=1).value == 'Sequencing Technology':
result.technology = self._sheet.cell(row=i + 1, column=2).value
if self._sheet.cell(row=i + 1, column=1).value == 'Study Accession number':
result.accession = self.__extract_text_value_xlsx(i + 1, 2)
if self._sheet.cell(row=i + 1, column=1).value == 'Total size of files in GBytes':
result.size = float(self._sheet.cell(row=i + 1, column=2).value)
if self._sheet.cell(row=i + 1, column=1).value == 'Data to be kept until':
result.limit = self._sheet.cell(row=i + 1, column=2).value.strftime('%d/%m/%Y')
if self._sheet.cell(row=i + 1, column=1).value == 'Filename' or self._sheet.cell(row=i + 1, column=1).value == 'Run Accession':
data_row = i + 2
header_row = i + 1
break
filename_column = None
run_accession_column = None
for i in range(self._sheet.max_column):
if self._sheet.cell(row=header_row, column=i + 1).value == 'Filename':
filename_column = i +1
if self._sheet.cell(row=header_row, column=i + 1).value == 'Run Accession':
run_accession_column = i +1
if filename_column is not None:
if self._sheet.cell(row=header_row, column=i + 1).value == 'Mate File':
mate_filename_column = i + 1
if run_accession_column is not None:
if self._sheet.cell(row=header_row, column=i + 1).value == 'Double-ended Reads':
double_ended_reads_column = i + 1
if self._sheet.cell(row=header_row, column=i + 1).value == 'Sample Name':
sample_name_column = i + 1
if self._sheet.cell(row=header_row, column=i + 1).value == 'Sample Accession number':
sample_accession_column = i + 1
if self._sheet.cell(row=header_row, column=i + 1).value == 'Taxon ID':
taxon_id_column = i + 1
if self._sheet.cell(row=header_row, column=i + 1).value == 'Library Name':
library_name_column = i + 1
reads = []
for i in range(data_row, self._sheet.max_row+1):
sample_name = self.__extract_float_value_xlsx(i, sample_name_column)
library_name = self.__extract_float_value_xlsx(i, library_name_column)
if library_name is None:
library_name = sample_name
if filename_column is not None:
reads.append(RawRead(
self.__extract_text_value_xlsx(i, filename_column),
self.__extract_text_value_xlsx(i, mate_filename_column),
sample_name,
self.__extract_text_value_xlsx(i, sample_accession_column),
self.__extract_float_value_xlsx(i, taxon_id_column),
library_name))
if run_accession_column is not None:
reads.append(RawRead(
(self.__extract_text_value_xlsx(i, run_accession_column)),
self.__extract_text_value_xlsx(i, double_ended_reads_column),
sample_name,
self.__extract_text_value_xlsx(i, sample_accession_column),
self.__extract_float_value_xlsx(i, taxon_id_column),
library_name))
result.reads = reads
return result
def load_xls(self):
result = Spreadsheet()
data_row = 0
header_row = 0
for i in range(self._sheet.nrows):
if self._sheet.cell_value(i, 0) == 'Study Name':
result.name = self._sheet.cell_value(i, 1)
if self._sheet.cell_value(i, 0) == 'Supplier Name':
result.supplier = self._sheet.cell_value(i, 1)
if self._sheet.cell_value(i, 0) == 'Supplier Organisation':
result.organisation = self._sheet.cell_value(i, 1)
if self._sheet.cell_value(i, 0) == 'Sanger Contact Name':
result.contact = self._sheet.cell_value(i, 1)
if self._sheet.cell_value(i, 0) == 'Sequencing Technology':
result.technology = self._sheet.cell_value(i, 1)
if self._sheet.cell_value(i, 0) == 'Study Accession number':
result.accession = self.__extract_text_value_xls(i, 1)
if self._sheet.cell_value(i, 0) == 'Total size of files in GBytes':
result.size = self._sheet.cell_value(i, 1)
if self._sheet.cell_value(i, 0) == 'Data to be kept until':
year, month, day, hour, minute, second = xlrd.xldate_as_tuple(self._sheet.cell_value(i, 1),
self._workbook.datemode)
result.limit = "%02d/%02d/%04d" % (day, month, year)
if self._sheet.cell_value(i, 0) == 'Filename' or self._sheet.cell_value(i, 0) == 'Run Accession':
data_row = i + 1
header_row = i
break
filename_column = None
run_accession_column = None
for i in range(self._sheet.ncols):
if self._sheet.cell_value(header_row, i) == 'Filename':
filename_column = i
if self._sheet.cell_value(header_row, i) == 'Run Accession':
run_accession_column = i
if filename_column is not None:
if self._sheet.cell_value(header_row, i) == 'Mate File':
mate_filename_column = i
if run_accession_column is not None:
if self._sheet.cell_value(header_row, i) == 'Double-ended Reads':
double_ended_reads_column = i
if self._sheet.cell_value(header_row, i) == 'Sample Name':
sample_name_column = i
if self._sheet.cell_value(header_row, i) == 'Sample Accession number':
sample_accession_column = i
if self._sheet.cell_value(header_row, i) == 'Taxon ID':
taxon_id_column = i
if self._sheet.cell_value(header_row, i) == 'Library Name':
library_name_column = i
reads = []
for i in range(data_row, self._sheet.nrows):
sample_name = self.__extract_float_value_xls(i, sample_name_column)
library_name = self.__extract_float_value_xls(i, library_name_column)
if library_name is None:
library_name = sample_name
if filename_column is not None:
reads.append(RawRead(
self.__extract_text_value_xls(i, filename_column),
self.__extract_text_value_xls(i, mate_filename_column),
sample_name,
self.__extract_text_value_xls(i, sample_accession_column),
self.__extract_float_value_xls(i, taxon_id_column),
library_name))
if run_accession_column is not None:
reads.append(RawRead(
(self.__extract_text_value_xls(i, run_accession_column)),
self.__extract_text_value_xls(i, double_ended_reads_column),
sample_name,
self.__extract_text_value_xls(i, sample_accession_column),
self.__extract_float_value_xls(i, taxon_id_column),
library_name))
result.reads = reads
return result