Commit bca90f1e authored by Bryan  BRANCOTTE's avatar Bryan BRANCOTTE

remove wrapped biosample field in favor of direct biosample field access

parent f0474e68
......@@ -15,11 +15,6 @@ if __name__ == '__main__':
output_header = [
"Strain", "BioSample", "Assembly",
"Date",
"Location",
"Source",
"Origin",
"Host",
"Sequencing",
"Assembling",
"Coverage",
......@@ -31,11 +26,6 @@ if __name__ == '__main__':
strain_output_pos = output_header.index('Strain')
bio_sample_output_pos = output_header.index('BioSample')
assembly_output_pos = output_header.index('Assembly')
host_output_pos = output_header.index('Host')
location_output_pos = output_header.index('Location')
date_output_pos = output_header.index('Date')
source_output_pos = output_header.index('Source')
origin_output_pos = output_header.index('Origin')
sequencing_output_pos = output_header.index('Sequencing')
coverage_output_pos = output_header.index('Coverage')
assembling_output_pos = output_header.index('Assembling')
......@@ -61,11 +51,6 @@ if __name__ == '__main__':
for relative_pos, biosample_attr in enumerate(output_header[selected_attributes_start_at:]):
results[relative_pos + selected_attributes_start_at] = strain.bio_sample_sample_data_attr(
biosample_attr)
# results[host_output_pos] = strain.host
# results[location_output_pos] = strain.location
# results[date_output_pos] = strain.isolation_date
# results[source_output_pos] = strain.source
# results[origin_output_pos] = strain.origin
results[sequencing_output_pos] = strain.sequencing
results[coverage_output_pos] = strain.coverage
results[assembling_output_pos] = strain.assembling
......
......@@ -62,11 +62,6 @@ class StrainWrapped:
# return bio_sample_record(self.bio_sample)["DocumentSummarySet"]["DocumentSummary"][0]["Date"]
return self.bio_sample_sample_data_attr("collection_date")
@property
def origin(self):
# prélévement sanguin ? bucale ? ...
return self._bio_sample_sample_data_attr("isolation_source")
@property
def coverage(self):
try:
......
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