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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,33 +1,44 @@ | ||
| """ | ||
| Basic tests to check that the core functionalities are at least running. | ||
| Complex validation test. | ||
| """ | ||
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| import matplotlib | ||
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| matplotlib.use("Agg") | ||
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| import os | ||
| from collections import OrderedDict | ||
| from bandwitch import (ClonesObservations) | ||
| from Bio import SeqIO, Restriction | ||
| import pytest | ||
| from bandwitch import ClonesObservations | ||
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| def test_complex_validation(tmpdir): | ||
| data_dir = os.path.join('tests', 'test_data', 'complex_validation_data') | ||
| records_path = os.path.join(data_dir, 'constructs_sequences.zip') | ||
| constructs_map_path = os.path.join(data_dir, 'constructs_map.xls') | ||
| digestions_map_path = os.path.join(data_dir, 'digestions_map.xls') | ||
| aati_zip_path = os.path.join(data_dir, 'digestion_results.zip') | ||
| data_dir = os.path.join("tests", "test_data", "complex_validation_data") | ||
| records_path = os.path.join(data_dir, "constructs_sequences.zip") | ||
| constructs_map_path = os.path.join(data_dir, "constructs_map.xls") | ||
| digestions_map_path = os.path.join(data_dir, "digestions_map.xls") | ||
| aati_zip_path = os.path.join(data_dir, "digestion_results.zip") | ||
| clones = ClonesObservations.from_files( | ||
| records_path=records_path, | ||
| constructs_map_path=constructs_map_path, | ||
| aati_zip_path=aati_zip_path, | ||
| digestions_map_path=digestions_map_path | ||
| digestions_map_path=digestions_map_path, | ||
| ) | ||
| validations = clones.validate_all_clones(relative_tolerance=0.03) | ||
| clones.plot_validations_plate_map(validations) | ||
| clones.plot_all_validations_patterns(validations) | ||
| partial_digest_analysis = clones.partial_digests_analysis() | ||
| clones.plot_partial_digests_analysis(partial_digest_analysis) | ||
| summary_table = clones.validations_summary_table( | ||
| validations, target=os.path.join(str(tmpdir), 'table.csv')) | ||
| validations, target=os.path.join(str(tmpdir), "table.csv") | ||
| ) | ||
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| # Chosen digestions, for reference: | ||
| # C00 EcoRI,PvuI | ||
| # C01 EcoRI,PvuI | ||
| # C02 EcoRI,PvuI | ||
| # C03 EcoRI,PvuI | ||
| # C04 EcoRI,PvuI | ||
| # C05 EcoRI,PvuI | ||
| # C06 AseI,EcoRI | ||
| # C07 AseI,EcoRI | ||
| # C08 AseI,EcoRI |