def __init__(self, cleaned_data):
# skip sequences with accession numbers and building GenBank Fasta file
self.sequences_skipped = []
self.cleaned_data = cleaned_data
self.translations = None
self.degen_translations = None
self.clean_translations()
self.errors = []
self.seq_objs = []
self.minimum_number_of_genes = cleaned_data['number_genes']
self.aminoacids = cleaned_data['aminoacids']
try:
self.codon_positions = clean_positions(cleaned_data['positions'])
except exceptions.InadequateCodonPositions as e:
self.codon_positions = None
self.errors = [e]
self.file_format = cleaned_data['file_format']
self.partition_by_positions = cleaned_data['partition_by_positions']
self.voucher_codes = get_voucher_codes(cleaned_data)
self.gene_codes = get_gene_codes(cleaned_data)
self.gene_codes_and_lengths = None
self.taxon_names = cleaned_data['taxon_names']
self.voucher_codes_metadata = dict()
self.gene_codes_metadata = self.get_gene_codes_metadata()
self.warnings = []
self.outgroup = cleaned_data['outgroup']
self.dataset_file = None
self.aa_dataset_file = None
self.charset_block = None
self.dataset_str = self.create_dataset()
def __init__(self, cleaned_data):
# skip sequences with accession numbers and building GenBank Fasta file
self.sequences_skipped = []
self.cleaned_data = cleaned_data
self.translations = None
self.degen_translations = None
self.clean_translations()
self.errors = []
self.seq_objs = []
self.minimum_number_of_genes = cleaned_data['number_genes']
self.aminoacids = cleaned_data['aminoacids']
try:
self.codon_positions = clean_positions(cleaned_data['positions'])
except exceptions.InadequateCodonPositions as e:
self.codon_positions = None
self.errors = [e]
self.file_format = cleaned_data['file_format']
self.partition_by_positions = cleaned_data['partition_by_positions']
self.voucher_codes = get_voucher_codes(cleaned_data)
self.gene_codes = get_gene_codes(cleaned_data)
self.gene_codes_and_lengths = None
self.taxon_names = cleaned_data['taxon_names']
self.voucher_codes_metadata = dict()
self.gene_codes_metadata = self.get_gene_codes_metadata()
self.warnings = []
self.outgroup = cleaned_data['outgroup']
self.dataset_file = None
self.aa_dataset_file = None
self.charset_block = None
self.dataset_str = self.create_dataset()
def __init__(self, cleaned_data):
self.cleaned_data = cleaned_data
self.translations = None
self.degen_translations = None
self.clean_translations()
self.errors = []
self.seq_objs = []
self.minimum_number_of_genes = cleaned_data["number_genes"]
self.aminoacids = cleaned_data["aminoacids"]
try:
self.codon_positions = clean_positions(cleaned_data["positions"])
except exceptions.InadequateCodonPositions as e:
self.codon_positions = None
self.errors = [e]
self.file_format = cleaned_data["file_format"]
self.partition_by_positions = cleaned_data["partition_by_positions"]
self.voucher_codes = get_voucher_codes(cleaned_data)
self.gene_codes = get_gene_codes(cleaned_data)
self.gene_codes_and_lengths = None
self.taxon_names = cleaned_data["taxon_names"]
self.voucher_codes_metadata = dict()
self.gene_codes_metadata = self.get_gene_codes_metadata()
self.warnings = []
self.outgroup = cleaned_data["outgroup"]
self.dataset_file = None
self.aa_dataset_file = None
self.charset_block = None
self.dataset_str = self.create_dataset()
def test_clean_positions(self):
self.assertEqual(clean_positions(["ALL", "1st"]), ["ALL"], 'Has "ALL" in list.')
self.assertEqual(clean_positions(["ALL", "2nd"]), ["ALL"], 'Has "ALL" in list.')
self.assertEqual(clean_positions(["ALL", "3rd"]), ["ALL"], 'Has "ALL" in list.')
self.assertEqual(clean_positions(["ALL", "1st", "2nd"]), ["ALL"], 'Has "ALL" in list.')
self.assertEqual(clean_positions(["ALL", "1st", "3rd"]), ["ALL"], 'Has "ALL" in list.')
self.assertEqual(clean_positions(["ALL", "2nd", "3rd"]), ["ALL"], 'Has "ALL" in list.')
self.assertEqual(clean_positions(["ALL", "1st", "2nd", "3rd"]), ["ALL"], 'Has "ALL" in list.')
self.assertEqual(clean_positions(["1st", "2nd", "3rd"]), ["ALL"], "All codon positions were required.")
self.assertEqual(clean_positions(["1st", "2nd"]), ["1st-2nd"], "Only some codon positions were required.")
self.assertRaises(exceptions.InadequateCodonPositions, clean_positions, ["1st", "3rd"])
self.assertRaises(exceptions.InadequateCodonPositions, clean_positions, ["2nd", "3rd"])
self.assertEqual(clean_positions(["1st"]), ["1st"], "All codon positions were required.")
self.assertEqual(clean_positions(["2nd"]), ["2nd"], "All codon positions were required.")
self.assertEqual(clean_positions(["3rd"]), ["3rd"], "All codon positions were required.")
def test_clean_positions(self):
self.assertEqual(clean_positions(['ALL', '1st']), ['ALL'],
'Has "ALL" in list.')
self.assertEqual(clean_positions(['ALL', '2nd']), ['ALL'],
'Has "ALL" in list.')
self.assertEqual(clean_positions(['ALL', '3rd']), ['ALL'],
'Has "ALL" in list.')
self.assertEqual(clean_positions(['ALL', '1st', '2nd']), ['ALL'],
'Has "ALL" in list.')
self.assertEqual(clean_positions(['ALL', '1st', '3rd']), ['ALL'],
'Has "ALL" in list.')
self.assertEqual(clean_positions(['ALL', '2nd', '3rd']), ['ALL'],
'Has "ALL" in list.')
self.assertEqual(clean_positions(['ALL', '1st', '2nd', '3rd']),
['ALL'], 'Has "ALL" in list.')
self.assertEqual(clean_positions(['1st', '2nd', '3rd']), ['ALL'],
'All codon positions were required.')
self.assertEqual(clean_positions(['1st', '2nd']), ['1st-2nd'],
'Only some codon positions were required.')
self.assertRaises(exceptions.InadequateCodonPositions, clean_positions,
['1st', '3rd'])
self.assertRaises(exceptions.InadequateCodonPositions, clean_positions,
['2nd', '3rd'])
self.assertEqual(clean_positions(['1st']), ['1st'],
'All codon positions were required.')
self.assertEqual(clean_positions(['2nd']), ['2nd'],
'All codon positions were required.')
self.assertEqual(clean_positions(['3rd']), ['3rd'],
'All codon positions were required.')