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src/p/y/pycogent-HEAD/tests/test_parse/test_genbank.py   pycogent(Download)
#!/usr/bin/env python
"""Unit tests for the GenBank database parsers.
"""
from cogent.parse.genbank import parse_locus, parse_single_line, \
    indent_splitter, parse_sequence, block_consolidator, parse_organism, \
                     EYSSMGSALFFLGEYANMILMSGLCTSLSPGGWPPILDLPISKRIPGSIWFSIKVILF
                     LFLYIWVRAAFPRYRYDQLMGLGRKVFLPLSLARVVAVSGVLVTFQWLP"""
        result = parse_feature(example_feature.split('\n'))
        self.assertEqual(result['type'], 'CDS')
        self.assertEqual(result['raw_location'], \
 
        short_feature = ['D-loop          15418..16866']
        result = parse_feature(short_feature)
        self.assertEqual(result['type'], 'D-loop')
        self.assertEqual(result['raw_location'], ['15418..16866'])
                     /product="tRNA-Ile"
                     /anticodon=(pos:1203..1205,aa:Ile)"""
        result = parse_feature(bad_feature.split('\n'))
        self.assertEqual(result['note'], \
            ['codon recognized: AUC; Cove score = 16.56'])
     /citation=[6]
     /product="H-strand"'''
        result = parse_feature(bad_feature.split('\n'))
        self.assertEqual(result['partial'], [''])
 

src/c/o/cogent-1.5.3/tests/test_parse/test_genbank.py   cogent(Download)
#!/usr/bin/env python
"""Unit tests for the GenBank database parsers.
"""
from cogent.parse.genbank import parse_locus, parse_single_line, \
    indent_splitter, parse_sequence, block_consolidator, parse_organism, \
                     EYSSMGSALFFLGEYANMILMSGLCTSLSPGGWPPILDLPISKRIPGSIWFSIKVILF
                     LFLYIWVRAAFPRYRYDQLMGLGRKVFLPLSLARVVAVSGVLVTFQWLP"""
        result = parse_feature(example_feature.split('\n'))
        self.assertEqual(result['type'], 'CDS')
        self.assertEqual(result['raw_location'], \
 
        short_feature = ['D-loop          15418..16866']
        result = parse_feature(short_feature)
        self.assertEqual(result['type'], 'D-loop')
        self.assertEqual(result['raw_location'], ['15418..16866'])
                     /product="tRNA-Ile"
                     /anticodon=(pos:1203..1205,aa:Ile)"""
        result = parse_feature(bad_feature.split('\n'))
        self.assertEqual(result['note'], \
            ['codon recognized: AUC; Cove score = 16.56'])
     /citation=[6]
     /product="H-strand"'''
        result = parse_feature(bad_feature.split('\n'))
        self.assertEqual(result['partial'], [''])