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Revert rna feature translate #19

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merged 3 commits into from
Mar 3, 2015
Merged

Revert rna feature translate #19

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690c8b9
dont convert 16s product
andrewjpage Mar 3, 2015
44425ab
new version
andrewjpage Mar 3, 2015
8ec2481
add in comma in exception
andrewjpage Mar 3, 2015
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2 changes: 1 addition & 1 deletion gff3toembl/convert.py
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Expand Up @@ -8,7 +8,7 @@ class Convert(object):
feature_attributes_to_ignore = {'ID': 1, 'protein_id': 1}
feature_attributes_translations = {'eC_number': 'EC_number'}
feature_attributes_to_split_on_multiple_lines = {'inference': 1, 'EC_number': 1}
feature_attributes_regex_to_change_feature_name = {'^16S ribosomal RNA': 'rRNA'}
feature_attributes_regex_to_change_feature_name = {}

feature_attributes_inference_to_dbxref = {'similar to AA sequence:UniProtKB': 'UniProtKB/Swiss-Prot', 'protein motif:Pfam': 'PFAM', 'protein motif:CLUSTERS': "CDD", 'protein motif:Cdd': "CDD", 'protein motif:TIGRFAMs': "TIGRFAM"}

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17 changes: 0 additions & 17 deletions gff3toembl/tests/EMBLWriter_test.py
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Expand Up @@ -97,22 +97,5 @@ def test_chromosome_list_conversion(self):
assert filecmp.cmp(os.path.join(data_dir, 'expected_chromosome_list.txt'), 'chromosome_list.txt', shallow=False)
os.remove('chromosome_list.embl')
os.remove('chromosome_list.txt')

def test_renaming_16s_features(self):
'''test renaming the feature type to rRNA if the product is 16S'''
emblwriter = EMBLWriter(os.path.join(data_dir,'input_16s.gff'),
'Organism',
1234,
'ABC',
'My description',
'John',
'Some title',
'Some journal',
'circular',
'PROK',
'16s.embl', None, 11, None )
emblwriter.parse_and_run()
assert filecmp.cmp(os.path.join(data_dir, 'expected_16s.embl'), '16s.embl', shallow=False)
os.remove('16s.embl')


181 changes: 0 additions & 181 deletions gff3toembl/tests/data/expected_16s.embl
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20 changes: 0 additions & 20 deletions gff3toembl/tests/data/input_16s.gff
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -7,7 +7,7 @@ def read(fname):

setup(
name='gff3toembl',
version='0.3.8',
version='0.3.9',
description='Convert a GFF3 file to EMBL format for submission',
long_description=read('README.md'),
packages = find_packages(),
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