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allow .ent & .ent.gz file extensions #82

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Apr 7, 2021
Merged

allow .ent & .ent.gz file extensions #82

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2 changes: 1 addition & 1 deletion biopandas/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,5 +24,5 @@
# 'X.Y.dev0' is the canonical version of 'X.Y.dev'
#

__version__ = '0.2.8'
__version__ = '0.2.9dev'
__author__ = "Sebastian Raschka <mail@sebastianraschka.com>"
8 changes: 5 additions & 3 deletions biopandas/pdb/pandas_pdb.py
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Expand Up @@ -263,14 +263,16 @@ def _init_get_dict():
def _read_pdb(path):
"""Read PDB file from local drive."""
r_mode = 'r'
if path.endswith('.pdb'):
if path.endswith(('.pdb', '.ent')):
openf = open
elif path.endswith('pdb.gz'):
elif path.endswith(('pdb.gz', '.ent.gz')):
r_mode = 'rb'
openf = gzip.open
else:
allowed_formats = ", ".join(('.pdb', '.pdb.gz', '.ent', '.ent.gz'))
raise ValueError(
'Wrong file format; allowed file formats are .pdb and .pdb.gz.'
('Wrong file format; allowed file formats are %s'
% allowed_formats)
)

with openf(path, r_mode) as f:
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4 changes: 2 additions & 2 deletions biopandas/pdb/tests/test_read_pdb.py
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Expand Up @@ -61,8 +61,8 @@ def test__read_pdb_raises():
"""Test private _read_pdb:
Test if ValueError is raised for wrong file formats."""

expect = ('Wrong file format; allowed file formats'
' are .pdb and .pdb.gz.')
expect = ('Wrong file format; allowed file formats are '
'.pdb, .pdb.gz, .ent, .ent.gz')

def run_code_1():
PandasPdb()._read_pdb("protein.mol2")
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19 changes: 19 additions & 0 deletions docs/CHANGELOG.md
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Expand Up @@ -4,6 +4,25 @@ The CHANGELOG for the current development version is available at
[https://github.com/rasbt/biopandas/blob/master/docs/sources/CHANGELOG.md](https://github.com/rasbt/biopandas/blob/master/docs/sources/CHANGELOG.md).


### 0.2.9 (TBD)

##### Downloads

- -
- -

##### New Features

- -

##### Changes

- Now also allow `.ent` and `.ent.gz` file endings for PDB files. (via PR [82](https://github.com/rasbt/biopandas/pull/82/files)

##### Bug Fixes

- -

### 0.2.8 (03-30-2021)

##### Downloads
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