Merge e2b15e7 into 04042d5

.travis.yml

@@ -1,27 +1,25 @@
-# Config file for automatic testing at travis-ci.org
-# This file will be regenerated if you run travis_pypi_setup.py
-
-language: python
-python: 3.6
-
-env:
-  - TOXENV=py36
-
-# command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -U tox
-
-# command to run tests, e.g. python setup.py test
-script: tox -e ${TOXENV}
-
-# After you create the Github repo and add it to Travis, run the
-# travis_pypi_setup.py script to finish PyPI deployment setup
+# This file was autogenerated and will overwrite each time you run travis_pypi_setup.py
 deploy:
-  provider: pypi
+  true:
+    condition: $TOXENV == py36
+    repo: nmdp-bioinformatics/pyhml
+    tags: true
   distributions: sdist bdist_wheel
-  user: mhalagan
   password:
-    secure: PLEASE_REPLACE_ME
-  on:
-    tags: true
-    repo: nmdp-bioinformatics/pyhml
-    condition: $TOXENV == py36
+    secure: 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
+  provider: pypi
+  user: mhalagan
+env:
+- TOXENV=py36
+install: pip install -U tox
+before_script:
+  - pip install -r requirements.txt
+  - pip install python-coveralls coveralls
+language: python
+python: 3.6
+script:
+  - tox -e ${TOXENV}
+  - coverage run -m unittest discover -v tests
+  - coverage report -m
+after_success:
+  - coveralls

HISTORY.rst

@@ -2,6 +2,12 @@
 History
 =======
 
+0.0.5 (2017-04-16)
+------------------
+
+* Improved documentation
+* Fixed issues with parsing HML files with NMDP-CORRECTION
+
 0.0.4 (2017-04-15)
 ------------------
 

README.rst

@@ -6,8 +6,11 @@ pyHML
 .. image:: https://img.shields.io/pypi/v/pyhml.svg
         :target: https://pypi.python.org/pypi/pyhml
 
-.. image:: https://img.shields.io/travis/nmdp-bioinformatics/pyhml.svg
-        :target: https://travis-ci.org/nmdp-bioinformatics/pyhml
+.. image:: https://img.shields.io/travis/nmdp-bioinformatics/pyHML.svg
+        :target: https://travis-ci.org/nmdp-bioinformatics/pyHML
+
+.. image:: https://coveralls.io/repos/github/nmdp-bioinformatics/pyHML/badge.svg?branch=master
+		:target: https://coveralls.io/github/nmdp-bioinformatics/pyHML?branch=master
 
 .. image:: https://readthedocs.org/projects/pyhml/badge/?version=latest
         :target: https://pyhml.readthedocs.io/en/latest/?badge=latest
@@ -39,7 +42,7 @@ Features
     hml.tobiotype(outdir, dtype='fasta', by='subject')
 
     # Print out the full HML file in IMGT dat file format
-    hml.tobiotype(outdir, dtype='imgt', by='hml')
+    hml.tobiotype(outdir, dtype='imgt', by='file')
 
     # Get pandas DF from HML object
     pandasdf = hml.toPandas()

pyhml/pyhml.py

@@ -95,7 +95,6 @@ def parse(self, hml_file: str) -> HML:
         Parses an HML file into a python object.
 
             >>> hml = hmlparser.parse(hml_file)
-            >>> hml_df = hml.toPandas()
 
         :param hml_file: A valid HML file
         :type: str
@@ -160,7 +159,7 @@ def parse(self, hml_file: str) -> HML:
                                               type=hap['@type'])
                             haploids.append(haploid)
                     gls = [gl.strip() for gl in assignment['hmlns:glstring']
-                           if re.search("\*\d", gl)]
+                           if gl and re.search("\*\d", gl)]
                     allele_assignment = AlleleAssignment(allele_db=allele_db,
                                                          allele_version=db,
                                                          date=type_date,
@@ -299,6 +298,8 @@ def _unzip_clean(self, hmlfile):
         """
         gunzip(hmlfile)
         hml_unzipped = ".".join(hmlfile.split(".")[0:len(hmlfile.split("."))-1])
+        cmd = "perl -p -i -e 's/<\?X-NMDP-CORRECTION TRUE\?><\?X-NMDP-NOREPORTS\?>//g' " + hml_unzipped
+        os.system(cmd)
         cmd4 = "perl -p -i -e 's/<\?xml.+\?>//g' " + hml_unzipped
         os.system(cmd4)
         cmd1 = "perl -p -i -e 's/\?//g' " + hml_unzipped

pyhml/util.py

@@ -133,7 +133,6 @@ def _deserialize_list(data, boxed_type):
             for sub_data in data]
 
 
-
 def _deserialize_dict(data, boxed_type):
     """
     Deserializes a dict and its elements.

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.4
+current_version = 0.0.5
 commit = True
 tag = True
 

setup.py

@@ -33,7 +33,7 @@
     history = history_file.read()
 
 requirements = [
-    'biopython==1.70',
+    'biopython==1.71',
     'pandas==0.20.3',
     'numpy==1.14.2',
     'six==1.11.0',
@@ -50,7 +50,7 @@
 
 setup(
     name='pyhml',
-    version='0.0.4',
+    version='0.0.5',
     description="Python HML parser",
     long_description=readme + '\n\n' + history,
     author="Mike Halagan",

tests/test_pyhml.py

@@ -36,9 +36,12 @@
 import sys
 import unittest
 
+from pyhml.models.sample import Sample
+from pyhml.models.typing import Typing
 from pyhml.pyhml import HmlParser
 from pyhml.models.hml import HML
 
+
 from Bio import SeqIO
 from pandas import DataFrame
 
@@ -79,4 +82,27 @@ def test_002_gzip(self):
         os.system(cmd_zip)
         pass
 
+    def test_003_sample(self):
+        sample = Sample(center_code='000', id='100000',
+                        collection_method='DNA')
+        self.assertIsInstance(sample, Sample)
+        self.assertEqual(sample.id, '100000')
+        self.assertEqual(sample.center_code, '000')
+        self.assertEqual(sample.collection_method, 'DNA')
+        pass
+
+    def test_004_sampleTyping(self):
+        sample = Sample(center_code='000', id='100000',
+                        collection_method='DNA')
+        typing = Typing(date='04-11-2011', gene_family='HLA')
+        sample.typing = [typing]
+        self.assertIsInstance(typing, Typing)
+        self.assertIsInstance(sample, Sample)
+        self.assertEqual(typing.gene_family, 'HLA')
+        self.assertIsInstance(sample.typing[0], Typing)
+        self.assertEqual(sample.id, '100000')
+        self.assertEqual(sample.center_code, '000')
+        self.assertEqual(sample.collection_method, 'DNA')
+        pass
+
 

tox.ini

@@ -12,6 +12,15 @@ setenv =
 
 commands = python -m unittest
 
+passenv =
+    TRAVIS
+    TRAVIS_BRANCH
+    TRAVIS_JOB_ID
+
+[travis]
+python =
+  3.6: py36, flake8
+
 ; If you want to make tox run the tests with the same versions, create a
 ; requirements.txt with the pinned versions and uncomment the following lines:
 ; deps =