Merge pull request #3 from bewt85/bt5_rename_everything

Rename project to snpEffWrapper

.travis.yml

@@ -12,4 +12,4 @@ before_install:
   - "source install_dependencies.sh"
 install:
   - "python setup.py develop"
-script: ./annotateVCF/tests/test_annotateVCF.py
+script: ./snpEffWrapper/tests/test_wrapper.py

MANIFEST.in

@@ -1,2 +1,2 @@
-recursive-include annotateVCF/data *
-recursive-include annotateVCF/tests/data *
+recursive-include snpEffWrapper/data *
+recursive-include snpEffWrapper/tests/data *

README.md

@@ -1,24 +1,24 @@
-# AnnotateVCF
+# SnpEffWrapper
 
-[![Build Status](https://travis-ci.org/sanger-pathogens/AnnotateVCF.svg?branch=master)](https://travis-ci.org/sanger-pathogens/AnnotateVCF)
+[![Build Status](https://travis-ci.org/sanger-pathogens/SnpEffWrapper.svg?branch=master)](https://travis-ci.org/sanger-pathogens/SnpEffWrapper)
 
-Takes a VCF and applies annotations from a GFF using [SnpEff](http://snpeff.sourceforge.net/)
+Takes a VCF and infers annotations and variant effects from a GFF using [SnpEff](http://snpeff.sourceforge.net/)
 
 If you use this, please consider [citing SnpEff](http://snpeff.sourceforge.net/SnpEff.html#citing); it
-made making this tool a lot easier.
+made making this tool a lot easier.  This software is not endorsed in any respect by the original authors.
 
 ## Usage
 
 ```
-$ annotateVCF annotateVCF/tests/data/minimal.gff annotateVCF/tests/data/minimal.vcf -o minimal.annotated.vcf
+$ snpEffBuildAndRun snpEffWrapper/tests/data/minimal.gff snpEffWrapper/tests/data/minimal.vcf -o minimal.annotated.vcf
 ```
 
 ```
-$ annotateVCF --help
-usage: annotateVCF [-h] [--snpeff-exec SNPEFF_EXEC] [--java-exec JAVA_EXEC]
-                   [--coding-table CODING_TABLE] [-o OUTPUT_VCF] [--debug]
-                   [--keep]
-                   gff_file vcf_file
+$ snpEffBuildAndRun --help
+usage: snpEffBuildAndRun [-h] [--snpeff-exec SNPEFF_EXEC]
+                         [--java-exec JAVA_EXEC] [--coding-table CODING_TABLE]
+                         [-o OUTPUT_VCF] [--debug] [--keep]
+                         gff_file vcf_file
 
 Takes a VCF and applies annotations from a GFF using SnpEff
 
@@ -45,30 +45,30 @@ optional arguments:
                         debugging)
 ```
 
-* annotateVCF will look for SnpEFF.jar in the following locations:
+* snpEffBuildAndRun will look for SnpEFF.jar in the following locations:
   * the file specified by `--snpeff-exec`
   * `snpEff.jar` in your local directory
   * `snpEff.jar` in your `PATH`
-* SnpEff needs Java 1.7 to run; annotateVCF will look in the following locations:
+* SnpEff needs Java 1.7 to run; snpEffBuildAndRun will look in the following locations:
   * the file specified by `--java-exec`
   * `java` in your `PATH`
 
 ## Alternative coding tables
 
 You can provide a coding table for each VCF contig otherwise it'll default to
 SnpEff's 'Bacterial_and_Plant_Plastid'.  You can do this by providing a mapping for
-each contig in your VCF to the relevant table in [annotateVCF/data/config.template](annotateVCF/data/config.template)
+each contig in your VCF to the relevant table in [snpEffWrapper/data/config.template](snpEffWrapper/data/config.template)
 in YAML format.
 
 For example:
 ```
-annotateVCF minimal.gff minimal.vcf \
+snpEffBuildAndRun minimal.gff minimal.vcf \
   --coding-table 'default: Standard'
   
-annotateVCF minimal.gff minimal.vcf \
+snpEffBuildAndRun minimal.gff minimal.vcf \
   --coding-table '{CHROM1: Standard, MITO1: Mitochondrial}'
   
-annotateVCF minimal.gff minimal.vcf \
+snpEffBuildAndRun minimal.gff minimal.vcf \
   --coding-table '{default: Standard, MITO1: Mitochondrial}'
 ```
 
@@ -81,10 +81,12 @@ NB you don't need curly brackets if you're only mapping one contig (or setting a
 * At least one of the contigs in the VCF must have annotation data in the GFF
   (you'll get warnings for each VCF config not in the GFF)
 * You cannot provide unknown coding tables (i.e. that can't be found in
-  [config.template](annotateVCF/data/config.template))
+  [config.template](snpEffWrapper/data/config.template))
 
 ## Installation
 
+Install [snpEff](http://snpeff.sourceforge.net/) and Java 1.7 then
+
 ```
-pip install git+https://github.com/sanger-pathogens/AnnotateVCF.git
+pip install git+https://github.com/sanger-pathogens/SnpEffWrapper.git
 ```

scripts/annotateVCF → scripts/snpEffBuildAndRun

@@ -5,7 +5,7 @@ import logging
 import shutil
 import sys
 
-from annotateVCF.annotateVCF import annotate_vcf, check_and_amend_executables
+from snpEffWrapper.wrapper import annotate_vcf, check_and_amend_executables
 
 def parse_arguments():
   parser = argparse.ArgumentParser(
@@ -42,5 +42,5 @@ if __name__ == '__main__':
   else:
     logging.basicConfig(format="[%(asctime)s] %(levelname)s: %(message)s",
                         level=logging.INFO)
-  logger = logging.getLogger('annotateVCF')
+  logger = logging.getLogger('snpEffWrapper')
   annotate_vcf(args)

setup.py

@@ -2,10 +2,10 @@
 from setuptools import setup, find_packages
 import multiprocessing
 
-setup(name='annotateVCF',
-      version='0.1.0',
+setup(name='snpEffWrapper',
+      version='0.2.0',
       scripts=[
-        'scripts/annotateVCF'
+        'scripts/snpEffBuildAndRun'
       ],
       install_requires=[
         'Jinja2',
@@ -14,8 +14,8 @@
       ],
       include_package_data=True,
       package_data={
-        'data': 'annotateVCF/data/*',
-        'test_data': 'annotateVCF/tests/data/*'
+        'data': 'snpEffWrapper/data/*',
+        'test_data': 'snpEffWrapper/tests/data/*'
       },
       packages=find_packages(),
       zip_safe=False

annotateVCF/tests/test_annotateVCF.py → snpEffWrapper/tests/test_wrapper.py

@@ -8,18 +8,18 @@
 from io import StringIO
 from unittest.mock import patch, MagicMock
 
-from annotateVCF.annotateVCF import *
-from annotateVCF.annotateVCF import _java_version_ok, _choose_java
+from snpEffWrapper.wrapper import *
+from snpEffWrapper.wrapper import _java_version_ok, _choose_java
 
-class TestAnnotateVCF(unittest.TestCase):
+class TestSnpEffWrapper(unittest.TestCase):
   def setUp(self):
     class FakeArgs(object):
       pass
     self.fake_args = FakeArgs()
 
-  @patch('annotateVCF.annotateVCF.os.path.isfile')
-  @patch('annotateVCF.annotateVCF._java_version_ok')
-  @patch('annotateVCF.annotateVCF.shutil')
+  @patch('snpEffWrapper.wrapper.os.path.isfile')
+  @patch('snpEffWrapper.wrapper._java_version_ok')
+  @patch('snpEffWrapper.wrapper.shutil')
   def test_snpeff_not_in_path(self, shutil_mock, java_ok, isfile_mock):
     isfile_mock.side_effect = lambda path: path in ['/foo/snpEff.jar', '/bin/snpEff.jar']
     parsed_args = MagicMock()
@@ -99,7 +99,7 @@ def test_get_vcf_contigs(self):
     actual_contigs = get_vcf_contigs(fake_vcf)
     self.assertEqual(actual_contigs, expected_contigs)
 
-  @patch('annotateVCF.annotateVCF.logger.warn')
+  @patch('snpEffWrapper.wrapper.logger.warn')
   def test_check_contigs(self, warn_mock):
     vcf_contigs = ['CHROM1']
     gff_contigs = ['CHROM1']
@@ -196,17 +196,17 @@ def __init__(self, name):
     gff_file = FakeFile('foo.gz')
     self.assertEqual(get_genome_name(gff_file), 'foo.gz')
 
-  @patch('annotateVCF.annotateVCF.open', create=True)
+  @patch('snpEffWrapper.wrapper.open', create=True)
   def test_create_config_file(self, open_mock):
     try:
       fake_output_file = tempfile.NamedTemporaryFile(mode='w',
-                                                     prefix='annotateVCF_tmp_',
+                                                     prefix='snpEffWrapper_tmp_',
                                                      dir=os.getcwd(),
                                                      delete=False)
       open_mock.return_value = fake_output_file
       fake_output_filename = fake_output_file.name
 
-      tests_dir = pkg_resources.resource_filename('annotateVCF', 'tests')
+      tests_dir = pkg_resources.resource_filename('snpEffWrapper', 'tests')
       expected_config_filename = os.path.join(tests_dir, 'data', 'config')
       temp_database_dir = '/tmp/fake_dir'
       genome_name = 'fake_genome'
@@ -229,8 +229,8 @@ def test_create_config_file(self, open_mock):
     finally:
       os.remove(fake_output_filename)
 
-  @patch('annotateVCF.annotateVCF.shutil.which')
-  @patch('annotateVCF.annotateVCF._java_version_ok')
+  @patch('snpEffWrapper.wrapper.shutil.which')
+  @patch('snpEffWrapper.wrapper._java_version_ok')
   def test_choose_java(self, java_ok_mock, which_mock):
     which_mock.return_value = '/foo/bar/java'
     java_ok_mock.side_effect = lambda java: java in list_of_ok_javas
@@ -255,7 +255,7 @@ def test_choose_java(self, java_ok_mock, which_mock):
     list_of_ok_javas = []
     self.assertRaises(WrongJavaError, _choose_java)
 
-  @patch('annotateVCF.annotateVCF.logger.warn')
+  @patch('snpEffWrapper.wrapper.logger.warn')
   def test_check_annotations(self, warn_mock):
     fake_vcf = StringIO("""\
 ##fileformat=VCFv4.1
@@ -274,8 +274,8 @@ def test_check_annotations(self, warn_mock):
     expected_warning = "1 instances of 'ERROR_CHROMOSOME_NOT_FOUND': A contig in your VCF could not be found in your GFF. Are you sure that contigs use consitent names between your input data and the reference?"
     warn_mock.assert_called_once_with(expected_warning)
 
-  @patch('annotateVCF.annotateVCF.delete_temp_database')
-  @patch('annotateVCF.annotateVCF._get_snpeff_output_files')
+  @patch('snpEffWrapper.wrapper.delete_temp_database')
+  @patch('snpEffWrapper.wrapper._get_snpeff_output_files')
   def test_happy_case(self, output_mock, delete_database_mock):
     delete_database_mock.side_effect = shutil.rmtree
     temp_annotated_vcf = tempfile.NamedTemporaryFile(mode='w', delete=False,
@@ -300,7 +300,7 @@ def test_happy_case(self, output_mock, delete_database_mock):
 
     fake_args.coding_table = 'default: Bacterial_and_Plant_Plastid'
 
-    tests_dir = pkg_resources.resource_filename('annotateVCF', 'tests')
+    tests_dir = pkg_resources.resource_filename('snpEffWrapper', 'tests')
     minimal_gff_filename = os.path.join(tests_dir, 'data', 'minimal.gff')
     minimal_vcf_filename = os.path.join(tests_dir, 'data', 'minimal.vcf')
     fake_args.gff_file = open(minimal_gff_filename, 'r')

annotateVCF/annotateVCF.py → snpEffWrapper/wrapper.py

@@ -192,7 +192,7 @@ def get_genome_name(gff_file):
 
 def create_config_file(temp_database_dir, genome_name, vcf_contigs,
                        coding_table):
-  env = Environment(loader=PackageLoader('annotateVCF', 'data'))
+  env = Environment(loader=PackageLoader('snpEffWrapper', 'data'))
   template = env.get_template('config.template')
   output_filename = os.path.join(temp_database_dir, 'config')
   config_content = template.render(