Merge pull request #49 from eppinglen/master

Bug fix due to ariba --max_noncoding_length parameter

.travis.yml

@@ -8,7 +8,7 @@ addons:
     - libgfortran3
     - libncurses5-dev
 python:
-  - "3.4"
+  - "3.7"
 sudo: false
 install:
   - "source ./install_dependencies.sh"
@@ -17,4 +17,4 @@ before_script:
 script:
   - "coverage run setup.py test"
 after_success:
-  - codecov
+  - codecov

README.md

@@ -139,7 +139,7 @@ Clone the git repository:
 git clone https://github.com/sanger-pathogens/seroba.git
 ```
 
-Copy the databse to a directory:
+Copy the database to a directory:
 ```
 cp -r seroba/database my_directory
 ```

seroba/ref_db_creator.py

@@ -128,7 +128,7 @@ def _check_meta_data(meta_tsv,gene_fasta):
     @staticmethod
     def _create_ariba_db(fasta_file,cluster_meta_data,cdhit_clusters,serogroup,out_dir,subdir):
         ariba_dir = os.path.join(out_dir,'ariba_db',serogroup,subdir)
-        command = ['ariba prepareref','-f',fasta_file,'-m',cluster_meta_data,'--cdhit_clusters',cdhit_clusters, ariba_dir]
+        command = ['ariba prepareref','-f',fasta_file,'-m',cluster_meta_data,'--max_noncoding_length 50000 --cdhit_clusters',cdhit_clusters, ariba_dir]
         print(' '.join(command))
         os.system(' '.join(command))
 
@@ -155,7 +155,7 @@ def _create_complete_cdhit_cluster(meta_data_tsv,out_dir):
     def _create_complete_ariba_db(self,complete_cdhit_cluster):
         temp_dir = tempfile.mkdtemp(prefix = 'temp_ariba', dir=os.getcwd())
         temp_dir = os.path.join(temp_dir,'ariba')
-        command = ['ariba prepareref','-f',self.ref_fasta,'--all_coding no --cdhit_clusters',complete_cdhit_cluster, temp_dir]
+        command = ['ariba prepareref','-f',self.ref_fasta,'--all_coding no --max_noncoding_length 50000 --cdhit_clusters',complete_cdhit_cluster, temp_dir]
         os.system(' '.join(command))
         shutil.copyfile(os.path.join(temp_dir,'02.cdhit.clusters.tsv'),os.path.join(self.out_dir,'cd_cluster.tsv'))
         shutil.rmtree(temp_dir)

seroba/tests/ref_db_creator_test.py

@@ -123,8 +123,8 @@ def test__create_ariba_db(self):
 
         for i in range(len(db_files)):
             with self.subTest (i= i):
-                exp = os.path.join(data_dir,'ariba_db',db_files[i])
-
+                exp = os.path.join(out_dir,'ariba_db','06A','ref',db_files[i])
+                print(exp)
                 self.assertTrue(os.path.isfile(exp) , 'files does not exists')
         shutil.rmtree(out_dir)
 

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name='seroba',
-    version='1.0.1',
+    version='1.0.2',
     description='SEROBA: Serotyping for illumina reads',
     packages = find_packages(),
     author='Lennard Epping',