Merge pull request #7787 from wm75/snpeff-dm-more-fixes

More fixes and improvements for the SnpEff data manager

Author: wm75

data_managers/data_manager_snpeff/data_manager/data_manager_snpEff_databases.py

@@ -2,10 +2,24 @@
 import json
 import optparse
 import os
+import re
 import subprocess
 import sys
 
 
+def getSnpeffVersion():
+    snpeff_version = 'SnpEff ?.?'
+    args = ['snpEff', '-version']
+    try:
+        version_output = subprocess.check_output(args, shell=False).decode()
+    except subprocess.CalledProcessError as e:
+        sys.exit(e.returncode)
+    m = re.match(r'^(SnpEff)\s*(\d+\.\d+).*$', version_output)
+    if m:
+        snpeff_version = m.groups()[0] + m.groups()[1]
+    return snpeff_version
+
+
 def fetch_databases(data_manager_dict, target_directory):
     if not os.path.exists(target_directory):
         os.makedirs(target_directory)
@@ -18,6 +32,8 @@ def fetch_databases(data_manager_dict, target_directory):
     data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
     data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get('snpeffv_databases', [])
     data_table_entries = []
+    snpeff_version = getSnpeffVersion()
+
     with open(databases_path, 'r') as fh:
         for line in fh:
             fields = line.split('\t')
@@ -29,7 +45,7 @@ def fetch_databases(data_manager_dict, target_directory):
                 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                     continue
                 description = fields[1].strip() + ' : ' + genome_version
-                data_table_entries.append(dict(value=genome_version, name=description))
+                data_table_entries.append(dict(key=snpeff_version + '_' + genome_version, version=snpeff_version, value=genome_version, name=description))
     data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
     return data_manager_dict
 

data_managers/data_manager_snpeff/data_manager/data_manager_snpEff_databases.xml

@@ -16,7 +16,7 @@ python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file'
             <output name="out_file">
                 <assert_contents>
                     <!-- Check that a genome was added -->
-                    <has_text text="GRCh38.86" />
+                    <has_text text="ebola_zaire" />
                 </assert_contents>
             </output>
         </test>

data_managers/data_manager_snpeff/data_manager/data_manager_snpEff_download.py

@@ -47,18 +47,14 @@ def getOrganismNames(genomes, organisms):
 
 def getSnpeffVersion():
     snpeff_version = 'SnpEff ?.?'
-    stderr_path = 'snpeff.err'
-    args = ['snpEff', '-h']
-    with open(stderr_path, 'w') as stderr_fh:
-        return_code = subprocess.call(args=args, shell=False, stderr=stderr_fh.fileno())
-    if return_code != 255:
-        sys.exit(return_code)
-    with open(stderr_path) as fh:
-        for line in fh:
-            m = re.match(r'^[Ss]npEff version (SnpEff)\s*(\d+\.\d+).*$', line)
-            if m:
-                snpeff_version = m.groups()[0] + m.groups()[1]
-                break
+    args = ['snpEff', '-version']
+    try:
+        version_output = subprocess.check_output(args, shell=False).decode()
+    except subprocess.CalledProcessError as e:
+        sys.exit(e.returncode)
+    m = re.match(r'^(SnpEff)\s*(\d+\.\d+).*$', version_output)
+    if m:
+        snpeff_version = m.groups()[0] + m.groups()[1]
     return snpeff_version
 
 
@@ -124,7 +120,7 @@ def download_database(data_manager_dict, target_directory, genome_version, organ
                 name=genomedb_name,
                 path=f"snpEff/{db_version}/data"
             )
-            _add_data_table_entry(data_manager_dict, 'snpeffv_genomedb', data_table_entry)
+            data_manager_dict['data_tables']['snpeffv_genomedb'].append(data_table_entry)
 
         if regulationdb_name:
             data_table_entry = dict(
@@ -134,16 +130,7 @@ def download_database(data_manager_dict, target_directory, genome_version, organ
                 value=regulationdb_name,
                 name=regulationdb_name
             )
-            _add_data_table_entry(data_manager_dict, 'snpeffv_regulationdb', data_table_entry)
-
-    return data_manager_dict
-
-
-def _add_data_table_entry(data_manager_dict, data_table, data_table_entry):
-    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
-    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
-    data_manager_dict['data_tables'][data_table].append(data_table_entry)
-    return data_manager_dict
+            data_manager_dict['data_tables']['snpeffv_regulationdb'].append(data_table_entry)
 
 
 def main():
@@ -158,7 +145,12 @@ def main():
         params = json.load(fh)
     target_directory = params['output_data'][0]['extra_files_path']
     os.mkdir(target_directory)
-    data_manager_dict = {}
+    data_manager_dict = {
+        'data_tables': {
+            'snpeffv_genomedb': [],
+            'snpeffv_regulationdb': []
+        }
+    }
 
     # Create SnpEff Reference Data
     for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.genome_version, options.organism).split(',')):