Merge pull request #282 from /issues/281-export-transgene-fusions

Export transgene fusions (resolves #281)

Author: arkal

src/protect/mutation_translation.py

@@ -139,5 +139,11 @@ def run_transgene(job, snpeffed_file, rna_bam, univ_options, transgene_options,
         os.rename('transgened_transgened.vcf', 'mutations.vcf')
         export_results(job, job.fileStore.writeGlobalFile('mutations.vcf'), 'mutations.vcf',
                        univ_options, subfolder='mutations/transgened')
+    if fusion_calls:
+        # There won't be an output bedpe if there's no input
+        os.rename('transgened_transgened.bedpe', 'fusions.bedpe')
+        export_results(job, job.fileStore.writeGlobalFile('fusions.bedpe'), 'fusions.bedpe',
+                       univ_options, subfolder='mutations/transgened')
+
     job.fileStore.logToMaster('Ran transgene on %s successfully' % univ_options['patient'])
     return output_files

src/protect/test/ci/test_protect.py

@@ -140,9 +140,12 @@ def _test_ran_successfully(self, expected_dirs):
                                 'snpeffed': ('/mnt/ephemeral/done/TEST/mutations/snpeffed',
                                              [],
                                              ['mutations.vcf']),
-                                'transgened': ('/mnt/ephemeral/done/TEST/mutations/transgened',
-                                               [],
-                                               ['mutations.vcf']),
+                                'transgened_f': ('/mnt/ephemeral/done/TEST/mutations/transgened',
+                                                 [],
+                                                 ['fusions.bedpe', 'mutations.vcf']),
+                                'transgened_v': ('/mnt/ephemeral/done/TEST/mutations/transgened',
+                                                 [],
+                                                 ['mutations.vcf']),
                             },
                             'peptides': ('/mnt/ephemeral/done/TEST/peptides',
                                          [],
@@ -185,6 +188,13 @@ def _test_ran_successfully(self, expected_dirs):
                                 contents_per_dir['mutations']['strelka']['indel']
                             expected_contents['mutations_strelka_3'] = \
                                 contents_per_dir['mutations']['strelka']['snv']
+                        elif caller == 'transgened':
+                            if 'fusions' in dir['mutations']:
+                                expected_contents['mutations_' + caller] = \
+                                    contents_per_dir['mutations'][caller + '_f']
+                            else:
+                                expected_contents['mutations_' + caller] = \
+                                    contents_per_dir['mutations'][caller + '_v']
                         else:
                             expected_contents['mutations_' + caller] = \
                                 contents_per_dir['mutations'][caller]