Transgene now returns None with an empty VCF and does not fail.

If Transgene returns None, all subsequent tools which rely on Transgene’s
return value return None as well.

Resolves #214

src/protect/binding_prediction/common.py

@@ -58,6 +58,10 @@ def spawn_antigen_predictors(job, transgened_files, phlat_files, univ_options, m
                             +- 'normal': fsID
     :rtype: tuple(dict, dict)
     """
+    if transgened_files is None:
+        job.fileStore.logToMaster('Spawn antigen predictors failed to find any pepetides for %s.'
+                                  % univ_options['patient'])
+        return None
     work_dir = os.getcwd()
     mhci_options, mhcii_options = mhc_options
     pept_files = {
@@ -498,6 +502,10 @@ def merge_mhc_peptide_calls(job, antigen_predictions, transgened_files, univ_opt
     :rtype: dict
     """
     job.fileStore.logToMaster('Merging MHC calls')
+    if antigen_predictions is None and transgened_files is None:
+        job.fileStore.logToMaster('Merge_mhc_peptide_calls failed to find any peptides for %s.'
+                                  % univ_options['patient'])
+        return None
     work_dir = os.getcwd()
     pept_files = {
         '10_mer.faa': transgened_files['transgened_tumor_10_mer_peptides.faa'],

src/protect/mutation_translation.py

@@ -90,7 +90,8 @@ def run_transgene(job, snpeffed_file, rna_bam, univ_options, transgene_options,
                   '--pep_lens', '9,10,15',
                   '--cores', str(transgene_options['n']),
                   '--genome', input_files['genome.fa'],
-                  '--annotation', input_files['annotation.gtf']]
+                  '--annotation', input_files['annotation.gtf'],
+                  '--log_file', '/data/transgene.log']
 
     if snpeffed_file is not None:
         parameters.extend(['--snpeff', input_files['snpeffed_muts.vcf']])
@@ -111,11 +112,15 @@ def run_transgene(job, snpeffed_file, rna_bam, univ_options, transgene_options,
         parameters += ['--transcripts', fusion_files['transcripts.fa'],
                        '--fusions', fusion_files['fusion_calls']]
 
-    docker_call(tool='transgene',
-                tool_parameters=parameters,
-                work_dir=work_dir,
-                dockerhub=univ_options['dockerhub'],
-                tool_version=transgene_options['version'])
+    try:
+        docker_call(tool='transgene',
+                    tool_parameters=parameters,
+                    work_dir=work_dir,
+                    dockerhub=univ_options['dockerhub'],
+                    tool_version=transgene_options['version'])
+    finally:
+        logfile = os.path.join(os.getcwd(), 'transgene.log')
+        export_results(job, job.fileStore.writeGlobalFile(logfile), logfile, univ_options, subfolder='peptides')
 
     output_files = defaultdict()
     for peplen in ['9', '10', '15']:
@@ -128,7 +133,10 @@ def run_transgene(job, snpeffed_file, rna_bam, univ_options, transgene_options,
                 if tissue_type == 'tumor':
                     os.rename(os.path.join(work_dir, old_pepfile + '.map'),
                               os.path.join(work_dir, pepfile + '.map'))
-
+            if not os.path.exists(pepfile):
+                job.fileStore.logToMaster('Transgene failed to find any pepetides for %s.'
+                                          % univ_options['patient'])
+                return None
             output_files[pepfile] = job.fileStore.writeGlobalFile(os.path.join(work_dir, pepfile))
             export_results(job, output_files[pepfile], pepfile, univ_options, subfolder='peptides')
         mapfile = '_'.join(['transgened_tumor', peplen, 'mer_peptides.faa.map'])

src/protect/rankboost.py

@@ -36,6 +36,10 @@ def wrap_rankboost(job, rsem_files, merged_mhc_calls, transgene_out, univ_option
                 +- 'mhci_rankboost_detailed_results.txt': fsID
     :rtype: dict
     """
+    if merged_mhc_calls is None:
+        job.fileStore.logToMaster('Wrap_rankboost failed to find any pepetides for %s.'
+                                  % univ_options['patient'])
+        return None
     rankboost = job.addChildJobFn(boost_ranks, rsem_files['rsem.isoforms.results'],
                                   merged_mhc_calls, transgene_out, univ_options, rankboost_options)