Merge pull request #14 from B-UMMI/minor_fix

Control if assembly is produced when SPAdes doesn't crash
B-UMMI · Feb 16, 2018 · 0add1c0 · 0add1c0
2 parents 74a0817 + 97c9b50
commit 0add1c0
Showing 1 changed file with 33 additions and 25 deletions.
diff --git a/modules/spades.py b/modules/spades.py
@@ -7,10 +7,13 @@
 
 
 # Run Spades
-def spades(spades_folder, threads, fastq_files, notUseCareful, maxMemory, minCoverageAssembly, kmers, assembled_se_reads):
+def spades(spades_folder, threads, fastq_files, notUseCareful, maxMemory, minCoverageAssembly, kmers,
+           assembled_se_reads):
     contigs = os.path.join(spades_folder, 'contigs.fasta')
 
-    command = ['spades.py', '', '--only-assembler', '--threads', str(threads), '--memory', str(maxMemory), '--cov-cutoff', str(minCoverageAssembly), '', '-1', fastq_files[0], '-2', fastq_files[1], '', '-o', spades_folder]
+    command = ['spades.py', '', '--only-assembler', '--threads', str(threads), '--memory', str(maxMemory),
+               '--cov-cutoff', str(minCoverageAssembly), '', '-1', fastq_files[0], '-2', fastq_files[1], '',
+               '-o', spades_folder]
 
     if not notUseCareful:
         command[1] = '--careful'
@@ -231,8 +234,7 @@ def decide_filter_parameters(sequence_dict, minContigsLength, minCoverageContigs
 @spades_timer
 def runSpades(sampleName, outdir, threads, fastq_files, notUseCareful, maxMemory, minCoverageAssembly, minContigsLength, estimatedGenomeSizeMb, kmers, maximumReadsLength, defaultKmers, minCoverageContigs, assembled_se_reads, saveExcludedContigs, maxNumberContigs):
     pass_qc = True
-    failing = {}
-    failing['sample'] = False
+    failing = {'sample': False}
     warnings = {}
 
     # Create SPAdes output directory
@@ -250,40 +252,46 @@ def runSpades(sampleName, outdir, threads, fastq_files, notUseCareful, maxMemory
         else:
             print 'SPAdes will use the following k-mers: ' + str(kmers)
 
-    run_successfully, contigs = spades(spades_folder, threads, fastq_files, notUseCareful, maxMemory, minCoverageAssembly, kmers, assembled_se_reads)
+    run_successfully, contigs = spades(spades_folder, threads, fastq_files, notUseCareful, maxMemory,
+                                       minCoverageAssembly, kmers, assembled_se_reads)
 
     if run_successfully:
-        shutil.copyfile(contigs, os.path.join(outdir, str('SPAdes_original_assembly.contigs.fasta')))
+        if os.path.isfile(contigs):
+            shutil.copyfile(contigs, os.path.join(outdir, str('SPAdes_original_assembly.contigs.fasta')))
 
-        contigs_link = os.path.join(outdir, str(sampleName + '.contigs.fasta'))
-        os.symlink(contigs, contigs_link)
+            contigs_link = os.path.join(outdir, str(sampleName + '.contigs.fasta'))
+            os.symlink(contigs, contigs_link)
 
-        contigs = contigs_link
+            contigs = contigs_link
 
-        minContigsLength = define_minContigsLength(maximumReadsLength, minContigsLength)
+            minContigsLength = define_minContigsLength(maximumReadsLength, minContigsLength)
 
-        sequence_dict = get_SPAdes_sequence_information(contigs)
+            sequence_dict = get_SPAdes_sequence_information(contigs)
 
-        warnings, sequence_dict, filtered_sequences_sufix, spades_report_general = decide_filter_parameters(sequence_dict, minContigsLength, minCoverageContigs, estimatedGenomeSizeMb, maxNumberContigs)
+            warnings, sequence_dict, filtered_sequences_sufix, spades_report_general = \
+                decide_filter_parameters(sequence_dict, minContigsLength, minCoverageContigs, estimatedGenomeSizeMb,
+                                         maxNumberContigs)
 
-        if filtered_sequences_sufix is not None:
-            filtered_sequence_file = os.path.splitext(contigs)[0] + '.' + filtered_sequences_sufix + '.fasta'
-            write_filtered_sequences_and_stats(sequence_dict, spades_report_general, contigs, filtered_sequence_file, sampleName, False, saveExcludedContigs)
-            contigs = filtered_sequence_file
-        else:
-            filtered_sequence_file = os.path.splitext(contigs)[0] + '.original.fasta'
-            write_filtered_sequences_and_stats(sequence_dict, spades_report_general, contigs, filtered_sequence_file, sampleName, True, False)
-            contigs = filtered_sequence_file
-
-        os.remove(contigs_link)
+            if filtered_sequences_sufix is not None:
+                filtered_sequence_file = os.path.splitext(contigs)[0] + '.' + filtered_sequences_sufix + '.fasta'
+                write_filtered_sequences_and_stats(sequence_dict, spades_report_general, contigs,
+                                                   filtered_sequence_file, sampleName, False, saveExcludedContigs)
+                contigs = filtered_sequence_file
+            else:
+                filtered_sequence_file = os.path.splitext(contigs)[0] + '.original.fasta'
+                write_filtered_sequences_and_stats(sequence_dict, spades_report_general, contigs,
+                                                   filtered_sequence_file, sampleName, True, False)
+                contigs = filtered_sequence_file
 
+            os.remove(contigs_link)
+        else:
+            run_successfully = False
+            failing['sample'] = 'Assembly was not produced'
     else:
         failing['sample'] = 'Did not run'
-        print failing['sample']
-        contigs = None
-        pass_qc = False
 
     if not run_successfully:
+        print failing['sample']
         pass_qc = False
 
     utils.removeDirectory(spades_folder)