Merge branch 'master' of github.com:RabadanLab/arcasHLA

scripts/convert.py

@@ -78,25 +78,25 @@ def convert_allele(allele, resolution):
 
         # Output: P-group allele
         elif resolution == 'p-group': 
-            if allele[:-1] in p_group[i]:
-                allele = p_group[i][allele[:-1]]
+            if allele[:-1] in p_group[str(i)]:
+                allele = p_group[str(i)][allele[:-1]]
 
-            elif process_allele(allele[:-1], i - 1) in p_group[i]:
-                allele = p_group[i][process_allele(allele[:-1], i -1)]
+            elif process_allele(allele[:-1], i - 1) in p_group[str(i)]:
+                allele = p_group[str(i)][process_allele(allele[:-1], i -1)]
 
     # Input: ungrouped allele
     # Output: G-group allele
     elif resolution == 'g-group':
-        if allele in g_group[i]:
-            allele = g_group[i][allele]
+        if allele in g_group[str(i)]:
+            allele = g_group[str(i)][allele]
         elif allele[-1] != 'N':
             allele = process_allele(allele,3)
 
     # Input: ungrouped allele
     # Output: P-group allele
     elif resolution == 'p-group':
-        if allele in p_group[i]:
-            allele = p_group[i][allele]
+        if allele in p_group[str(i)]:
+            allele = p_group[str(i)][allele]
 
     # Input: ungrouped allele
     # Output: reduced resolution, ungrouped allele

scripts/extract.py

@@ -67,8 +67,6 @@ def extract_reads(bam, outdir, paired, unmapped, alts, temp, threads):
 
     hla_filtered = ''.join([temp, sample, '.hla.sam'])
     file_list.append(hla_filtered)
-    hla_filtered_bam = ''.join([temp, sample, '.hla.bam'])
-    file_list.append(hla_filtered_bam)
 
     # Get bam header to check for chromosome nomenclature
     output = run_command(['samtools', 'view', '-@'+threads, '-H', bam])
@@ -115,21 +113,13 @@ def extract_reads(bam, outdir, paired, unmapped, alts, temp, threads):
             command.extend([bam, alt+':', '>>', hla_filtered])
             run_command(command)
 
-
-    # Convert SAM to BAM
-    message = '[extract] Converting SAM to BAM: '
-    command = ['samtools', 'view', '-Sb', '-@'+threads,
-                hla_filtered, '>', hla_filtered_bam]    
-    run_command(command, message)
-
-
-    # Sort BAM
+    # Sort and convert to BAM
     hla_sorted = ''.join([temp, sample, '.hla.sorted.bam'])
     file_list.append(hla_sorted)
     file_list.append(hla_sorted + '.bai')
     message = '[extract] Sorting bam: '
     command = ['samtools', 'sort', '-n', '-@'+threads, 
-                hla_filtered_bam, '-o', hla_sorted]
+                hla_filtered, '-o', hla_sorted]
     run_command(command, message)
 
     # Convert BAM to FASTQ and compress