add extensions to tmp files

CHANGES.md

@@ -70,4 +70,5 @@ v1.5.1
 - bugfix: size and copy range of alleles only include "full" supporting reads even if partials were included, but "partial" reads will be reported in support counts
 - bugfix: allele motif equivalence checked to perform proper tallying for determining consensus motif in variant
 - used read name as tiebreaker for choosing support read sequence as ALT
+- add extensions (`.fa`, `.blastn`, `.bed`) to temporary files to help debugging
 - `MOTIF` renamed to `RU`, `COPIES` to `REF` in VCF fields

src/ins.py

@@ -456,7 +456,7 @@ def create_tmp_bed(self, ins_list, include_read=False):
         for ins in ins_list:
             ins_bed += '{}\n'.format(INS.to_bed(ins, include_read=include_read))
 
-        ins_bed_file = create_tmp_file(ins_bed)
+        ins_bed_file = create_tmp_file(ins_bed, '.bed')
         self.tmp_files.add(ins_bed_file)
 
         return ins_bed_file
@@ -469,7 +469,7 @@ def merge(self, ins_list, d=50):
         ins_all = BedTool(ins_bed_file)
         ins_merged = ins_all.sort().merge(d=d, c='4,5', o='distinct,count_distinct')
         if self.debug:
-            ins_merged_file = create_tmp_file('')
+            ins_merged_file = create_tmp_file('', '.bed')
             ins_merged.saveas(ins_merged_file)
             print('ins merged {}'.format(ins_merged_file))
 
@@ -516,7 +516,7 @@ def get_examine_regions(self, bam, chroms, chunk_size=1000000, regions_bed_file=
                 chrom_spans = ''
                 for chrom in sorted(chroms):
                     chrom_spans += '{}\n'.format('\t'.join(map(str, [chrom, 0, chrom_lens[chrom]])))
-                chrom_bed_file = create_tmp_file(chrom_spans)
+                chrom_bed_file = create_tmp_file(chrom_spans, '.bed')
                 self.tmp_files.add(chrom_bed_file)
 
                 chrom_bed = BedTool(chrom_bed_file)

src/utils.py

@@ -35,8 +35,8 @@ def combine_batch_results(batch_results, data_type):
 
     return all_results
 
-def create_tmp_file(content):
-    fd, path = tempfile.mkstemp()
+def create_tmp_file(content, ext=None):
+    fd, path = tempfile.mkstemp(suffix=ext)
     try:
         with os.fdopen(fd, 'w') as out:
             out.write(content)