Merge branch 'master' of https://github.com/dawe/scatACC

dawe · Jun 17, 2021 · 2b7710e · 2b7710e
2 parents 9d16955 + 3e73c0f
commit 2b7710e
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/bc2rg.py b/bc2rg.py
@@ -45,13 +45,15 @@ def build_header(in_header, coder, group = '', keep_unmatched=True):
       header[k] = in_header[k]
 
   # read groups
+  _pl = _pu = _lb = _cn = 'default'
   if 'RG' in in_header:
-    _pl = in_header['RG'][0]['PL']
-    _pu = in_header['RG'][0]['PU']
-    _lb = in_header['RG'][0]['LB']
-    _cn = in_header['RG'][0]['CN']
-  else:
-    _pl = _pu = _lb = _cn = 'default'
+    try:
+      _pl = in_header['RG'][0]['PL']
+      _pu = in_header['RG'][0]['PU']
+      _lb = in_header['RG'][0]['LB']
+      _cn = in_header['RG'][0]['CN']
+    except KeyError:
+      1
   _rg = []
   for bc in coder.values():
     _rg.append({'ID': "%s-%s" % (bc, group),

diff --git a/separate_bam.py b/separate_bam.py
@@ -24,7 +24,7 @@ def main():
   if not options.output:
     prefix, _ = os.path.splitext(os.path.basename(options.bamfile))
   else:
-    prefix = 'output'
+    prefix = options.output
 
   try:
     clusters = pd.read_table(options.clusters, index_col=0, header=None)