now possible to run bed files in csv files

arontommi · Jan 12, 2018 · 01926ed · 01926ed
1 parent 3fc6a0b
commit 01926ed
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Showing 2 changed files with 34 additions and 27 deletions.
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
diff --git a/smallerbams/smallerbam.py b/smallerbams/smallerbam.py
@@ -12,10 +12,15 @@ def __init__(self):
 
     def runbams(self, bamfile, region, outputfile):
         """run samtools view"""
+        if str(region).endswith('.bed'):
+            region = '-L ' + region
+        else:
+            pass
         sp.call(['{}'.format(self.bashscript),
                  '{}'.format(bamfile),
                  '{}'.format(region),
                  '{}'.format(outputfile)])
+
     def runmultiple(self, csv):
         file = pd.read_csv(csv, header=None)
         for i, r in file.iterrows():