diff extract_aln_ends.py @ 50:0b9aab6aaebf draft

Uploaded 16cfcafe8b42055c5dd64e62c42b82b455027a40

--- a/extract_aln_ends.py	Sat Dec 19 06:16:22 2015 -0500
+++ b/extract_aln_ends.py	Tue Jan 26 04:38:27 2016 -0500
@@ -1,5 +1,17 @@
 #!/usr/bin/env python
 
+import argparse
+import logging
+from sys import stdout
+from shutil import rmtree
+from tempfile import mkdtemp
+from pybedtools import BedTool
+import pysam
+# avoid ugly python IOError when stdout output is piped into another program
+# and then truncated (such as piping to head)
+from signal import signal, SIGPIPE, SIG_DFL
+signal(SIGPIPE, SIG_DFL)
+
 tool_description = """
 Extract alignment ends from sam file.
 
@@ -32,25 +44,12 @@
 Status: Development
 """
 
-import argparse
-import logging
-from sys import stdout
-from shutil import rmtree
-from tempfile import mkdtemp
-from pybedtools import BedTool
-import pysam
-
 
 class DefaultsRawDescriptionHelpFormatter(argparse.ArgumentDefaultsHelpFormatter,
                                           argparse.RawDescriptionHelpFormatter):
     # To join the behaviour of RawDescriptionHelpFormatter with that of ArgumentDefaultsHelpFormatter
     pass
 
-# avoid ugly python IOError when stdout output is piped into another program
-# and then truncated (such as piping to head)
-from signal import signal, SIGPIPE, SIG_DFL
-signal(SIGPIPE, SIG_DFL)
-
 # parse command line arguments
 parser = argparse.ArgumentParser(description=tool_description,
                                  epilog=epilog,