diff coords2clnt.py @ 2:de4ea3aa1090 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coords2clnt.py	Thu Oct 22 10:26:45 2015 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+
+tool_description = """
+Given coordinates of the aligned reads, calculate positions of the crosslinked
+nucleotides. Crosslinked nts are assumed to be one nt upstream of the 5'-end of
+the read.
+
+By default output is written to stdout.
+
+Input:
+* bed6 file containing coordinates of aligned reads
+* bed6 file containing coordinates of crosslinking events
+
+Example usage:
+- convert read coordinates from file in.bed to coordinates of the crosslinking
+  events, written to out.bed:
+coords2clnt.py in.bed --outfile out.bed
+"""
+
+epilog = """
+Author: Daniel Maticzka
+Copyright: 2015
+License: Apache
+Email: [e-mail]
+Status: Testing
+"""
+
+import argparse
+import logging
+from sys import stdout
+from pybedtools import BedTool
+from pybedtools.featurefuncs import five_prime
+# 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,
+                                 formatter_class=argparse.RawDescriptionHelpFormatter)
+# positional arguments
+parser.add_argument(
+    "infile",
+    help="Path to bed input file.")
+# optional arguments
+parser.add_argument(
+    "-o", "--outfile",
+    help="Write results to this file.")
+parser.add_argument(
+    "-v", "--verbose",
+    help="Be verbose.",
+    action="store_true")
+parser.add_argument(
+    "-d", "--debug",
+    help="Print lots of debugging information",
+    action="store_true")
+parser.add_argument(
+    '--version',
+    action='version',
+    version='0.1.0')
+
+
+# handle arguments
+args = parser.parse_args()
+if args.debug:
+    logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
+elif args.verbose:
+    logging.basicConfig(level=logging.INFO, format="%(filename)s - %(levelname)s - %(message)s")
+else:
+    logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
+logging.info("Parsed arguments:")
+if args.outfile:
+    logging.info("  outfile: enabled writing to file")
+    logging.info("  outfile: '{}'".format(args.outfile))
+logging.info("  outfile: '{}'".format(args.outfile))
+logging.info("")
+
+# data processing
+alns = BedTool(args.infile)
+clnts = alns.each(five_prime, upstream=1, downstream=0)
+
+# write to file or to stdout
+if args.outfile:
+    clnts.saveas(args.outfile)
+else:
+    tmptool = clnts.saveas()
+    logging.debug("results written to temporary file :" + tmptool.fn)
+    tmp = open(tmptool.fn)
+    for line in tmp:
+        stdout.write(line)
+    tmp.close()