diff extract_aln_ends.py @ 14:570a7de9f151 draft

read from bam; fix header issue

--- a/extract_aln_ends.py	Fri Nov 27 04:33:02 2015 -0500
+++ b/extract_aln_ends.py	Mon Nov 30 07:53:36 2015 -0500
@@ -14,7 +14,7 @@
 By default output is written to stdout.
 
 Input:
-* sam file containing alignments (paired-end sequencing)
+* alignments in SAM or BAM format (paired-end sequencing)
 
 Output:
 * bed6 file containing outer coordinates (sorted by read id)
@@ -57,8 +57,8 @@
                                  formatter_class=DefaultsRawDescriptionHelpFormatter)
 # positional arguments
 parser.add_argument(
-    "sam",
-    help="Path to sam file containing alignments.")
+    "infile",
+    help="Path to alignments in SAM or BAM format.")
 # optional arguments
 parser.add_argument(
     "-o", "--outfile",
@@ -75,7 +75,7 @@
 parser.add_argument(
     '--version',
     action='version',
-    version='0.1.0')
+    version='0.2.0')
 
 args = parser.parse_args()
 
@@ -86,7 +86,7 @@
 else:
     logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
 logging.info("Parsed arguments:")
-logging.info("  sam: '{}'".format(args.sam))
+logging.info("  infile: '{}'".format(args.infile))
 if args.outfile:
     logging.info("  outfile: enabled writing to file")
     logging.info("  outfile: '{}'".format(args.outfile))
@@ -103,7 +103,7 @@
 
     # sort by id
     logging.debug("calling samtools sort")
-    pysam.sort(args.sam, "-n", "-o{}".format(fn_sorted), "-T sortprefix")
+    pysam.sort(args.infile, "-n", "-o{}".format(fn_sorted), "-T sortprefix")
 
     # fix mate information
     # also removes secondary and unmapped reads