Merge branch 'release_16.04' into release_16.07

lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+"""
+Uses pysam to bgzip a file
+
+usage: %prog in_file out_file
+"""
+
+import optparse
+import os.path
+
+from pysam import ctabix
+
+
+def main():
+    # Read options, args.
+    usage = "Usage: %prog [options] tabular_input_file bgzip_output_file"
+    parser = optparse.OptionParser(usage=usage)
+    parser.add_option( '-c', '--chr-col', type='int', default=0, dest='chrom_col' )
+    parser.add_option( '-s', '--start-col', type='int', default=1, dest='start_col' )
+    parser.add_option( '-e', '--end-col', type='int', default=1, dest='end_col' )
+    (options, args) = parser.parse_args()
+    if len(args) != 2:
+        parser.print_usage()
+        exit(1)
+    input_fname, output_fname = args
+    output_dir = os.path.dirname(output_fname)
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+    ctabix.tabix_compress(input_fname, output_fname, force=True)
+    # Column indices are 0-based.
+    ctabix.tabix_index(output_fname, seq_col=options.chrom_col, start_col=options.start_col, end_col=options.end_col)
+
+if __name__ == "__main__":
+    main()