diff seal-galaxy-cc1b1911/seal/merge_alignments.py @ 0:244073d9abc1 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seal-galaxy-cc1b1911/seal/merge_alignments.py	Wed Oct 15 09:41:10 2014 -0400
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+
+# Copyright (C) 2011-2014 CRS4.
+#
+# This file is part of Seal.
+#
+# Seal is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option)
+# any later version.
+#
+# Seal is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+# for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with Seal.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+import os
+import subprocess
+import sys
+import tempfile
+
+import hadoop_galaxy.pathset as pathset
+import hadoop_galaxy.cat_paths as cat_paths
+
+def usage_error(msg=None):
+  if msg:
+    print >> sys.stderr, msg
+  print >> sys.stderr, os.path.basename(__file__), "INPUT_PATHSET OUTPUT [args...]"
+  sys.exit(1)
+
+def main(args):
+  if len(args) < 2:
+    usage_error()
+
+  # We generate the header with seal_merge_alignments, insert it at the
+  # top of a copy of the input pathset, and then use cat_parts to
+  # join everything into a single file.
+
+  input_pathset, output_path = map(os.path.abspath, args[0:2])
+
+  with tempfile.NamedTemporaryFile() as header_file:
+    print "generating header"
+    gen_header_cmd = [ 'seal', 'merge_alignments', '--header-only' ]
+    gen_header_cmd.extend(args[2:])
+    header_text = subprocess.check_output(gen_header_cmd)
+
+    header_file.write(header_text)
+    header_file.flush()
+    print "header ready"
+    print "generating new pathset"
+
+    original_pathset = pathset.FilePathset.from_file(input_pathset)
+    new_pathset = pathset.FilePathset()
+    new_pathset.append(header_file.name)
+    for p in original_pathset:
+      new_pathset.append(p)
+
+    with tempfile.NamedTemporaryFile() as temp_pathset:
+      new_pathset.write(temp_pathset)
+      temp_pathset.flush()
+
+      print "concatenating pathset"
+      # TODO:  Add ability to use dist_cat_paths
+      cat_paths.main([temp_pathset.name, output_path])
+      print "operation complete"
+
+if __name__ == '__main__':
+  main(sys.argv[1:])