Mercurial > repos > sanbi-uwc > build_ctb_gene

annotate build_ctb_gene.py @ 4:714cbeae0b96 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
author sanbi-uwc
date Mon, 16 May 2016 04:20:19 -0400
parents
children 6098213127d7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
1 #!/usr/bin/env python
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
2 from __future__ import print_function
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
3 import argparse
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
4 import os
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
5 import sys
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
6 import glob
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
7
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
8 import logging
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
9 log = logging.getLogger( __name__ )
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
10
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
11 def build_ctb_gene(output_file1, output_dir, input_file, mount_point ):
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
12 #cmdline_str = "build_ctb_gene goterms ${}".format(input_file)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
13 cmdline_str = "echo goterms"
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
14 build_ctb = False
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
15 try:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
16 os.system(cmdline_str)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
17 build_ctb = True
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
18 except:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
19 log.debug("Error running the build_ctb_gene goterms", file=sys.stderr)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
20
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
21 # Read the files at the mount point and load the html file
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
22 if build_ctb == True:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
23 files=glob.glob(mount_point)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
24 output_file1 = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
25 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
26 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
27 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
28 <title></title>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
29 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
30 </head>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
31 <body>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
32 <div class="toolFormBody">
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
33 <table>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
34 <th>Files</th>
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
35 """
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
36 for file in files:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
37 output_file1 += """<tr><td>file</td></tr>"""
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
38 output_file1 += """</table></div></body></html>\n"""
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
39
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
40
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
41 def main():
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
42 parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
43 parser.add_argument('output_file1')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
44 parser.add_argument('output_dir')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
45 parser.add_argument('--input_file')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
46 parser.add_argument('--mount_point')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
47 parser.add_argument('--username')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
48 parser.add_argument('--password')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
49 parser.add_argument('--url')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
50 parser.add_argument('--port')
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
51 args = parser.parse_args()
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
52
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
53 export_cmd = "export NEO4J_REST_URL=http://${neo4j_db_username}:${neo4j_db_password}@${neo4j_db_url}:${neo4j_db_port}/db/data/"
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
54 try:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
55 os.system(export_cmd)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
56 except:
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
57 log.debug("Error exporting the NEO4J db environmental values")
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
58
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
59 build_ctb_gene(args.output_file1, args.output_dir, args.input_file, args.mount_point)
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
60
714cbeae0b96 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 43f091b6ac53f9754906c0be9ab6ced467cb3535
sanbi-uwc
parents:
diff changeset
61 if __name__ == "__main__": main()