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comparison span_wrapper.py @ 0:1f0c4f0a9c3b draft

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Initial version of SPAN for ToolShed
author jetbrains
date Thu, 15 Nov 2018 11:04:49 -0500
parents
children 5b99943c4627
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-1:000000000000 0:1f0c4f0a9c3b
1 #!/usr/bin/env python
2
3 import os
4 import sys
5 import subprocess
6 argv = sys.argv[1:]
7 print 'Arguments {0}'.format(argv)
8
9 SPAN_JAR = os.environ.get("SPAN_JAR")
10 # span.jar from Docker container
11 # SPAN_JAR = "/root/span.jar"
12 print 'Using SPAN Peak Analyzer distributive file {0}'.format(SPAN_JAR)
13
14 # #if $action.action_selector
15 # #if str($control.control_selector) == "with_control"
16 # span_wrapper.py model with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}"
17 # #else
18 # span_wrapper.py model without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}"
19 # #end if
20 # #else
21 # #if $control.control_selector
22 # span_wrapper.py peaks with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" "${fdr}" "${gap}" "${action.peaks_file}"
23 # #else
24 # span_wrapper.py peaks without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${fdr}" "${gap}" "${action.peaks_file}"
25 # #end if
26 # #end if
27
28 # See http://artyomovlab.wustl.edu/aging/span.html for command line options
29 action = argv[0]
30 control = argv[1]
31 if action == 'model':
32 if control == 'with_control':
33 (chrom_sizes, treatment_file, bin, model_file, control_file) = argv[2:]
34 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {}'.format(
35 SPAN_JAR, chrom_sizes, treatment_file, control_file, bin
36 )
37 print "MODEL FILE" + model_file
38 elif control == 'without_control':
39 (chrom_sizes, treatment_file, bin, model_file) = argv[2:]
40 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {}'.format(
41 SPAN_JAR, argv[2], argv[3], argv[4]
42 )
43 print "MODEL FILE" + model_file
44 else:
45 raise Exception("Unknown control option {}".format(control))
46
47 elif action == "peaks":
48 if control == 'with_control':
49 (chrom_sizes, treatment_file, bin, model_file, control_file, fdr, gap, peaks_file) = argv[2:]
50 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {} --fdr {} --gap {} --peaks {}'.format(
51 SPAN_JAR, chrom_sizes, treatment_file, control_file, bin, fdr, gap, peaks_file
52 )
53 print "MODEL FILE" + model_file
54 elif control == 'without_control':
55 (chrom_sizes, treatment_file, bin, model_file, fdr, gap, peaks_file) = argv[2:]
56 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {} --fdr {} --gap {} --peaks {}'.format(
57 SPAN_JAR, chrom_sizes, treatment_file, bin, fdr, gap, peaks_file
58 )
59 print "MODEL FILE" + model_file
60 else:
61 raise Exception("Unknown control option {}".format(control))
62 else:
63 raise Exception("Unknown action command {}".format(action))
64
65
66 print 'Launching SPAN: {0}'.format(cmd)
67 subprocess.check_call(cmd, cwd=None, shell=True)