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comparison span_wrapper.py @ 2:5b99943c4627 draft

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Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
author jetbrains
date Sun, 18 Nov 2018 08:20:27 -0500
parents 1f0c4f0a9c3b
children 4130e95bd6c8
comparison
equal deleted inserted replaced
1:dfb1e66235c5 2:5b99943c4627
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 2
3 import os 3 import os
4 import shutil
5 import subprocess
4 import sys 6 import sys
5 import subprocess 7
6 argv = sys.argv[1:] 8 argv = sys.argv[1:]
7 print 'Arguments {0}'.format(argv) 9 print 'Arguments {0}'.format(argv)
8 10
9 SPAN_JAR = os.environ.get("SPAN_JAR") 11 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) 12 print 'Using SPAN Peak Analyzer distributive file {0}'.format(SPAN_JAR)
13 13
14 # #if $action.action_selector 14 # #if str($action.action_selector) == "model"
15 # #if str($control.control_selector) == "with_control" 15 # #if $control.control_selector
16 # span_wrapper.py model with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" 16 # span_wrapper.py model with_control
17 # "${genome_identifier}" "${genome_file}"
18 # "${treatment_identifier}" "${treatment_file}"
19 # "${bin}" "${action.model_file}"
20 # "${control_identifier}" "${control.control_file}"
17 # #else 21 # #else
18 # span_wrapper.py model without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" 22 # span_wrapper.py model without_control
23 # "${genome_identifier}" "${genome_file}"
24 # "${treatment_identifier}" "${treatment_file}"
25 # "${bin}" "${action.model_file}"
19 # #end if 26 # #end if
20 # #else 27 # #else
21 # #if $control.control_selector 28 # #if $control.control_selector
22 # span_wrapper.py peaks with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" "${fdr}" "${gap}" "${action.peaks_file}" 29 # span_wrapper.py peaks with_control
30 # "${genome_identifier}" "${genome_file}"
31 # "${treatment_identifier}" "${treatment_file}"
32 # "${bin}" "${action.model_file}"
33 # "${control_identifier}" "${control.control_file}"
34 # "${fdr}" "${gap}" "${action.peaks_file}"
23 # #else 35 # #else
24 # span_wrapper.py peaks without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${fdr}" "${gap}" "${action.peaks_file}" 36 # span_wrapper.py peaks with_control
37 # "${genome_identifier}" "${genome_file}"
38 # "${treatment_identifier}" "${treatment_file}"
39 # "${bin}" "${action.model_file}"
40 # "${fdr}" "${gap}" "${action.peaks_file}"
25 # #end if 41 # #end if
26 # #end if 42 # #end if
27 43
28 # See http://artyomovlab.wustl.edu/aging/span.html for command line options 44 # See https://research.jetbrains.org/groups/biolabs/tools/span-peak-analyzer for command line options
29 action = argv[0] 45 action = argv[0]
30 control = argv[1] 46 control = argv[1]
47
48 working_dir = os.path.abspath('.')
49 print 'WORKING DIRECTORY: {}'.format(working_dir)
50
51
52 def link(name, f):
53 """ SPAN uses file extension to detect input type, so original names are necessary, instead of Galaxy .dat files"""
54 result = os.path.join(working_dir, name)
55 os.symlink(f, result)
56 return result
57
58
31 if action == 'model': 59 if action == 'model':
32 if control == 'with_control': 60 if control == 'with_control':
33 (chrom_sizes, treatment_file, bin, model_file, control_file) = argv[2:] 61 (chrom_sizes, chrom_sizes_file,
62 treatment, treatment_file,
63 bin, model_file,
64 control, control_file) = argv[2:]
34 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {}'.format( 65 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {}'.format(
35 SPAN_JAR, chrom_sizes, treatment_file, control_file, bin 66 SPAN_JAR,
67 link(chrom_sizes, chrom_sizes_file),
68 link(treatment, treatment_file),
69 link(control, control_file),
70 bin
36 ) 71 )
37 print "MODEL FILE" + model_file
38 elif control == 'without_control': 72 elif control == 'without_control':
39 (chrom_sizes, treatment_file, bin, model_file) = argv[2:] 73 (chrom_sizes, chrom_sizes_file,
74 treatment, treatment_file,
75 bin, model_file) = argv[2:]
40 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {}'.format( 76 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {}'.format(
41 SPAN_JAR, argv[2], argv[3], argv[4] 77 SPAN_JAR,
78 link(chrom_sizes, chrom_sizes_file),
79 link(treatment, treatment_file),
80 bin
42 ) 81 )
43 print "MODEL FILE" + model_file
44 else: 82 else:
45 raise Exception("Unknown control option {}".format(control)) 83 raise Exception("Unknown control option {}".format(control))
46 84
47 elif action == "peaks": 85 elif action == "peaks":
48 if control == 'with_control': 86 if control == 'with_control':
49 (chrom_sizes, treatment_file, bin, model_file, control_file, fdr, gap, peaks_file) = argv[2:] 87 (chrom_sizes, chrom_sizes_file,
88 treatment, treatment_file,
89 bin, model_file,
90 control, control_file,
91 fdr, gap, peaks_file) = argv[2:]
50 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {} --fdr {} --gap {} --peaks {}'.format( 92 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 93 SPAN_JAR,
94 link(chrom_sizes, chrom_sizes_file),
95 link(treatment, treatment_file),
96 link(control, control_file),
97 bin, fdr, gap,
98 os.path.join(working_dir, peaks_file)
52 ) 99 )
53 print "MODEL FILE" + model_file
54 elif control == 'without_control': 100 elif control == 'without_control':
55 (chrom_sizes, treatment_file, bin, model_file, fdr, gap, peaks_file) = argv[2:] 101 (chrom_sizes, chrom_sizes_file,
102 treatment, treatment_file,
103 bin, model_file,
104 fdr, gap, peaks_file) = argv[2:]
56 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {} --fdr {} --gap {} --peaks {}'.format( 105 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {} --fdr {} --gap {} --peaks {}'.format(
57 SPAN_JAR, chrom_sizes, treatment_file, bin, fdr, gap, peaks_file 106 SPAN_JAR,
107 link(chrom_sizes, chrom_sizes_file),
108 link(treatment, treatment_file),
109 bin, fdr, gap,
110 os.path.join(working_dir, peaks_file)
58 ) 111 )
59 print "MODEL FILE" + model_file
60 else: 112 else:
61 raise Exception("Unknown control option {}".format(control)) 113 raise Exception("Unknown control option {}".format(control))
62 else: 114 else:
63 raise Exception("Unknown action command {}".format(action)) 115 raise Exception("Unknown action command {}".format(action))
64 116
65 117
66 print 'Launching SPAN: {0}'.format(cmd) 118 print 'Launching SPAN: {}'.format(cmd)
119 print 'Model file: {}'.format(model_file)
120 try:
121 print 'Peaks file: {}'.format(peaks_file)
122 except NameError:
123 pass
124
67 subprocess.check_call(cmd, cwd=None, shell=True) 125 subprocess.check_call(cmd, cwd=None, shell=True)
126
127 # Move model to the the working dir with given name
128 fit_dir = os.path.join(working_dir, 'fit')
129 model_original = os.path.join(fit_dir, os.listdir(fit_dir)[0])
130 shutil.move(model_original, os.path.join(working_dir, model_file))
131
132 # Move log file
133 logs_dir = os.path.join(working_dir, 'logs')
134 log_original = os.path.join(logs_dir, os.listdir(logs_dir)[0])
135 shutil.move(log_original, os.path.join(working_dir, "span.log"))