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