annotate breseq_wrapper.py @ 3:77c1ee3bad82 draft

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author dsobral
date Sat, 03 Mar 2018 11:44:15 -0500
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1 # -*- coding: utf-8 -*-
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2
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3 from __future__ import print_function
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4 import sys
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5 import os
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6 import shutil
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7 from subprocess import call
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8 from glob import glob
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9
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10 """
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11 Expected input format:
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12 ./thiscript output_file output_folder zipfile (args)
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13 """
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14
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15
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16 def fail(exitcode):
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17 sys.stderr.write("Breseq did not finish successfully\n")
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18 sys.stderr.write("Exit code was: {0}\n".format(exitcode))
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19 sys.exit(1)
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20
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21
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22 def main(args):
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23 output, outdir = args[1:3]
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24 cmd = ["breseq"] + args[3:]
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25
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26 returncode = call(cmd)
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27
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28 if returncode != 0:
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29 fail(returncode)
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30
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31 # the short HTML report
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32 summary = "output/summary.html"
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33 if not os.path.isfile(summary):
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34 fail(returncode)
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35
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36 # Data will be in the zipfile together will all the content of "output"
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37 shutil.move("data", "output/")
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38
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39 if not os.path.isfile(outdir):
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40 os.mkdir(outdir)
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41
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42 # Zip the whole folder
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43 shutil.make_archive("results", "zip", os.path.dirname(outdir), "output/")
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44 shutil.move("results.zip", outdir)
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45
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46 shutil.copy(summary, output)
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47
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48 # move all the files needed for preview of HTML
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49 for file in glob("output/*"):
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50 dest = file.split("/", 1)[1]
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51 # Folder "data" only needs to go in the zipfile not the HTML preview
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52 if file == "data":
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53 continue
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54
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55 shutil.move(file, os.path.join(outdir, dest))
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56
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57
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58 def usage():
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59 err = sys.stderr
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60 err.write("Usage:\n")
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61 err.write(" {0} output_filename output_folder [args]\n".format(
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62 sys.argv[0]))
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63 sys.exit(1)
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64
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65 if __name__ == "__main__":
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66 args = sys.argv
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67
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68 if len(args) <= 3:
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69 usage()
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71 main(args)
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72
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73 # vim: ai sts=4 et sw=4