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1 #!/usr/bin/env python
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2
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3 # Copyright (C) 2011-2014 CRS4.
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4 #
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5 # This file is part of Seal.
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6 #
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7 # Seal is free software: you can redistribute it and/or modify it
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8 # under the terms of the GNU General Public License as published by the Free
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9 # Software Foundation, either version 3 of the License, or (at your option)
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10 # any later version.
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11 #
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12 # Seal is distributed in the hope that it will be useful, but
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13 # WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
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14 # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
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15 # for more details.
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16 #
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17 # You should have received a copy of the GNU General Public License along
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18 # with Seal. If not, see <http://www.gnu.org/licenses/>.
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19
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20
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21
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22 import os
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23 import subprocess
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24 import sys
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25 import tempfile
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26
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27 import hadoop_galaxy.pathset as pathset
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28 import hadoop_galaxy.cat_paths as cat_paths
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29
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30 def usage_error(msg=None):
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31 if msg:
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32 print >> sys.stderr, msg
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33 print >> sys.stderr, os.path.basename(__file__), "INPUT_PATHSET OUTPUT [args...]"
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34 sys.exit(1)
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35
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36 def main(args):
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37 if len(args) < 2:
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38 usage_error()
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39
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40 # We generate the header with seal_merge_alignments, insert it at the
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41 # top of a copy of the input pathset, and then use cat_parts to
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42 # join everything into a single file.
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43
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44 input_pathset, output_path = map(os.path.abspath, args[0:2])
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45
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46 with tempfile.NamedTemporaryFile() as header_file:
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47 print "generating header"
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48 gen_header_cmd = [ 'seal', 'merge_alignments', '--header-only' ]
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49 gen_header_cmd.extend(args[2:])
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50 header_text = subprocess.check_output(gen_header_cmd)
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51
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52 header_file.write(header_text)
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53 header_file.flush()
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54 print "header ready"
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55 print "generating new pathset"
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56
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57 original_pathset = pathset.FilePathset.from_file(input_pathset)
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58 new_pathset = pathset.FilePathset()
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59 new_pathset.append(header_file.name)
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60 for p in original_pathset:
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61 new_pathset.append(p)
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62
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63 with tempfile.NamedTemporaryFile() as temp_pathset:
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64 new_pathset.write(temp_pathset)
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65 temp_pathset.flush()
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66
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67 print "concatenating pathset"
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68 # TODO: Add ability to use dist_cat_paths
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69 cat_paths.main([temp_pathset.name, output_path])
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70 print "operation complete"
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71
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72 if __name__ == '__main__':
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73 main(sys.argv[1:])
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