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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 """
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23 Calls the Seal RecabTable tool. Then, it calls recab_table_fetch to
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24 concatenate all the partial tables and create a single csv file.
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25 """
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26
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27
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28 # parameters:
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29 # INPUT_DATA
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30 # OUTPUT
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31 # VCF
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32 # NUM_REDUCERS
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33 # [OTHER]
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34
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35 import os
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36 import sys
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37
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38 import hadoop_galaxy.pathset as pathset
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39 import subprocess
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40 import tempfile
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41 import pydoop.hdfs as phdfs
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42
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43 # XXX: add --append-python-path to the possible arguments?
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44
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45 def usage_error(msg=None):
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46 if msg:
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47 print >> sys.stderr, msg
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48 print >> sys.stderr, os.path.basename(sys.argv[0]), "INPUT_DATA OUTPUT VCF NUM_REDUCERS [OTHER]"
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49 sys.exit(1)
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50
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51
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52 def run_recab(input_path, output_path, vcf, num_red, other_args):
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53 mydir = os.path.abspath(os.path.dirname(__file__))
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54 cmd = [
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55 'hadoop_galaxy',
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56 '--input', input_path,
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57 '--output', output_path,
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58 '--executable', 'seal',
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59 'recab_table',
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60 '--vcf-file', vcf,
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61 '--num-reducers', num_red
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62 ]
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63
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64 if other_args:
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65 cmd.extend(other_args)
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66
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67 # now execute the hadoop job
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68 subprocess.check_call(cmd)
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69
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70 def collect_table(pset, output_path):
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71 # finally, fetch the result into the final output file
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72 cmd = ['seal', 'recab_table_fetch']
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73 cmd.extend(pset.get_paths())
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74 cmd.append(output_path)
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75 try:
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76 # remove the file that galaxy creates. recab_table_fetch refuses to
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77 # overwrite it
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78 os.unlink(output_path)
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79 except IOError:
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80 pass
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81 subprocess.check_call(cmd)
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82
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83 def cleanup(out_pathset):
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84 # clean-up job output
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85 for path in out_pathset:
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86 try:
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87 print >> sys.stderr, "Deleting output path", path
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88 phdfs.rmr(path)
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89 except StandardError as e:
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90 print >> sys.stderr, "Error!", str(e)
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91
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92 def main(args):
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93 if len(args) < 5:
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94 usage_error()
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95
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96 input_data = args[0]
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97 final_output = args[1]
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98 vcf = args[2]
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99 num_reducers = args[3]
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100 other = args[4:]
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101
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102 # Create a temporary pathset to reference the recab_table
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103 # output directory
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104 with tempfile.NamedTemporaryFile(mode='rwb') as tmp_pathset_file:
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105 try:
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106 run_recab(input_data, tmp_pathset_file.name, vcf, num_reducers, other)
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107 tmp_pathset_file.seek(0)
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108 out_paths = pathset.FilePathset.from_file(tmp_pathset_file)
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109 collect_table(out_paths, final_output)
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110 finally:
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111 cleanup(out_paths)
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112
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113 if __name__ == "__main__":
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114 main(sys.argv[1:])
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115
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116 # vim: et ai ts=2 sw=2
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