Mercurial > repos > devteam > data_manager_twobit_builder

annotate data_manager/twobit_builder.py @ 2:9946bc39c834 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:16:29 -0400
parents 74b09c8e5f6e
children 5c77d4091880
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74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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1 #!/usr/bin/env python
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2 # Dan Blankenberg
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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3 from __future__ import print_function
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4
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5 import optparse
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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6 import os
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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7 import subprocess
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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8 import sys
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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9 import tempfile
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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10 from json import dumps, loads
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11
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12 CHUNK_SIZE = 2**20 # 1mb
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15 def get_id_name( params, dbkey, fasta_description=None):
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16 # TODO: ensure sequence_id is unique and does not already appear in location file
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17 sequence_id = params['param_dict']['sequence_id']
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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18 if not sequence_id:
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19 sequence_id = dbkey # uuid.uuid4() generate and use an uuid
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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21 sequence_name = params['param_dict']['sequence_name']
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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22 if not sequence_name:
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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23 sequence_name = fasta_description
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24 if not sequence_name:
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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25 sequence_name = dbkey
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26 return sequence_id, sequence_name
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27
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29 def build_twobit( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ):
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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30 twobit_base_name = "%s.2bit" % ( sequence_id )
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31 twobit_filename = os.path.join( target_directory, twobit_base_name )
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33 args = [ 'faToTwoBit', fasta_filename, twobit_filename ]
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34 tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-twobit-builder-stderr" )
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74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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35 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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36 return_code = proc.wait()
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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37 if return_code:
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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38 tmp_stderr.flush()
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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39 tmp_stderr.seek(0)
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40 print("Error building index:", file=sys.stderr)
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41 while True:
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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42 chunk = tmp_stderr.read( CHUNK_SIZE )
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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43 if not chunk:
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44 break
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45 sys.stderr.write( chunk )
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46 sys.exit( return_code )
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47 tmp_stderr.close()
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48 # lastz_seqs
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49 data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name )
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51 _add_data_table_entry( data_manager_dict, "lastz_seqs", data_table_entry )
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52 # twobit.loc
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53 data_table_entry = dict( value=sequence_id, path=twobit_base_name )
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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55 _add_data_table_entry( data_manager_dict, "twobit", data_table_entry )
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56 # alignseq
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57 data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name )
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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59 _add_data_table_entry( data_manager_dict, "alignseq_seq", data_table_entry )
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62 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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63 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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64 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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65 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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66 return data_manager_dict
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69 def main():
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70 parser = optparse.OptionParser()
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71 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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72 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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73 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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74 (options, args) = parser.parse_args()
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76 filename = args[0]
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78 params = loads( open( filename ).read() )
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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79
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80 target_directory = params[ 'output_data' ][0]['extra_files_path']
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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81 os.mkdir( target_directory )
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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82 data_manager_dict = {}
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83
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74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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84 dbkey = options.fasta_dbkey
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85
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74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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86 if dbkey in [ None, '', '?' ]:
74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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87 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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88
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74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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89 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
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90
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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91 # build the index
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74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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92 build_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name )
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93
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94 # save info to json file
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74b09c8e5f6e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
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95 open( filename, 'wb' ).write( dumps( data_manager_dict ) )
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96
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97
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98 if __name__ == "__main__":
9946bc39c834 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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99 main()