Mercurial > repos > devteam > data_manager_twobit_builder

annotate data_manager/twobit_builder.py @ 1:298d15849a14 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
author devteam
date Thu, 19 Jan 2017 11:45:29 -0500
parents 26e3ae5f74ed
children c9896bb1f03c
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26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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4 import sys, os, tempfile, optparse, uuid, subprocess
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6 from json import loads, dumps
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9 CHUNK_SIZE = 2**20 #1mb
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11 def get_id_name( params, dbkey, fasta_description=None):
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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12 #TODO: ensure sequence_id is unique and does not already appear in location file
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13 sequence_id = params['param_dict']['sequence_id']
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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14 if not sequence_id:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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15 sequence_id = dbkey #uuid.uuid4() generate and use an uuid
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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17 sequence_name = params['param_dict']['sequence_name']
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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18 if not sequence_name:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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19 sequence_name = fasta_description
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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20 if not sequence_name:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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21 sequence_name = dbkey
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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22 return sequence_id, sequence_name
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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24 def build_twobit( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ):
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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25 twobit_base_name = "%s.2bit" % ( sequence_id )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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26 twobit_filename = os.path.join( target_directory, twobit_base_name )
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28 args = [ 'faToTwoBit', fasta_filename, twobit_filename ]
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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29 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-twobit-builder-stderr" )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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30 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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31 return_code = proc.wait()
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32 if return_code:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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33 tmp_stderr.flush()
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34 tmp_stderr.seek(0)
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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35 print >> sys.stderr, "Error building index:"
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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36 while True:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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37 chunk = tmp_stderr.read( CHUNK_SIZE )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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38 if not chunk:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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39 break
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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40 sys.stderr.write( chunk )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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41 sys.exit( return_code )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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42 tmp_stderr.close()
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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43 #lastz_seqs
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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44 data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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46 _add_data_table_entry( data_manager_dict, "lastz_seqs", data_table_entry )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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47 #twobit.loc
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48 data_table_entry = dict( value=sequence_id, path=twobit_base_name )
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50 _add_data_table_entry( data_manager_dict, "twobit", data_table_entry )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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51 #alignseq
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52 data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name )
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54 _add_data_table_entry( data_manager_dict, "alignseq_seq", data_table_entry )
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56 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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57 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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58 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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59 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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60 return data_manager_dict
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62 def main():
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63 #Parse Command Line
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64 parser = optparse.OptionParser()
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65 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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66 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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67 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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68 (options, args) = parser.parse_args()
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70 filename = args[0]
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72 params = loads( open( filename ).read() )
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74 target_directory = params[ 'output_data' ][0]['extra_files_path']
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75 os.mkdir( target_directory )
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76 data_manager_dict = {}
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78 dbkey = options.fasta_dbkey
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26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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80 if dbkey in [ None, '', '?' ]:
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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81 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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83 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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85 #build the index
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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86 build_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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88 #save info to json file
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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89 open( filename, 'wb' ).write( dumps( data_manager_dict ) )
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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91 if __name__ == "__main__": main()
26e3ae5f74ed planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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