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annotate data_manager/data_manager_sam_fasta_index_builder.py @ 3:1f54e98616af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:13:56 -0400
parents 2a1ac1abc3f7
children cc4ef4d38cf9
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1 #!/usr/bin/env python
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2 # Dan Blankenberg
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4 import json
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5 import optparse
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6 import os
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7 import subprocess
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8 import sys
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9 import tempfile
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10
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11 CHUNK_SIZE = 2**20
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12
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13 DEFAULT_DATA_TABLE_NAME = "fasta_indexes"
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14
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16 def get_id_name( params, dbkey, fasta_description=None):
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17 # TODO: ensure sequence_id is unique and does not already appear in location file
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18 sequence_id = params['param_dict']['sequence_id']
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19 if not sequence_id:
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20 sequence_id = dbkey
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1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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21
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22 sequence_name = params['param_dict']['sequence_name']
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23 if not sequence_name:
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24 sequence_name = fasta_description
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25 if not sequence_name:
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26 sequence_name = dbkey
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27 return sequence_id, sequence_name
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30 def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
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31 # TODO: allow multiple FASTA input files
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32 assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename
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33 fasta_base_name = os.path.split( fasta_filename )[-1]
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34 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
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35 os.symlink( fasta_filename, sym_linked_fasta_filename )
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36
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37 args = [ 'samtools', 'faidx' ]
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38 args.append( sym_linked_fasta_filename )
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1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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39 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-sam_fa_index_builder-stderr")
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40 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
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41 return_code = proc.wait()
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42 if return_code:
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43 tmp_stderr.flush()
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44 tmp_stderr.seek( 0 )
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45 sys.stderr.write( "Error building index:\n" )
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46 while True:
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47 chunk = tmp_stderr.read( CHUNK_SIZE )
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48 if not chunk:
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49 break
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50 sys.stderr.write( chunk )
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51 sys.exit( return_code )
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52 tmp_stderr.close()
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53 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
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54 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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55
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56
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57 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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58 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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59 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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60 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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61 return data_manager_dict
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62
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63
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64 def main():
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65 parser = optparse.OptionParser()
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66 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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67 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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68 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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69 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
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70 (options, args) = parser.parse_args()
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72 filename = args[0]
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74 params = json.loads( open( filename ).read() )
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75 target_directory = params[ 'output_data' ][0]['extra_files_path']
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76 os.mkdir( target_directory )
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77 data_manager_dict = {}
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78
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79 if options.fasta_dbkey in [ None, '', '?' ]:
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80 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
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81
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82 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
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84 # build the index
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85 build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
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87 # save info to json file
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88 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
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91 if __name__ == "__main__":
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92 main()