Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder

annotate data_manager/novocraft_index_builder.py @ 7:d04a59b76845 draft

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planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 03f281362d5cf7c4d2a813203b83f5d12eb8ca46
author sanbi-uwc
date Sat, 05 Mar 2016 09:19:21 -0500
parents 8dd4b25716d1
children 56e8324519c4
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6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
sanbi-uwc
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1 #!/usr/bin/env python
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
sanbi-uwc
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2 # Z. Mashologu (SANBI-UWC)
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3 # import dict as dict
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sanbi-uwc
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4 from __future__ import print_function
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5 import os
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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6 import sys
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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7 import urllib2
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8 import logging
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9 import argparse
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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10 import shlex
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11 from subprocess import check_call, CalledProcessError
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13 log = logging.getLogger(__name__)
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15 from json import loads, dumps
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17 DEFAULT_DATA_TABLE_NAME = "novocraft_index"
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19 def get_dbkey_id_name(params, dbkey_description=None):
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20 dbkey = params['param_dict']['dbkey']
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
sanbi-uwc
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21 # TODO: ensure sequence_id is unique and does not already appear in location file
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sanbi-uwc
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22 sequence_id = params['param_dict']['sequence_id']
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sanbi-uwc
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23 if not sequence_id:
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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24 sequence_id = dbkey # uuid.uuid4() generate and use an uuid instead?
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26 sequence_name = params['param_dict']['sequence_name']
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27 if not sequence_name:
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28 sequence_name = dbkey_description
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29 if not sequence_name:
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
sanbi-uwc
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30 sequence_name = dbkey
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31 return dbkey, sequence_id, sequence_name
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32
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33 def _make_novocraft_index(data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME):
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34 if os.path.exists(target_directory) and not os.path.isdir(target_directory):
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35 print("Output directory path already exists but is not a directory: {}".format(target_directory),
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36 file=sys.stderr)
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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37 elif not os.path.exists(target_directory):
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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38 os.mkdir(target_directory)
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40 if 'GALAXY_SLOTS' in os.environ:
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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41 nslots = os.environ['GALAXY_SLOTS']
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42 else:
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43 nslots = 1
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45 #cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format(
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46 # target_directory,
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47 # fasta_filename,
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48 # nslots)
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49 #cmdline = shlex.split(cmdline_str)
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50 index_filename = 'foo.nix'
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51 cmdline = ('touch', '{}/{}'.format(target_directory, index_filename))
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52 try:
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53 check_call(cmdline)
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54 except CalledProcessError:
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55 print("Error building RNA STAR index", file=sys.stderr)
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57 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=target_directory )
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58 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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59 return ( index_filename )
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61 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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62 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
c276a826fc4b planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 1e4e16c747ca6ef261d3307f47a09ff1d49756a1
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63 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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64 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
c276a826fc4b planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 1e4e16c747ca6ef261d3307f47a09ff1d49756a1
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65 return data_manager_dict
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66
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67 def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
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6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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68 # TODO: we should automatically do decompression here
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69 urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n')))
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70 fasta_reader = [urllib2.urlopen(url) for url in urls]
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72 _make_novocraft_index(data_manager_dict, fasta_reader, target_directory, dbkey, sequence_id, sequence_name, data_table_name)
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74 def download_from_history( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
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6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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75 # TODO: allow multiple FASTA input files
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76 input_filename = params['param_dict']['reference_source']['input_fasta']
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78 _make_novocraft_index(data_manager_dict, input_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name)
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80 REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history)
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82 def main():
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83 parser = argparse.ArgumentParser(description="Generate Novo-craft genome index and JSON describing this")
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84 parser.add_argument('output_filename')
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85 parser.add_argument('--dbkey_description')
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86 parser.add_argument('--data_table_name', default='novocraft_index')
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87 args = parser.parse_args()
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88
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89 filename = args.output_filename
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91 params = loads(open(filename).read())
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92 target_directory = params['output_data'][0]['extra_files_path']
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93 os.makedirs(target_directory)
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94 data_manager_dict = {}
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96 dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description)
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97
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98 if dbkey in [None, '', '?']:
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99 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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101 # Fetch the FASTA
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102 REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\
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103 (data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=args.data_table_name or DEFAULT_DATA_TABLE_NAME)
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104
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105 open(filename, 'wb').write(dumps( data_manager_dict ))
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106
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107 if __name__ == "__main__": main()