Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder

annotate data_manager/novocraft_index_builder.py @ 17:db293ee25be5 draft

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planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 0745f158bbb0d5d190cc4503157d2d3092ab8cc5
author sanbi-uwc
date Fri, 15 Apr 2016 09:03:40 -0400
parents d053e7b179b5
children 2b89ba1c0057
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sanbi-uwc
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1 #!/usr/bin/env python
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sanbi-uwc
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2 # Z. Mashologu (SANBI-UWC)
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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
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6 import sys
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7 import urllib2
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8 import logging
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9 import argparse
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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 # TODO: ensure sequence_id is unique and does not already appear in location file
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sanbi-uwc
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21 sequence_id = params['param_dict']['sequence_id']
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sanbi-uwc
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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 = dbkey_description
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sanbi-uwc
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25 return sequence_id, sequence_name
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sanbi-uwc
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27 def _make_novocraft_index(data_manager_dict, fasta_filename, target_directory, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME):
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28 if os.path.exists(target_directory) and not os.path.isdir(target_directory):
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29 print("Output directory path already exists but is not a directory: {}".format(target_directory),
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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30 file=sys.stderr)
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31 elif not os.path.exists(target_directory):
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32 os.mkdir(target_directory)
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34 nix_file = sequence_id + ".nix"
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35 index_filename = os.path.join(target_directory, nix_file)
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36 cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename)
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37 cmdline = shlex.split(cmdline_str)
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39 try:
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40 check_call(cmdline)
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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41 except CalledProcessError:
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42 print("Error building RNA STAR index", file=sys.stderr)
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44 data_table_entry = dict( value=sequence_id, dbkey=sequence_id, name=sequence_name, path=index_filename )
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45 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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47 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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48 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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49 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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50 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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51 return data_manager_dict
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53 def download_from_url( data_manager_dict, params, target_directory, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
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54 # TODO: we should automatically do decompression here
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55 urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n')))
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56 fasta_reader = [urllib2.urlopen(url) for url in urls]
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58 _make_novocraft_index(data_manager_dict, fasta_reader, target_directory, sequence_id, sequence_name, data_table_name)
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60 def download_from_history( data_manager_dict, params, target_directory, 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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61 # TODO: allow multiple FASTA input files
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62 input_filename = params['param_dict']['reference_source']['input_fasta']
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64 _make_novocraft_index(data_manager_dict, input_filename, target_directory, sequence_id, sequence_name, data_table_name )
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66 REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history)
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68 def main():
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69 parser = argparse.ArgumentParser(description="Generate Novo-craft genome index and JSON describing this")
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70 parser.add_argument('output_filename')
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71 parser.add_argument('--dbkey_description')
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72 parser.add_argument('--data_table_name', default='novocraft_index')
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73 args = parser.parse_args()
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75 filename = args.output_filename
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77 params = loads(open(filename).read())
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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78 target_directory = params['output_data'][0]['extra_files_path']
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79 os.makedirs(target_directory)
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80 data_manager_dict = {}
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82 sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description)
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6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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84 # Fetch the FASTA
6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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85 REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\
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db293ee25be5 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 0745f158bbb0d5d190cc4503157d2d3092ab8cc5
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86 (data_manager_dict, params, target_directory, sequence_id, sequence_name, data_table_name=args.data_table_name or 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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87
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c276a826fc4b planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 1e4e16c747ca6ef261d3307f47a09ff1d49756a1
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88 open(filename, 'wb').write(dumps( data_manager_dict ))
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6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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6cddc1a6e282 planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 3a0b36e3ee66f35f7e2d5e1220cd883a9d528fac
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90 if __name__ == "__main__": main()