Mercurial > repos > sanbi-uwc > data_manager_novoalign_index_builder

annotate data_manager/novoalign_index_builder.py @ 2:e51fb8188ed9 draft

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planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
author sanbi-uwc
date Thu, 03 Mar 2016 08:40:42 -0500
parents 85fbd52dbb36
children b63a406719c5
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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
1 #!/usr/bin/env python
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
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4 import os
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sanbi-uwc
parents: 0
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5 import sys
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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
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6 import urllib2
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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7 import logging
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sanbi-uwc
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8 import argparse
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
parents: 0
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9 import shlex
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
parents: 0
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10 from subprocess import check_call, CalledProcessError
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
parents: 0
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11 from __future__ import print_function
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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13 log = logging.getLogger(__name__)
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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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15 from json import loads, dumps
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16
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sanbi-uwc
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17 def get_dbkey_id_name(params, dbkey_description=None):
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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18 dbkey = params['param_dict']['dbkey']
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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19 # TODO: ensure sequence_id is unique and does not already appear in location file
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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20 sequence_id = params['param_dict']['sequence_id']
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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21 if not sequence_id:
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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22 sequence_id = dbkey # uuid.uuid4() generate and use an uuid instead?
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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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23
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24 sequence_name = params['param_dict']['sequence_name']
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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25 if not sequence_name:
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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26 sequence_name = dbkey_description
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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27 if not sequence_name:
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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28 sequence_name = dbkey
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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29 return dbkey, sequence_id, sequence_name
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32 def _make_novocraft_index(fasta_filename, target_directory):
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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33 if os.path.exists(target_directory) and not os.path.isdir(target_directory):
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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34 print("Output directory path already exists but is not a directory: {}".format(target_directory),
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
sanbi-uwc
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35 file=sys.stderr)
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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36 elif not os.path.exists(target_directory):
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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37 os.mkdir(target_directory)
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39 if 'GALAXY_SLOTS' in os.environ:
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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40 nslots = os.environ['GALAXY_SLOTS']
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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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41 else:
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sanbi-uwc
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42 nslots = 1
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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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43
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44 cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format(
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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45 target_directory,
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46 fasta_filename,
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47 nslots)
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48 cmdline = shlex.split(cmdline_str)
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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49 try:
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50 check_call(cmdline)
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51 except CalledProcessError:
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52 print("Error building RNA STAR index", file=sys.stderr)
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53 return (target_directory)
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55
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56 def download_from_url(params, target_directory):
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57 # TODO: we should automatically do decompression here
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58 urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n')))
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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59 fasta_reader = [urllib2.urlopen(url) for url in urls]
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61 _make_novocraft_index(fasta_reader, target_directory)
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62
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64 def download_from_history( params, target_directory):
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sanbi-uwc
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65 # TODO: allow multiple FASTA input files
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66 input_filename = params['param_dict']['reference_source']['input_fasta']
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68 _make_novocraft_index(input_filename, target_directory)
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70 REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history)
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72 def main():
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73 parser = argparse.ArgumentParser(description="Generate Novo-align genome index and JSON describing this")
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74 parser.add_argument('output_filename')
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75 parser.add_argument('--data_table_name', default='novocraft_index')
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76 (options, args) = parser.parse_args()
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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78 filename = args.output_filename
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80 params = loads(open(filename).read())
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81 target_directory = params['output_data'][0]['extra_files_path']
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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82 os.mkdir(target_directory)
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84 dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=options.dbkey_description)
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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85 if dbkey in [None, '', '?']:
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86 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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88 # Fetch the FASTA
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89 REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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90 (params, target_directory, dbkey, sequence_id, sequence_name)
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91
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92 data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=target_directory)
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85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
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93
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94 output_datatable_dict = dict(data_tables={args.data_table_name: [data_table_entry]})
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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95 open(filename, 'wb').write(dumps(output_datatable_dict))
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96
e51fb8188ed9 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20
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97 if __name__ == "__main__": main()