Mercurial > repos > devteam > data_manager_twobit_builder

annotate data_manager/twobit_builder.py @ 5:ced9f4a48806 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
author iuc
date Mon, 18 Nov 2019 22:43:06 +0000
parents c9896bb1f03c
children 94bffa4fdedc
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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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c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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2 # Dan Blankenberg
c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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3 from __future__ import print_function
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4
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5 import optparse
c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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6 import os
c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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7 import subprocess
c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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8 import sys
c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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9 import tempfile
c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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10 from json import dumps, loads
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11
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12 CHUNK_SIZE = 2**20 # 1mb
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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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ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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15 def get_id_name(params, dbkey, fasta_description=None):
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16 # TODO: ensure sequence_id is unique and does not already appear in location file
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17 sequence_id = params['param_dict']['sequence_id']
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18 if not sequence_id:
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19 sequence_id = dbkey # uuid.uuid4() generate and use an uuid
c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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21 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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22 if not sequence_name:
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23 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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24 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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25 sequence_name = dbkey
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26 return sequence_id, sequence_name
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29 def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name):
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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30 twobit_base_name = "%s.2bit" % (sequence_id)
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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31 twobit_filename = os.path.join(target_directory, twobit_base_name)
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33 args = ['faToTwoBit', fasta_filename, twobit_filename]
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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34 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-twobit-builder-stderr")
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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35 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno())
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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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36 return_code = proc.wait()
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 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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38 tmp_stderr.flush()
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39 tmp_stderr.seek(0)
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40 print("Error building index:", file=sys.stderr)
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41 while True:
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42 chunk = tmp_stderr.read(CHUNK_SIZE)
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43 if not chunk:
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44 break
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45 sys.stderr.write(chunk)
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46 sys.exit(return_code)
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47 tmp_stderr.close()
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48 # lastz_seqs
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49 data_table_entry = dict(value=sequence_id, name=sequence_name, path=twobit_base_name)
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51 _add_data_table_entry(data_manager_dict, "lastz_seqs", data_table_entry)
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52 # twobit.loc
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53 data_table_entry = dict(value=sequence_id, path=twobit_base_name)
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55 _add_data_table_entry(data_manager_dict, "twobit", data_table_entry)
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56 # alignseq
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57 data_table_entry = dict(type="seq", value=sequence_id, path=twobit_base_name)
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59 _add_data_table_entry(data_manager_dict, "alignseq_seq", data_table_entry)
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62 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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63 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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64 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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65 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
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66 return data_manager_dict
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69 def 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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70 parser = optparse.OptionParser()
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71 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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72 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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73 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
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74 (options, args) = parser.parse_args()
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75
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76 filename = args[0]
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78 params = loads(open(filename).read())
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80 target_directory = params['output_data'][0]['extra_files_path']
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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81 os.mkdir(target_directory)
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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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82 data_manager_dict = {}
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84 dbkey = options.fasta_dbkey
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86 if dbkey in [None, '', '?']:
ced9f4a48806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 82ad45497a7b2277a710c634378a4122fb75ce1f"
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87 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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89 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
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91 # build the index
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92 build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name)
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94 # save info to json file
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95 open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True))
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97
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98 if __name__ == "__main__":
c9896bb1f03c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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99 main()