Mercurial > repos > dfornika > data_manager_build_mash_sketch

annotate data_manager/mash_build_sketch.py @ 8:8c4654df4d58 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mash_sketch/ commit 423cf96266f6ac433052ff72edb1397502313010-dirty
author dfornika
date Thu, 25 Jul 2019 14:56:00 -0400
parents 628353238ad1
children 97170f449e08
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1 #!/usr/bin/env python
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3 from __future__ import print_function
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5 import argparse
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6 import datetime
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7 import errno
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8 import json
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9 import os
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10 import string
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11 import subprocess
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12 import sys
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13 import uuid
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16 DATA_TABLE_NAME = "mash_sketches"
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19 def mash_build_sketch(target_directory, mash_args, database_name, data_table_name=DATA_TABLE_NAME):
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21 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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23 database_value = str(uuid.uuid4())
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25 database_name = database_name
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27 database_path = database_value
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29 try:
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30 os.mkdir( os.path.join(target_directory, database_path) )
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31 except OSError as exc:
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32 if exc.errno == errno.EEXIST and os.path.isdir( os.path.join(target_directory, database_path) ):
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33 pass
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34 else:
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35 raise
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37 mash_sketch_args_list = [
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38 '-p', mash_args['threads'],
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39 '-k', mash_args['kmer_size'],
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40 '-s', mash_args['sketch_size'],
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41 '-i', mash_args['input'],
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42 '-o', 'sketch',
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43 ]
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45 subprocess.check_call(['mash', 'sketch'] + mash_sketch_args_list,
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46 cwd=str(os.path.join(target_directory, database_path)))
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48 bagit_args_list = [
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49 database_path,
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50 ]
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52 subprocess.call(['bagit.py'] + bagit_args_list, cwd=target_directory)
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54 data_table_entry = {
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55 "data_tables": {
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56 data_table_name: [
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57 {
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58 "value": database_value,
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59 "name": database_name,
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60 "path": os.path.join(database_path, 'data'),
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61 }
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62 ]
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63 }
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64 }
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66 return data_table_entry
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69 def main():
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70 parser = argparse.ArgumentParser()
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71 parser.add_argument('data_manager_json')
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72 parser.add_argument('--threads', dest='threads', default=1, help='threads' )
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73 parser.add_argument('--input', dest='input', help='Plasmid Assemblies (.fasta)')
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74 parser.add_argument('--kmer-size', dest='kmer_size', help='K-mer size' )
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75 parser.add_argument('--sketch-size', dest='sketch_size', help='Sketch size' )
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76 parser.add_argument('--database-name', dest='database_name', help='Database Name')
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77 args = parser.parse_args()
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78
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79 data_manager_input = json.loads(open(args.data_manager_json).read())
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80
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81 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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82
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83 mash_args = {
5
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84 'input': args.input,
0
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85 'kmer_size': args.kmer_size,
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86 'sketch_size': args.kmer_size,
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87 'threads': args.threads,
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88 }
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89
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90 try:
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91 os.mkdir( target_directory )
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92 except OSError as exc:
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93 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
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94 pass
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95 else:
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96 raise
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97
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98 data_manager_output = {}
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99
1
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100 data_manager_output = mash_build_sketch(
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101 target_directory,
0
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102 mash_args,
1
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103 args.database_name,
0
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104 )
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105
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106 open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
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107
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108
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109 if __name__ == "__main__":
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110 main()