Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder

annotate data_manager/rnastar_index_builder.py @ 12:a42dbab7917c draft

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planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
author sanbi-uwc
date Mon, 15 Feb 2016 06:55:55 -0500
parents 6096741e8d83
children e905fcc6fd15
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2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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1 #!/usr/bin/env python
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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3 from __future__ import print_function
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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4 import argparse
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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5 from subprocess import check_call, CalledProcessError
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6 from json import load, dump, dumps
aed097239724 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 9d7fb6d7c47e94fb113e0fe26427086935122ff0
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7 from os import environ, mkdir, makedirs
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8 from os.path import isdir, exists
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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9 import shlex
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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10 import sys
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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13 def get_id_name(params, dbkey, fasta_description=None):
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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14 # TODO: ensure sequence_id is unique and does not already appear in location file
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15 sequence_id = params['param_dict']['sequence_id']
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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16 if not sequence_id:
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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17 sequence_id = dbkey
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19 sequence_name = params['param_dict']['sequence_name']
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20 if not sequence_name:
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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21 sequence_name = fasta_description
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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22 if not sequence_name:
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23 sequence_name = dbkey
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24 return sequence_id, sequence_name
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27 def make_rnastar_index(output_directory, fasta_filename):
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28 if exists(output_directory) and not isdir(output_directory):
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29 print("Output directory path already exists but is not a directory: {}".format(output_directory),
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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30 file=sys.stderr)
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31 elif not exists(output_directory):
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32 mkdir(output_directory)
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34 if 'GALAXY_SLOTS' in environ:
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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35 nslots = environ['GALAXY_SLOTS']
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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36 else:
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37 nslots = 1
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39 cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadsN {}'.format(
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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40 output_directory,
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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41 fasta_filename,
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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42 nslots)
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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43 cmdline = shlex.split(cmdline_str)
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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44 # cmdline = ('touch', '{}/foo'.format(output_directory))
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45 try:
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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46 check_call(cmdline)
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47 except CalledProcessError:
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48 print("Error building RNA STAR index", file=sys.stderr)
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49 return (output_directory)
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52 def main():
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53 parser = argparse.ArgumentParser(description="Generate RNA STAR genome index and JSON describing this")
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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54 parser.add_argument('output_filename')
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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55 parser.add_argument('--fasta_filename')
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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56 parser.add_argument('--fasta_dbkey')
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57 parser.add_argument('--fasta_description', default=None)
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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58 parser.add_argument('--data_table_name', default='rnastar_index')
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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59 args = parser.parse_args()
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61 filename = args.output_filename
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63 params = load(open(filename, 'rb'))
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64 output_directory = params['output_data'][0]['extra_files_path']
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65 makedirs(output_directory)
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67 make_rnastar_index(output_directory, args.fasta_filename)
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68 (sequence_id, sequence_name) = get_id_name(params, args.fasta_dbkey, args.fasta_description)
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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69 data_table_entry = dict(value=sequence_id, dbkey=args.fasta_dbkey, name=sequence_name, path=output_directory)
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71 output_datatable_dict = dict(data_tables={args.data_table_name: [data_table_entry]})
a42dbab7917c planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
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72 open(filename, 'wb').write(dumps(output_datatable_dict))
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74 if __name__ == "__main__": main()