Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder

annotate data_manager/rnastar_index_builder.py @ 0:2883a3b7dc56 draft

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planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
author sanbi-uwc
date Mon, 08 Feb 2016 03:23:34 -0500
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children aed097239724
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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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2
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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
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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6 from json import load, dump
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7 from os import environ, mkdir
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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
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10 import sys
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12 def get_id_name( params, dbkey, fasta_description=None):
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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13 #TODO: ensure sequence_id is unique and does not already appear in location file
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14 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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15 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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16 sequence_id = dbkey
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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18 sequence_name = params['param_dict']['sequence_name']
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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19 if not sequence_name:
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20 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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21 if not sequence_name:
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22 sequence_name = dbkey
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23 return sequence_id, sequence_name
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25 def make_rnastar_index(output_directory, fasta_filename):
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26 # STAR
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27 # --runMode genomeGenerate
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28 # --genomeDir tempstargenomedir
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29 # --genomeFastaFiles $input1
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30 # --runThreadsN \${GALAXY_SLOTS:-1}
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31 # --genomeChrBinNbits $advanced_options.chr_bin_nbits
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32
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33 if exists(output_directory) and not isdir(output_directory):
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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34 print("Output directory path already exists but is not a directory: {}".format(output_directory), file=sys.stderr)
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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35 elif not exists(output_directory):
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36 mkdir(output_directory)
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37
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38 if 'GALAXY_SLOTS' in environ:
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39 nslots = environ['GALAXY_SLOTS']
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40 else:
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41 nslots = 1
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42
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43 # cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadsN {}'.format(output_directory,
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44 # fasta_filename,
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45 # nslots)
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46 # cmdline = shlex.split(cmdline_str)
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47 cmdline = ('touch', '{}/foo'.format(output_directory))
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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48 try:
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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49 check_call(cmdline)
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50 except CalledProcessError:
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51 print("Error building RNA STAR index", file=sys.stderr)
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52 return(output_directory)
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53
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54 parser = argparse.ArgumentParser(description="Generate RNA STAR genome index and JSON describing this")
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55 parser.add_argument('output_filename')
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56 parser.add_argument('--fasta_filename')
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57 parser.add_argument('--fasta_dbkey')
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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58 parser.add_argument('--fasta_description', default=None)
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59 parser.add_argument('--data_table_name', default='rnastar_indexes')
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60 args = parser.parse_args()
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62 params = load(open(args.output_filename, 'rb'))
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64 output_directory = params['output_data'][0]['extra_files_path']
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65
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66 make_rnastar_index(output_directory, args.fasta_filename)
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67 (sequence_id, sequence_name) = get_id_name(params, args.fasta_dbkey, args.fasta_description)
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68 data_table_entry = dict(value=sequence_id, dbkey=args.fasta_dbkey, name=sequence_name, path=output_directory)
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69 output_datatable_dict = dict('data_tables', dict(args.data_table_name, [data_table_entry]))
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70
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71 dump(output_datatable_dict(open(args.output_file, 'wb')))