Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_download.py @ 9:db4c810682ee draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
author iuc
date Tue, 24 Nov 2020 07:27:05 +0000
parents fbb459120c29
children
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
diff changeset
1 #!/usr/bin/env python
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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2 import json
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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3 import optparse
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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4 import os
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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5 import re
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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6 import subprocess
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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7 import sys
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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8
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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9
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a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 3
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10 def fetch_databases(genome_list=None):
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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11 snpDBs = dict()
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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12 databases_path = 'databases.out'
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a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 3
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13 args = ['snpEff', 'databases']
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db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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14 with open(databases_path, 'w') as databases_output:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
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15 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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16 if return_code:
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fbb459120c29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
iuc
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17 sys.exit(return_code)
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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18 try:
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db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
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19 with open(databases_path, 'r') as fh:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
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20 for line in fh:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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21 fields = line.split('\t')
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
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22 if len(fields) >= 2:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
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23 genome_version = fields[0].strip()
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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24 if genome_list and genome_version not in genome_list:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
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25 continue
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
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26 if genome_version.startswith("Genome") or genome_version.startswith("-"):
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
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27 continue
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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28 description = fields[1].strip()
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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29 snpDBs[genome_version] = description
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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30 except Exception as e:
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db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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31 sys.exit('Error parsing %s %s\n' % (databases_path, str(e)))
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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32 return snpDBs
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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34
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iuc
parents: 3
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35 def getOrganismNames(genomes, organisms):
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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36 genome_list = genomes.split(',')
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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37 organism_list = organisms.split(',') if organisms else []
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
parents:
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38 if len(genome_list) != len(organism_list):
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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39 descriptions = []
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a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
parents: 3
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40 snpDBdict = fetch_databases(genome_list=genome_list)
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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41 for genome in snpDBdict:
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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42 descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome)
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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43 return ','.join(descriptions)
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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44 return organisms
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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46
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a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
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47 def getSnpeffVersion():
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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48 snpeff_version = 'SnpEff ?.?'
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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49 stderr_path = 'snpeff.err'
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50 args = ['snpEff', '-h']
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db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
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51 with open(stderr_path, 'w') as stderr_fh:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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52 return_code = subprocess.call(args=args, shell=False, stderr=stderr_fh.fileno())
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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53 if return_code != 255:
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fbb459120c29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
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54 sys.exit(return_code)
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db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
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parents: 8
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55 with open(stderr_path) as fh:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
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56 for line in fh:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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57 m = re.match(r'^[Ss]npEff version (SnpEff)\s*(\d+\.\d+).*$', line)
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
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58 if m:
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
iuc
parents: 8
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59 snpeff_version = m.groups()[0] + m.groups()[1]
db4c810682ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
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60 break
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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61 return snpeff_version
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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62
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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64 # Download human database 'hg19'
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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65 # java -jar snpEff.jar download -v hg19
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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66 #
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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67 # <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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68 #
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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69 # snpEffectPredictor.bin
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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70 # regulation_HeLa-S3.bin
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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71 # regulation_pattern = 'regulation_(.+).bin'
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parents: 3
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72 def download_database(data_manager_dict, target_directory, genome_version, organism):
0
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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73 # get data_dir from config
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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74 # ---
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
iuc
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75 # Databases are stored here
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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76 # E.g.: Information for 'hg19' is stored in data_dir/hg19/
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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77 #
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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78 # Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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79 data_dir = target_directory
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iuc
parents: 3
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80 args = ['snpEff', 'download', '-dataDir', data_dir, '-v', genome_version]
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
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81 return_code = subprocess.call(args=args, shell=False)
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82 if return_code:
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83 sys.exit(return_code)
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84 # search data_dir/genome_version for files
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85 regulation_pattern = 'regulation_(.+).bin'
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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86 genome_path = os.path.join(data_dir, genome_version)
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87 snpeff_version = getSnpeffVersion()
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88 key = snpeff_version + '_' + genome_version
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89 if os.path.isdir(genome_path):
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90 for _, _, files in os.walk(genome_path):
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91 for fname in files:
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92 if fname.startswith('snpEffectPredictor'):
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93 # if snpEffectPredictor.bin download succeeded
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94 name = genome_version + (' : ' + organism if organism else '')
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95 data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir)
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96 _add_data_table_entry(data_manager_dict, 'snpeffv_genomedb', data_table_entry)
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97 else:
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98 m = re.match(regulation_pattern, fname)
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99 if m:
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100 name = m.groups()[0]
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101 data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=name, name=name)
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102 _add_data_table_entry(data_manager_dict, 'snpeffv_regulationdb', data_table_entry)
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103 return data_manager_dict
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104
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105
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106 def _add_data_table_entry(data_manager_dict, data_table, data_table_entry):
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107 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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108 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
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109 data_manager_dict['data_tables'][data_table].append(data_table_entry)
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110 return data_manager_dict
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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111
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112
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113 def main():
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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114 parser = optparse.OptionParser()
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115 parser.add_option('-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version')
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116 parser.add_option('-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name')
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117 (options, args) = parser.parse_args()
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118
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119 filename = args[0]
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120
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121 with open(filename) as fh:
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122 params = json.load(fh)
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123 target_directory = params['output_data'][0]['extra_files_path']
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124 os.mkdir(target_directory)
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125 data_manager_dict = {}
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126
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127 # Create SnpEff Reference Data
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128 for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.genome_version, options.organism).split(',')):
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129 download_database(data_manager_dict, target_directory, genome_version, organism)
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130
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131 # save info to json file
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132 with open(filename, 'w') as fh:
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133 json.dump(data_manager_dict, fh, sort_keys=True)
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134
3
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135
0
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136 if __name__ == "__main__":
111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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137 main()