Mercurial > repos > iuc > data_manager_snpsift_dbnsfp

annotate data_manager/data_manager_snpsift_dbnsfp.py @ 6:e57f0b0bc73b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:48:39 -0500
parents 09f9bfb2b33b
children fe8a9ab8daf9
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0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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1 #!/usr/bin/env python
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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2
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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3 import gzip
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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4 import json
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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5 import optparse
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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6 import os
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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7 import os.path
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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8 import re
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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9 import shutil
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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10 import sys
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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11 import urllib
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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12 import zipfile
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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14 from pysam import ctabix
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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16 """
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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17 # Install dbNSFP databases
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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18 # from DbNsfp site
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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19 # Download dbNSFP database
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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20 $ wget ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFPv2.4.zip
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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21 # Uncompress
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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22 $ unzip dbNSFP2.4.zip
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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23 # Create a single file version
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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24 $ (head -n 1 dbNSFP2.4_variant.chr1 ; cat dbNSFP2.4_variant.chr* | grep -v "^#") > dbNSFP2.4.txt
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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25 # Compress using block-gzip algorithm
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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26 bgzip dbNSFP2.4.txt
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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27 # Create tabix index
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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28 tabix -s 1 -b 2 -e 2 dbNSFP2.4.txt.gz
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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30 data_table:
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32 <table name="snpsift_dbnsfps" comment_char="#">
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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33 <columns>key, build, name, value, annotations</columns>
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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34 <file path="tool-data/snpsift_dbnsfps.loc" />
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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35 </table>
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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36
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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37 #id build description path annotations
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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38 #GRCh37_dbNSFP2.4 GRCh37 GRCh37 dbNSFP2.4 /depot/snpeff/dbNSFP2.4.gz SIFT_pred,Uniprot_acc
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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39 #GRCh38_dbNSFP2.7 GRCh38 GRCh38 dbNSFP2.7 /depot/snpeff/dbNSFP2.7.gz SIFT_pred,Uniprot_acc
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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40 """
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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41
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42 data_table = 'snpsift_dbnsfps'
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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43 softgenetics_url = 'ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/'
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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44 dbNSFP_file_pat = '(dbNSFP(.*)_variant|dbscSNV(.*)).chr(.*)'
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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45 tokenize = re.compile(r'(\d+)|(\D+)').findall
5
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46 dbNSFP_name_pat = r'dbNSFP(v|_light)?(\d*).*?'
0
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48
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49 def stop_err(msg):
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50 sys.stderr.write(msg)
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51 sys.exit(1)
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53
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54 def get_nsfp_genome_version(name):
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55 genome_version = 'hg19'
5
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56 dbNSFP_name_pat = r'(dbscSNV|dbNSFP(v|_light)?)(\d*).*?'
0
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57 m = re.match(dbNSFP_name_pat, name)
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58 if m:
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59 (base, mid, ver) = m.groups()
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60 if base == 'dbscSNV':
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61 genome_version = 'hg19'
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62 else:
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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63 genome_version = 'hg38' if ver == '3' else 'hg19' if ver == '2' else 'hg18'
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64 return genome_version
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65
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66
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67 def get_annotations(gzip_path):
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68 annotations = None
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69 fh = None
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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70 try:
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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71 fh = gzip.open(gzip_path, 'r')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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72 buf = fh.read(10000)
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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73 lines = buf.splitlines()
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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74 headers = lines[0].split('\t')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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75 annotations = ','.join([x.strip() for x in headers[4:]])
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76 except Exception as e:
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77 stop_err('Error Reading annotations %s : %s' % (gzip_path, e))
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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78 finally:
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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79 if fh:
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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80 fh.close()
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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81 return annotations
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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82
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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83
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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84 def tabix_file(input_fname, output_fname):
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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85 print >> sys.stdout, "tabix_file: %s -> %s" % (input_fname, output_fname)
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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86 ctabix.tabix_compress(input_fname, output_fname, force=True)
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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87 # Column indices are 0-based.
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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88 ctabix.tabix_index(output_fname, seq_col=0, start_col=1, end_col=1)
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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89
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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90
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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91 def natural_sortkey(string):
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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92 return tuple(int(num) if num else alpha for num, alpha in tokenize(string))
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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93
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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94
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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95 def download_dbnsfp_database(url, output_file):
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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96 dbnsfp_tsv = None
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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97 file_path = 'downloaded_file'
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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98 urllib.urlretrieve(url, file_path)
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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99 with zipfile.ZipFile(file_path, 'r') as my_zip:
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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100 dbnsfp_tsv = output_file if output_file else 'dbnsfp_tsv'
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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101 wtr = open(dbnsfp_tsv, 'w')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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102 allfiles = [info.filename for info in my_zip.infolist()]
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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103 files = [f for f in allfiles if re.match(dbNSFP_file_pat, f)]
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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104 files = sorted(files, key=natural_sortkey)
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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105 for j, file in enumerate(files):
2
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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106 tempfiles = []
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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107 tempfiles.append(file + "_%d" % len(tempfiles))
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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108 tfh = open(tempfiles[-1], 'w')
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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109 lastpos = None
0
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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110 fh = my_zip.open(file, 'rU')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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111 for i, line in enumerate(fh):
2
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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112 if i == 0:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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113 if j == 0:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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114 wtr.write(line)
0
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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115 continue
2
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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116 else:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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117 pos = int(line.split('\t')[1])
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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118 if lastpos and pos < lastpos:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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119 tfh.close()
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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120 tempfiles.append(file + "_%d" % len(tempfiles))
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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121 tfh = open(tempfiles[-1], 'w')
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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122 print >> sys.stderr, "%s [%d] pos: %d < %d" % (file, i, pos, lastpos)
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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123 lastpos = pos
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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124 tfh.write(line)
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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125 tfh.close()
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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126 if len(tempfiles) == 1:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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127 with open(tempfiles[0], 'r') as tfh:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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128 wtr.writelines(tfh.readlines())
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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129 else:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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130 tfha = [open(temp, 'r') for temp in tempfiles]
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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131 lines = [tfh.readline() for tfh in tfha]
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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132 curpos = [int(line.split('\t')[1]) for line in lines]
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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133 while len(tfha) > 0:
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134 k = curpos.index(min(curpos))
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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135 wtr.write(lines[k])
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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136 line = tfha[k].readline()
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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137 if line:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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138 lines[k] = line
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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139 curpos[k] = int(line.split('\t')[1])
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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140 else:
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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141 tfha[k].close()
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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142 del tfha[k]
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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143 del lines[k]
3d4cd0e3891f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 6eea2aa4bb66b329385e1f7324dafae805b555c8
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144 del curpos[k]
0
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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145 return dbnsfp_tsv
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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146
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147
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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148 def main():
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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149 # Parse Command Line
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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150 parser = optparse.OptionParser()
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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151 parser.add_option('-g', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='dbkey genome version')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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152 parser.add_option('-n', '--db_name', dest='db_name', action='store', type="string", default=None, help='A name for a history snpsiftdbnsfp dataset')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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153 parser.add_option('-s', '--softgenetics', dest='softgenetics', action='store', type="string", default=None, help='A name for softgenetics dbNSFP file')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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154 parser.add_option('-H', '--snpsiftdbnsfp', dest='snpsiftdbnsfp', action='store', type="string", default=None, help='A history snpsiftdbnsfp dataset')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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155 parser.add_option('-T', '--dbnsfp_tabular', dest='dbnsfp_tabular', action='store', type="string", default=None, help='A history dbnsfp_tabular dataset')
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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156 (options, args) = parser.parse_args()
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157
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158 filename = args[0]
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159 params = json.loads(open(filename).read())
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160 target_directory = params['output_data'][0]['extra_files_path']
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161 if not os.path.exists(target_directory):
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162 os.mkdir(target_directory)
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163 data_manager_dict = {}
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164 genome_version = options.dbkey if options.dbkey else 'unknown'
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165 dbnsfp_tsv = None
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166 db_name = None
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167 bzip_path = None
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168 if options.softgenetics:
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169 dbnsfp_url = softgenetics_url + options.softgenetics
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170 db_name = options.db_name if options.db_name else re.sub(r'\.zip$', '', options.softgenetics)
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171 genome_version = get_nsfp_genome_version(options.softgenetics)
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172 tsv = db_name + '.tsv'
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173 dbnsfp_tsv = download_dbnsfp_database(dbnsfp_url, tsv)
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174 elif options.dbnsfp_tabular:
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175 db_name = options.db_name
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176 dbnsfp_tsv = options.dbnsfp_tabular
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177 elif options.snpsiftdbnsfp:
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178 (dirpath, bgzip_name) = os.path.split(options.snpsiftdbnsfp)
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179 idxpath = options.snpsiftdbnsfp + '.tbi'
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180 shutil.copy(options.snpsiftdbnsfp, target_directory)
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181 shutil.copy(idxpath, target_directory)
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182 bzip_path = os.path.join(target_directory, bgzip_name)
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183 db_name = re.sub('(.txt)?.gz$', '', bgzip_name)
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184 else:
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185 stop_err('Either --softgenetics or --dbnsfp_tabular required')
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186 if dbnsfp_tsv:
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187 bgzip_name = '%s.txt.gz' % db_name
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188 bzip_path = os.path.join(target_directory, bgzip_name)
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189 tabix_file(dbnsfp_tsv, bzip_path)
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190 annotations = get_annotations(bzip_path)
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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191 # Create the SnpSift dbNSFP Reference Data
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192 data_table_entry = dict(key='%s_%s' % (genome_version, db_name), build=genome_version, name='%s %s' % (genome_version, db_name), value=bgzip_name, annotations=annotations)
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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193 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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194 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
0e9e3bb5776a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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195 data_manager_dict['data_tables'][data_table].append(data_table_entry)
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196
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197 # save info to json file
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e57f0b0bc73b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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198 open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
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199
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200
0
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201 if __name__ == "__main__":
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202 main()