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annotate export.py @ 8:860ca63f4a59 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 2488ac4ea447c45886ce5c7b102fb28c5839d26b
author gga
date Wed, 10 Apr 2019 13:58:21 -0400
parents 207c1c281360
children c6172b538caf
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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4 import argparse
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5 import json
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6 import sys
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8 from BCBio import GFF
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9
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10 from Bio import SeqIO
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11
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12 from webapollo import CnOrGuess, GuessCn, PermissionCheck, WAAuth, WebApolloInstance
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14 try:
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15 import StringIO as io
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16 except ImportError:
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17 import io
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20 def export(org_cn, seqs):
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21 org_data = wa.organisms.findOrganismByCn(org_cn)
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23 data = io.StringIO()
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25 kwargs = dict(
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26 exportType='GFF3',
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27 seqType='genomic',
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28 exportGff3Fasta=True,
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29 output="text",
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30 exportFormat="text",
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31 organism=org_cn,
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32 )
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33
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34 if len(seqs) > 0:
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35 data.write(wa.io.write(
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36 exportAllSequences=False,
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37 sequences=seqs,
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38 **kwargs
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39 ).encode('utf-8'))
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40 else:
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41 data.write(wa.io.write(
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42 exportAllSequences=True,
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43 sequences=[],
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44 **kwargs
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45 ).encode('utf-8'))
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46
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47 # Seek back to start
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48 data.seek(0)
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49
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50 records = list(GFF.parse(data))
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51 if len(records) == 0:
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52 print("Could not find any sequences or annotations for this organism + reference sequence")
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53 sys.exit(2)
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54 else:
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55 for record in records:
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56 record.annotations = {}
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57 record.features = sorted(record.features, key=lambda x: x.location.start)
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58 if args.gff:
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59 GFF.write([record], args.gff)
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60 record.description = ""
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61 if args.fasta:
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62 SeqIO.write([record], args.fasta, 'fasta')
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63
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64 return org_data
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65
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66
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67 if __name__ == '__main__':
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68 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
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69 WAAuth(parser)
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70 CnOrGuess(parser)
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71 parser.add_argument('--gff', type=argparse.FileType('w'))
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72 parser.add_argument('--fasta', type=argparse.FileType('w'))
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73 parser.add_argument('--json', type=argparse.FileType('w'))
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74 parser.add_argument('email', help='User Email')
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75 args = parser.parse_args()
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76
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77 wa = WebApolloInstance(args.apollo, args.username, args.password)
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78
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79 org_cn_list, seqs = GuessCn(args, wa)
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80
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81 # User must have an apollo account, if not, create it
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82 gx_user = wa.users.assertOrCreateUser(args.email)
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83
0
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84 org_data = []
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85 for org_cn in org_cn_list:
5
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86 # User must have read permission on organism
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87 if not PermissionCheck(gx_user, org_cn, "READ"):
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88 continue
0
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89 indiv_org_data = export(org_cn, seqs)
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90 org_data.append(indiv_org_data)
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91 args.json.write(json.dumps(org_data, indent=2))