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annotate export.py @ 0:99b348a1d355 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:47:45 -0400
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99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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3
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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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7
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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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12 from future import standard_library
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13
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14 from webapollo import CnOrGuess, GuessCn, WAAuth, WebApolloInstance
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16 standard_library.install_aliases()
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17 try:
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18 import StringIO as io
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19 except ImportError:
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20 import io
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23 def export(org_cn, seqs):
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24 org_data = wa.organisms.findOrganismByCn(org_cn)
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25
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26 data = io.StringIO()
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28 kwargs = dict(
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29 exportType='GFF3',
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30 seqType='genomic',
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31 exportGff3Fasta=True,
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32 output="text",
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33 exportFormat="text",
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34 organism=org_cn,
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35 )
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36
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37 if len(seqs) > 0:
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38 data.write(wa.io.write(
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39 exportAllSequences=False,
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40 sequences=seqs,
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41 **kwargs
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42 ).encode('utf-8'))
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43 else:
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44 data.write(wa.io.write(
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45 exportAllSequences=True,
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46 sequences=[],
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47 **kwargs
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48 ).encode('utf-8'))
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49
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50 # Seek back to start
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51 data.seek(0)
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52
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53 records = list(GFF.parse(data))
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54 if len(records) == 0:
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55 print("Could not find any sequences or annotations for this organism + reference sequence")
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56 sys.exit(2)
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57 else:
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58 for record in records:
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59 record.annotations = {}
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60 record.features = sorted(record.features, key=lambda x: x.location.start)
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61 if args.gff:
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62 GFF.write([record], args.gff)
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63 record.description = ""
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64 if args.fasta:
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65 SeqIO.write([record], args.fasta, 'fasta')
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66
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67 return org_data
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68
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69
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70 if __name__ == '__main__':
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71 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
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72 WAAuth(parser)
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73 CnOrGuess(parser)
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74 parser.add_argument('--gff', type=argparse.FileType('w'))
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75 parser.add_argument('--fasta', type=argparse.FileType('w'))
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76 parser.add_argument('--json', type=argparse.FileType('w'))
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77
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78 args = parser.parse_args()
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79
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80 wa = WebApolloInstance(args.apollo, args.username, args.password)
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81
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82 org_cn_list, seqs = GuessCn(args, wa)
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83
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84 org_data = []
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85 for org_cn in org_cn_list:
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86 indiv_org_data = export(org_cn, seqs)
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87 org_data.append(indiv_org_data)
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88 args.json.write(json.dumps(org_data, indent=2))