Mercurial > repos > yating-l > jbrowsearchivecreator

comparison util/Reader.py @ 32:7b955a58d8f2 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty
author yating-l
date Fri, 20 Oct 2017 11:22:21 -0400
parents 127037c49bc8
children 07cc5384dd61
comparison
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31:127037c49bc8 32:7b955a58d8f2
18 from datatypes.interval.BigPsl import BigPsl 18 from datatypes.interval.BigPsl import BigPsl
19 from datatypes.interval.BedBlatAlignments import BedBlatAlignments 19 from datatypes.interval.BedBlatAlignments import BedBlatAlignments
20 from datatypes.interval.BedBlastAlignments import BedBlastAlignments 20 from datatypes.interval.BedBlastAlignments import BedBlastAlignments
21 from datatypes.interval.Psl import Psl 21 from datatypes.interval.Psl import Psl
22 from datatypes.sequence.Fasta import Fasta 22 from datatypes.sequence.Fasta import Fasta
23 from apollo.ApolloUser import ApolloUser
24 from util import santitizer 23 from util import santitizer
25 24
26 class Reader(object): 25 class Reader(object):
27 26
28 DATATYPE_CLASS = [Bam, BigWig, Bed, BedSimpleRepeats, 27 DATATYPE_CLASS = [Bam, BigWig, Bed, BedSimpleRepeats,
72 71
73 def getTrackType(self): 72 def getTrackType(self):
74 track_type = self.args.get("track_type") 73 track_type = self.args.get("track_type")
75 return track_type 74 return track_type
76 75
77 def getApolloPath(self): 76 def getGenomeName(self):
78 apollo_path = self.args.get("apollo_path") 77 genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
79 return apollo_path 78 return genome_name
80
81 def getApolloHost(self):
82 apollo_host = self.args.get("apollo_host")
83 return apollo_host
84
85 79
86 def getRefGenome(self): 80 def getRefGenome(self):
87 array_inputs_reference_genome = self.args["fasta"] 81 array_inputs_reference_genome = self.args["fasta"]
88 # TODO: Replace these with the object Fasta 82 # TODO: Replace these with the object Fasta
89 input_fasta_file = array_inputs_reference_genome["false_path"] 83 input_fasta_file = array_inputs_reference_genome["false_path"]
90 input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"]) 84 input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"])
91 genome_name = santitizer.sanitize_name_input(self.args["genome_name"]) 85 #genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
86 genome_name = self.getGenomeName()
92 reference_genome = Fasta(input_fasta_file, 87 reference_genome = Fasta(input_fasta_file,
93 input_fasta_file_name, genome_name) 88 input_fasta_file_name, genome_name)
94 return reference_genome 89 return reference_genome
95
96 def getApolloUser(self):
97 user_info = self.args.get("apollo_user")
98 if not user_info:
99 firstname = "demo"
100 lastname = "user"
101 password = "gonramp"
102 user_email = self.getUserEmail()
103 else:
104 firstname = user_info['firstname']
105 lastname = user_info['lastname']
106 user_email = user_info['user_email']
107 password = user_info['password']
108 apollo_user = ApolloUser(user_email, firstname, lastname, password)
109 return apollo_user
110 90
111 def getTracksData(self): 91 def getTracksData(self):
112 self.logger = logging.getLogger(__name__) 92 self.logger = logging.getLogger(__name__)
113 all_datatype_dictionary = dict() 93 all_datatype_dictionary = dict()
114 for datatype in self.DATATYPE_CLASS: 94 for datatype in self.DATATYPE_CLASS: