forked from Ensembl/ensembl-io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
getters.txt
217 lines (191 loc) · 2.91 KB
/
getters.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
EMBL parser (Kieron):
getSequence
getAccessions
getDescription
getKeywords
getSpecies
getClassification
getRawID
getRawAccessions
getRawDescription
getRawKeywords
getRawDate
getRawSpecies
getRawClassification
getRawReferences
getRawFeatures
getRawComments
getRawAssemblyHeader
getRawAssembly
getRawContig
--------------------------------------
TrackBased parser (Anne) - common metadata for the following formats: BED, PSL, WIG
get_browser_switches
get_metadata_value
BED parser (Anne):
get_raw_seqname
get_seqname
get_raw_start
get_start
get_raw_end
get_end
get_raw_name
get_name
get_raw_score
get_score
get_raw_strand
get_strand
get_raw_thickStart
get_thickStart
get_raw_thickEnd
get_thickEnd
get_raw_itemRgb
get_itemRgb
get_raw_blockCount
get_blockCount
get_raw_blockSizes
get_blockSizes
get_raw_blockStarts
get_blockStarts
PSL parser (Anne)
get_raw_Matches
get_matches
get_raw_misMatches
get_misMatches
get_raw_repMatches
get_repMatches
get_raw_nCount
get_nCount
get_raw_qNumInsert
get_qNumInsert
get_raw_qBaseInsert
get_qBaseInsert
get_raw_tNumInsert
get_tNumInsert
get_raw_tBaseInsert
get_tBaseInsert
get_raw_strand
get_strand
get_raw_qName
get_qName
get_raw_qSize
get_qSize
get_raw_qStart
get_qStart
get_raw_qEnd
get_qEnd
get_raw_tName
get_tName
get_raw_tSize
get_tSize
get_raw_tStart
get_tStart
get_raw_tEnd
get_tEnd
get_raw_blockCount
get_blockCount
get_raw_blockSizes
get_blockSizes
get_raw_qStarts
get_qStarts
get_raw_tStarts
get_tStarts
WIG parser (Anne)
Metadata:
get_feature_count
get_wiggle_type
Fields:
get_raw_chrom
get_seqname
get_raw_start
get_start
get_raw_end
get_end
get_raw_score
get_score
--------------------------------------
GVF parser (Laurent):
get_metadata_key_list
get_gvf_version
get_genome_build
get_sequence_region_list
get_metadata_by_pragma
get_raw_seqname
get_seqname
get_raw_source
get_source
get_raw_type
get_type
get_raw_start
get_start
get_raw_end
get_end
get_raw_score
get_score
get_raw_strand
get_strand
get_raw_phase
get_phase
get_raw_attributes
get_attributes
get_ID
get_variant_seq
get_reference_seq
VCF parser (Laurent):
get_metadata_key_list
get_metadata_by_pragma
get_vcf_version
get_raw_seqname
get_seqname
get_raw_start
get_start
get_raw_end
get_end
get_outer_start
get_inner_start
get_inner_end
get_outer_end
get_raw_IDs
get_IDs
get_raw_reference
get_reference
get_raw_alternatives
get_alternatives
get_alternative_description
get_raw_score
get_score
get_raw_filter_results
get_filter_results
get_raw_info
get_info
get_info_description
get_raw_formats
get_formats
get_format_description
get_metadata_description
get_raw_individuals_info
get_individuals_info
get_individuals_genotypes
---------------------------------
EMF parser (Miguel)
get_sequences
get_score_types
tree
format
date
get_next_column
---------------------------------
BigBed Parser (Daniel)
get_chrom
get_start
get_end
get_score
get_parts
get_name
get_rgb
get_bedFeature
BigWig Parser (Daniel)
get_chrom
get_start
get_end
get_score