-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathvariants-config.yaml
205 lines (179 loc) · 8.52 KB
/
variants-config.yaml
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
name: Taccession variants configurations
#filesDirectory: /data/user/publications/trec17abstract/test/
filesDirectory: /data/user/publications/sample/sample70k/
#statsOutputFolder: /stats/stats-variants-trec2017
statsOutputFolder: /stats/stats-variants-trec2017
#dataOutputFolder: /data/user/results/result-variants-trec2017
dataOutputFolder: /data/user/anais/results/result-variants
sparkPartitions: 200
patterns:
#- patternName: variant-hgvs-protein-duplication
# pattern: (?:\b|^)(p)\.([A-Z])([a-z]{2})?(\d+)(?:_([A-Z])([a-z]{2})?(\d+))?dup(?:\b|$)
#
#- patternName: variant-hgvs-cDNA-duplication
# pattern: (?:\b|^)(c)\.((?:-|\*)?\d+)((?:\+|\-)\d+)?(?:_((?:-|\*)?\d+)((?:\+|\-)\d+)?)?dup(?:\b|$)
#
#- patternName: variant-hgvs-gDNA-duplication
# pattern: (?:\b|^)(g)\.(\d+)(?:_(\d+))?dup(?:\b|$)
#
#- patternName: variant-hgvs-mtDNA-duplication
# pattern: (?:\b|^)(m)\.(\d+)(?:_(\d+))?dup(?:\b|$)
#
#- patternName: variant-hgvs-protein-substitution
# pattern: (?:\b|^)(p)\.([A-Z])([a-z]{2})?(\d+)(?:([A-Z])([a-z]{2})?|(\*))(?:\b|$)
#
#- patternName: variant-hgvs-cDNA-substitution
# pattern: (?:\b|^)(c)\.((?:-|\*)?\d+)((?:\+|\-)\d+)?([A-Z])>([A-Z])(?:\b|$)
#
#- patternName: variant-hgvs-gDNA-substitution
# pattern: (?:\b|^)(g)\.(\d+)([A-Z])>([A-Z])(?:\b|$)
#
#- patternName: variant-hgvs-mtDNA-substitution
# pattern: (?:\b|^)(m)\.(\d+)([A-Z])>([A-Z])(?:\b|$)
#
#- patternName: variant-hgvs-protein-deletion
# pattern: (?:\b|^)(p)\.([A-Z])([a-z]{2})?(\d+)(?:_([A-Z])([a-z]{2})?(\d+))?del(?:\b|$)
#
#- patternName: variant-hgvs-cDNA-deletion
# pattern: (?:\b|^)(c)\.((?:-|\*)?\d+)((?:\+|\-)\d+)?(?:_((?:-|\*)?\d+)((?:\+|\-)\d+)?)?del[A-Z]*(?:\b|$)
#
#- patternName: variant-hgvs-gDNA-deletion
# pattern: (?:\b|^)(g)\.(\d+)(?:_(\d+))?del[A-Z]*(?:\b|$)
#
#- patternName: variant-hgvs-mtDNA-deletion
# pattern: (?:\b|^)(m)\.(\d+)(?:_(\d+))?del[A-Z]*(?:\b|$)
#
#- patternName: variant-hgvs-protein-insertion
# pattern: (?:\b|^)(p)\.([A-Z])([a-z]{2})?(\d+)_([A-Z])([a-z]{2})?(\d+)ins(?:((?:[A-Z\*]([a-z]{2})?)+)|(\d+))(?:\b|$)
#
#- patternName: variant-hgvs-cDNA-insertion
# pattern: (?:\b|^)(c)\.((?:-|\*)?\d+)((?:\+|\-)\d+)?_((?:-|\*)?\d+)((?:\+|\-)\d+)?ins[A-Z]+(?:\b|$)
#
#- patternName: variant-hgvs-gDNA-insertion
# pattern: (?:\b|^)(g)\.(\d+)_(\d+)ins[A-Z]+(?:\b|$)
#
#- patternName: variant-hgvs-mtDNA-insertion
# pattern: (?:\b|^)(m)\.(\d+)_(\d+)ins[A-Z]+(?:\b|$)
#
#- patternName: variant-hgvs-protein-deletion-insertion
# pattern: (?:\b|^)(p)\.([A-Z])([a-z]{2})?(\d+)(?:_([A-Z])([a-z]{2})?(\d+))?delins((?:[A-Z\*]([a-z]{2})?)+)(?:\b|$)
#
#- patternName: variant-hgvs-cDNA-deletion-insertion
# pattern: (?:\b|^)(c)\.((?:-|\*)?\d+)((?:\+|\-)\d+)?(?:_((?:-|\*)?\d+)((?:\+|\-)\d+)?)?delins[A-Z]+(?:\b|$)
#
#- patternName: variant-hgvs-gDNA-deletion-insertion
# pattern: (?:\b|^)(g)\.(\d+)(?:_(\d+))?delins[A-Z]+(?:\b|$)
#
#- patternName: variant-hgvs-mtDNA-deletion-insertion
# pattern: (?:\b|^)(m)\.(\d+)(?:_(\d+))?delins[A-Z]+(?:\b|$)
#
#- patternName: variant-hgvs-protein-repeatedsequences
# pattern: (?:\b|^)(p)\.([A-Z])([a-z]{2})?(\d+)(?:_([A-Z])([a-z]{2})?(\d+))?\[(\d+)\](?:\b|$)
#
#- patternName: variant-hgvs-cDNA-repeatedsequences-1
# pattern: (?:\b|^)(c)\.((?:\-|\*)?\d+)((?:\+|\-)\d+)?(?:_((?:\-|\*)?\d+)((?:\+|\-)\d+)?)?\[(\d+)\](?:\b|$)
#
#- patternName: variant-hgvs-gDNA-repeatedsequences-1
# pattern: (?:\b|^)(g)\.(\d+)(?:_(\d+))?\[(\d+)\](?:\b|$)
#
#- patternName: variant-hgvs-mtDNA-repeatedsequences-1
# pattern: (?:\b|^)(m)\.(\d+)(?:_(\d+))?\[(\d+)\](?:\b|$)
#
#- patternName: variant-hgvs-cDNA-repeatedsequences-2
# pattern: (?:\b|^)(c)\.((?:\-|\*)?\d+)((?:\+|\-)\d+)?[A-Z]+\[(\d+)\](?:\b|$)
#
#- patternName: variant-hgvs-gDNA-repeatedsequences-2
# pattern: (?:\b|^)(g)\.(\d+)[A-Z]+\[(\d+)\](?:\b|$)
#
#- patternName: variant-hgvs-mtDNA-repeatedsequences-2
# pattern: (?:\b|^)(m)\.(\d+)[A-Z]+\[(\d+)\](?:\b|$)
#
#- patternName: variant-hgvs-protein-extension
# pattern: (?:\b|^)(p)\.((?:Met|M|Ter|\*)\d+)([A-Z])([a-z]{2})?ext(?:([A-Z])([a-z]{2})?)*(\*|-)(\d+)(?:\b|$)
#
#- patternName: variant-hgvs-cDNA-inversion
# pattern: (?:\b|^)(c)\.((?:\-|\*)?\d+)((?:\+|\-)\d+)?_((?:\-|\*)?\d+)((?:\+|\-)\d+)?inv(?:\b|$)
#
#- patternName: variant-hgvs-gDNA-inversion
# pattern: (?:\b|^)(g)\.(\d+)_(\d+)inv(?:\b|$)
#
#- patternName: variant-hgvs-mtDNA-inversion
# pattern: (?:\b|^)(m)\.(\d+)_(\d+)inv(?:\b|$)
#
#- patternName: variant-hgvs-protein-frameshift
# pattern: p\.([A-Z])([a-z]{2})?(\d+)(?:([A-Z])([a-z]{2})?)?fs(?:(?:\*|Ter|X)(\d+))?(?:\b|$)
## Too much false positives !! (cristallography)
#- patternName: variant-literature-protein-DNA-substitution-1
# pattern: (?<!\.)(?:\b|^)([A-Z])([a-z]{2})?(\d{1,})(?:([A-Z])([a-z]{2})?|(\*))(?:\b|$)
## avoid e.g. IVS1-3G>T to match as 1-3GT, but misses -3G>T match
#- patternName: variant-literature-protein-DNA-substitution-2
# pattern: (?<!\.|\w|-|\*)((?:\-|\*)?\d+)((?:\+|\-)\d+)?\s*([A-Z])([a-z]{2})?\s*[- ]*>\s*(?:([A-Z])([a-z]{2})?|(\*))(?:\b|$)
#
#- patternName: variant-literature-protein-substitution-1
# pattern: (?<!\.)(?:\b|^)([A-Z])([a-z]{2})?(\d+)(?:([A-Z])([a-z]{2})?|(\*))(?:\b|$)
- patternName: variant-literature-protein-1lc-substitution-1a
pattern: (?<!\.)(?:\b|^|\w{3,8})([A-Z])(\d+)(?:([A-Z])|(\*))(?:\b|$)
- patternName: variant-literature-protein-1lc-substitution-1b
pattern: (?<!\.)(?:\b|^|\w{3,8})([a-z])(\d+)(?:([a-z])|(\*))(?:\b|$)
- patternName: variant-literature-protein-3lc-substitution-2a
pattern: (?<!\.)(?:\b|^|\w{3,8})([A-Z])([a-z]{2})(\d+)(?:([A-Z])([a-z]{2})|(\*))(?:\b|$)
- patternName: variant-literature-protein-3lc-substitution-2b
pattern: (?<!\.)(?:\b|^|\w{3,8})([a-z]{3})(\d+)(?:([a-z]{3})|(\*))(?:\b|$)
- patternName: variant-literature-protein-3lc-substitution-2c
pattern: (?<!\.)(?:\b|^|\w{3,8})([A-Z]{3})(\d+)(?:([A-Z]{3})|(\*))(?:\b|$)
#- patternName: variant-literature-protein-1AA-substitution-2
# pattern: (?<!\.)(?:\b|^)(\d+)\s*(?:([BD-FH-SU-Z])\s*[- ]*>\s*(?:([A-Z*]))|([A-Z])\s*[- ]*>\s*([BD-FH-SU-Z*]))(?:\b|$)
- patternName: variant-literature-protein-1lc-substitution-1
pattern: (?<!\.)(\d+)\s*(?:([BD-FH-SU-Z])\s*[- ]*>\s*(?:([A-Z*]))|([A-Z])\s*[- ]*>\s*([BD-FH-SU-Z*]))(?:\b|$)
#- patternName: variant-literature-protein-3AA-substitution-2
# pattern: (?<!\.)(?:\b|^)(\d+)\s*([A-Z][a-z]{2})\s*[- ]*>\s*(?:([A-Z][a-z]{2})|(\*))(?:\b|$)
- patternName: variant-literature-protein-3lc-substitution-2
pattern: (?<!\.)(\d+)\s*([A-Z][a-z]{2})\s*[- ]*>\s*(?:([A-Z][a-z]{2})|(\*))(?:\b|$)
##avoid e.g. IVS1-3G>T to match as -3GT but does not avoid to match c.-9-15G>T as -9-15G>T...
#- patternName: variant-literature-DNA-substitution
# pattern: (?<!\w)((?:\-|\*)?\d+)((?:\+|\-)\d+)?\s*([ATGC])\s*[- ]*>\s*([ATGC])(?:\b|$)
##avoid e.g. IVS1-3G>T to match as -3GT but does not avoid to match c.-9-15G>T as -9-15G>T...
#- patternName: variant-literature-DNA-substitution
# pattern: (?(?<!\w)((?:\-|\*)?\d+)|\d+)((?:\+|\-)\d+)?\s*([ATGC])\s*[- ]*>\s*([ATGC])(?:\b|$)
- patternName: dbSNP-rsid
pattern: (?:\b|^)(rs\d+)(?:\b|$)
- patternName: cosmic-id
pattern: (?:\b|^)(COSM\d+)(?:\b|$)
#- patternName: variant-literature-CNV
# pattern: (expansion|duplication|deletion)
# reference sequences found on https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly
#refseq_genomic=(?:\b|^)NC_\d+\.\d+
#refseq_genomic_alternate=(?:\b|^)AC_\d+\.\d+
#refseq_genomic_incomplete=(?:\b|^)NG_\d+\.\d+
#refseq_genomic_contig_clone_wgs=(?:\b|^)NT_\d+\.\d+
#refseq_genomic_contig_wgs=(?:\b|^)NW_\d+\.\d+
#refseq_genomic_environmental=(?:\b|^)NS_\d+\.\d+
#refseq_genomic_unfinished_wgs=(?:\b|^)NZ_\d+\.\d+
#refseq_mRNA=(?:\b|^)NM_\d+\.\d+
#refseq_RNA=(?:\b|^)NR_\d+\.\d+
#refseq_mRNA_predicted=(?:\b|^)XM_\d+\.\d+
#refseq_RNA_predicted=(?:\b|^)XR_\d+\.\d+
#refseq_protein=(?:\b|^)NP_\d+\.\d+
#refseq_protein_alternate=(?:\b|^)AP_\d+\.\d+
#refseq_protein_predicted=(?:\b|^)XP_\d+\.\d+
#refseq_protein_unfinished_wgs=(?:\b|^)ZP_\d+\.\d+
#- patternName: refseq_genomic
# pattern: (?:\b|^)[NA][CGTWSZ]_\d+\.\d+(?:\b|$)
#
#- patternName: refseq_mRNA
# pattern: (?:\b|^)[NX][MR]_\d+\.\d+(?:\b|$)
#
#- patternName: refseq_protein
# pattern: (?:\b|^)[NAXZ]P_\d+\.\d+(?:\b|$)
#
#- patternName: LRG_gene
# pattern: (?:\b|^)LRG_\d+(?:\b|$)
#
#- patternName: LRG_mRNA
# pattern: (?:\b|^)LRG_\d+t\d+(?:\b|$)
#
#- patternName: LRG_protein
# pattern: (?:\b|^)LRG_\d+p\d+(?:\b|$)
#
#- patternName: Genbank_locus_id
# pattern: (?:\b|^)AB\d+\.\d+(?:\b|$)