rbbt-util 5.20.8 → 5.20.9
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- checksums.yaml +4 -4
- data/lib/rbbt/util/misc/omics.rb +72 -6
- data/test/rbbt/util/misc/test_omics.rb +68 -0
- metadata +3 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 0dfd6e2f34b010a55ef904fe69c5d2f5d5c85363
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4
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+
data.tar.gz: b1b7fd04c9c94d2ec1a1c16cc4e883536f7a3500
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: e75cedcb0a224bdd4eb897578ed8bd08ef68b6b0c2196fb37bc31855457045d93dffa82d271ccaa47285df1b6395cd87b97a190f49cd4943a934f0ee903abb4e
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7
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+
data.tar.gz: dbf542a2d17b31f6975e8d3bc1fa53739d1fcc95c9aa9f805b2609833aff38fb8d0f8851ee90791434066e9165eaab4f636632868cdab7916cb43a9dc56da8a2
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data/lib/rbbt/util/misc/omics.rb
CHANGED
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@@ -148,11 +148,11 @@ module Misc
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148
148
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if ref == '-'
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149
149
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res = '+' + m
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150
150
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else
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151
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-
res = '-' * ref.length
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151
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+
res = '-' * ref.length
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152
152
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res << m unless m == '-'
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153
153
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end
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154
154
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Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"}
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155
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-
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155
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+
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156
156
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res
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157
157
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end
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158
158
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end
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@@ -183,11 +183,11 @@ module Misc
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183
183
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if ref == '-'
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184
184
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res = '+' + m
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185
185
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else
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186
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-
res = '-' * ref.length
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186
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+
res = '-' * ref.length
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187
187
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res << m unless m == '-'
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188
188
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end
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189
189
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Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"}
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190
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-
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190
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+
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191
191
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res
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192
192
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end
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193
193
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end
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@@ -195,6 +195,72 @@ module Misc
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195
195
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[pos, muts]
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196
196
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end
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197
197
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198
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+
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199
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+
def self.translate_dna_mutation_hgvs2rbbt(cds)
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200
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+
change = case
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201
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+
when cds =~ />/
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202
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+
cds.split(">").last
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203
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+
when cds =~ /del/
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204
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+
deletion = cds.split("del").last
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205
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+
case
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206
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+
when deletion =~ /^\d+$/
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207
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+
"-" * deletion.to_i
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208
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+
when deletion =~ /^[ACTG]+$/i
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209
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+
"-" * deletion.length
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210
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+
else
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211
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+
Log.debug "Unknown deletion: #{ deletion }"
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|
212
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+
deletion
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213
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+
end
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214
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+
when cds =~ /ins/
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215
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+
insertion = cds.split("ins").last
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|
216
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+
case
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|
217
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+
when insertion =~ /^\d+$/
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218
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+
"+" + "N" * insertion.to_i
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219
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+
when insertion =~ /^[NACTG]+$/i
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|
220
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+
"+" + insertion
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221
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+
else
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222
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+
Log.debug "Unknown insertion: #{insertion }"
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|
223
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+
insertion
|
|
224
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+
end
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225
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+
else
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226
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+
Log.debug "Unknown change: #{cds}"
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|
227
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+
"?(" << cds << ")"
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|
228
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+
end
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|
229
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+
change
|
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230
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+
end
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231
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+
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232
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+
def self.translate_prot_mutation_hgvs2rbbt(mutation)
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233
|
+
one_aa_code = THREE_TO_ONE_AA_CODE.values
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234
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+
one_aa_code << "X" << "B" << "Z" << "J" << "*" << "?"
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235
|
+
one_aa_code_re = one_aa_code*""
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|
236
|
+
subs = Regexp.new("^[#{one_aa_code_re}]\\d+[#{one_aa_code_re}]")
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237
|
+
f_aa = Regexp.new("^[#{one_aa_code_re}]\\d+")
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|
238
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+
mutation.sub!('p.', '')
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|
239
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+
mutation = case
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240
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+
when mutation =~ subs
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241
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+
mutation
|
|
242
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+
when mutation =~ /fs/
|
|
243
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+
mutation =~ f_aa
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|
244
|
+
if Regexp.last_match(0).nil?
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|
245
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+
Log.debug "Unknown Frameshift: #{mutation}"
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|
246
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+
nil
|
|
247
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+
else
|
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248
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+
Regexp.last_match(0) + "Frameshift"
|
|
249
|
+
end
|
|
250
|
+
when mutation =~ /ins|del|>/
|
|
251
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+
mutation =~ f_aa
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|
252
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+
if Regexp.last_match(0).nil?
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|
253
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+
Log.debug "Unknown Indel"
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|
254
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+
nil
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255
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+
else
|
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256
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+
Regexp.last_match(0) + "Indel"
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|
257
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+
end
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|
258
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+
else
|
|
259
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+
Log.debug "Unknown change: #{mutation}"
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|
260
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+
nil
|
|
261
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+
end
|
|
262
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+
end
|
|
263
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+
|
|
198
264
|
def self.IUPAC_to_base(iupac)
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|
199
265
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IUPAC2BASE[iupac]
|
|
200
266
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end
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|
@@ -286,7 +352,7 @@ module Misc
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|
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286
352
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pos2 = f2.pos
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287
353
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|
|
288
354
|
sline2, schr2, sstart2, seend2, srest2 = line2, chr2, start2, eend2, rest2
|
|
289
|
-
while chr1 == chr2 and ((start1 <= eend2 and eend1 >= start2))
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|
355
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+
while chr1 == chr2 and ((start1 <= eend2 and eend1 >= start2))
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|
290
356
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out.puts line1 + "\t" + line2
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|
291
357
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if f2.eof?
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|
292
358
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chr2 = 'next2'
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@@ -294,7 +360,7 @@ module Misc
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|
|
294
360
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line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep)
|
|
295
361
|
end
|
|
296
362
|
end
|
|
297
|
-
line2, chr2, start2, eend2, rest2 = sline2, schr2, sstart2, seend2, srest2
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|
363
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+
line2, chr2, start2, eend2, rest2 = sline2, schr2, sstart2, seend2, srest2
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|
298
364
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f2.seek(pos2)
|
|
299
365
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move = 1
|
|
300
366
|
end
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|
@@ -0,0 +1,68 @@
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|
|
1
|
+
require File.expand_path(File.dirname(__FILE__) + '/../../../test_helper')
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|
2
|
+
require 'test/unit'
|
|
3
|
+
require 'rbbt/util/misc/omics'
|
|
4
|
+
|
|
5
|
+
class TestMiscOmics < Test::Unit::TestCase
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|
6
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+
|
|
7
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+
def test_translate_dna_mutation_hgvs2rbbt
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|
8
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+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.395G>A"), "A"
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|
9
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-124C>T"), "T"
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|
10
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+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.639+6T>A"), "A"
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|
11
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.3386-2A>G"), "G"
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|
12
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+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.4090_4091insT"), "+T"
|
|
13
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.533_534insGGGG"), "+GGGG"
|
|
14
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.4249_4249delC"), "-"
|
|
15
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.464-2_465delAGTG"), "----"
|
|
16
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.209+1delGTAA"), "----"
|
|
17
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.371_397del27"), "---------------------------"
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|
18
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1359+2_1359+11delTTAGAAGAGC"), "----------"
|
|
19
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+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.ins?"), "?"
|
|
20
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?ins?"), "?"
|
|
21
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.184_185ins?"), "?"
|
|
22
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?ins57"), "+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
|
|
23
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?insCT"), "+CT"
|
|
24
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?del?"), "?"
|
|
25
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?"), "?(c.?)"
|
|
26
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(312)?"), "?(c.(312)?)"
|
|
27
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(1669_1671)>?"), "?"
|
|
28
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1050-?"), "?(c.1050-?)"
|
|
29
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(1347_1540)?"), "?(c.(1347_1540)?)"
|
|
30
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-?_850+?del"), "c.1-?_850+?"
|
|
31
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.2289_?del(7236)"), "(7236)"
|
|
32
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(3916_3927)del?"), "?"
|
|
33
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1705_?del?"), "?"
|
|
34
|
+
assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-?_421+?del"), "c.1-?_421+?"
|
|
35
|
+
end
|
|
36
|
+
|
|
37
|
+
def test_translate_prot_mutation_hgvs2rbbt
|
|
38
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E255K"), "E255K"
|
|
39
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E279Z"), "E279Z"
|
|
40
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.R132?"), "R132?"
|
|
41
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.*757?"), "*757?"
|
|
42
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.A2216>?"), "A2216Indel"
|
|
43
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.M552_W557>Z"), "M552Indel"
|
|
44
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.T1151_L1152insT"), "T1151Indel"
|
|
45
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.N771_P772ins?"), "N771Indel"
|
|
46
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.T310_?insKAAQRGA"), "T310Indel"
|
|
47
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.D579del"), "D579Indel"
|
|
48
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E746_A750delELREA"), "E746Indel"
|
|
49
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.P14fs*?"), "P14Frameshift"
|
|
50
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.*588fs?"), "*588Frameshift"
|
|
51
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs*(46_47)"), nil
|
|
52
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(A443)fs*?"), nil
|
|
53
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(574_1542)fs*?"), nil
|
|
54
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs"), nil
|
|
55
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.fs*?"), nil
|
|
56
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs*?"), nil
|
|
57
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(P1249)fs*?"), nil
|
|
58
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?"), nil
|
|
59
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.WQQSYLD25?"), nil
|
|
60
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(449_514)?"), nil
|
|
61
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("?"), nil
|
|
62
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.0?"), nil
|
|
63
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?_?ins?"), nil
|
|
64
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?_?insXXXX"), nil
|
|
65
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(A775)ins?"), nil
|
|
66
|
+
assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?del"), nil
|
|
67
|
+
end
|
|
68
|
+
end
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: rbbt-util
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 5.20.
|
|
4
|
+
version: 5.20.9
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Miguel Vazquez
|
|
@@ -433,6 +433,7 @@ files:
|
|
|
433
433
|
- test/rbbt/util/misc/test_bgzf.rb
|
|
434
434
|
- test/rbbt/util/misc/test_lock.rb
|
|
435
435
|
- test/rbbt/util/misc/test_multipart_payload.rb
|
|
436
|
+
- test/rbbt/util/misc/test_omics.rb
|
|
436
437
|
- test/rbbt/util/misc/test_pipes.rb
|
|
437
438
|
- test/rbbt/util/simpleopt/test_get.rb
|
|
438
439
|
- test/rbbt/util/simpleopt/test_parse.rb
|
|
@@ -495,6 +496,7 @@ test_files:
|
|
|
495
496
|
- test/rbbt/util/misc/test_multipart_payload.rb
|
|
496
497
|
- test/rbbt/util/misc/test_bgzf.rb
|
|
497
498
|
- test/rbbt/util/misc/test_pipes.rb
|
|
499
|
+
- test/rbbt/util/misc/test_omics.rb
|
|
498
500
|
- test/rbbt/util/test_concurrency.rb
|
|
499
501
|
- test/rbbt/util/test_R.rb
|
|
500
502
|
- test/rbbt/util/log/test_progress.rb
|