rbbt-util 5.20.8 → 5.20.9
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0dfd6e2f34b010a55ef904fe69c5d2f5d5c85363
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data.tar.gz: b1b7fd04c9c94d2ec1a1c16cc4e883536f7a3500
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SHA512:
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metadata.gz:
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data.tar.gz:
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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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if ref == '-'
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res = '+' + m
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else
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res = '-' * ref.length
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res = '-' * ref.length
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res << m unless m == '-'
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end
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Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"}
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-
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+
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res
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end
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end
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@@ -183,11 +183,11 @@ module Misc
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if ref == '-'
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res = '+' + m
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else
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-
res = '-' * ref.length
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res = '-' * ref.length
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res << m unless m == '-'
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end
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Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"}
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-
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+
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res
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end
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end
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@@ -195,6 +195,72 @@ module Misc
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[pos, muts]
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end
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def self.translate_dna_mutation_hgvs2rbbt(cds)
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change = case
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when cds =~ />/
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cds.split(">").last
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when cds =~ /del/
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deletion = cds.split("del").last
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case
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when deletion =~ /^\d+$/
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"-" * deletion.to_i
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when deletion =~ /^[ACTG]+$/i
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"-" * deletion.length
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else
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Log.debug "Unknown deletion: #{ deletion }"
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deletion
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end
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when cds =~ /ins/
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insertion = cds.split("ins").last
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case
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when insertion =~ /^\d+$/
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"+" + "N" * insertion.to_i
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when insertion =~ /^[NACTG]+$/i
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"+" + insertion
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else
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Log.debug "Unknown insertion: #{insertion }"
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insertion
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end
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else
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Log.debug "Unknown change: #{cds}"
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"?(" << cds << ")"
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end
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change
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end
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def self.translate_prot_mutation_hgvs2rbbt(mutation)
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one_aa_code = THREE_TO_ONE_AA_CODE.values
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one_aa_code << "X" << "B" << "Z" << "J" << "*" << "?"
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one_aa_code_re = one_aa_code*""
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subs = Regexp.new("^[#{one_aa_code_re}]\\d+[#{one_aa_code_re}]")
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f_aa = Regexp.new("^[#{one_aa_code_re}]\\d+")
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mutation.sub!('p.', '')
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mutation = case
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when mutation =~ subs
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mutation
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when mutation =~ /fs/
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mutation =~ f_aa
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if Regexp.last_match(0).nil?
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Log.debug "Unknown Frameshift: #{mutation}"
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nil
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else
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Regexp.last_match(0) + "Frameshift"
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end
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when mutation =~ /ins|del|>/
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mutation =~ f_aa
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if Regexp.last_match(0).nil?
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Log.debug "Unknown Indel"
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nil
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else
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Regexp.last_match(0) + "Indel"
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end
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else
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Log.debug "Unknown change: #{mutation}"
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nil
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end
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end
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def self.IUPAC_to_base(iupac)
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IUPAC2BASE[iupac]
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end
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@@ -286,7 +352,7 @@ module Misc
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pos2 = f2.pos
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sline2, schr2, sstart2, seend2, srest2 = line2, chr2, start2, eend2, rest2
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while chr1 == chr2 and ((start1 <= eend2 and eend1 >= start2))
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while chr1 == chr2 and ((start1 <= eend2 and eend1 >= start2))
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out.puts line1 + "\t" + line2
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if f2.eof?
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chr2 = 'next2'
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@@ -294,7 +360,7 @@ module Misc
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line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep)
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end
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end
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line2, chr2, start2, eend2, rest2 = sline2, schr2, sstart2, seend2, srest2
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line2, chr2, start2, eend2, rest2 = sline2, schr2, sstart2, seend2, srest2
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f2.seek(pos2)
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move = 1
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end
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@@ -0,0 +1,68 @@
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require File.expand_path(File.dirname(__FILE__) + '/../../../test_helper')
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require 'test/unit'
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require 'rbbt/util/misc/omics'
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class TestMiscOmics < Test::Unit::TestCase
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def test_translate_dna_mutation_hgvs2rbbt
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.395G>A"), "A"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-124C>T"), "T"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.639+6T>A"), "A"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.3386-2A>G"), "G"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.4090_4091insT"), "+T"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.533_534insGGGG"), "+GGGG"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.4249_4249delC"), "-"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.464-2_465delAGTG"), "----"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.209+1delGTAA"), "----"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.371_397del27"), "---------------------------"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1359+2_1359+11delTTAGAAGAGC"), "----------"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.ins?"), "?"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?ins?"), "?"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.184_185ins?"), "?"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?ins57"), "+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?insCT"), "+CT"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?del?"), "?"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?"), "?(c.?)"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(312)?"), "?(c.(312)?)"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(1669_1671)>?"), "?"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1050-?"), "?(c.1050-?)"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(1347_1540)?"), "?(c.(1347_1540)?)"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-?_850+?del"), "c.1-?_850+?"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.2289_?del(7236)"), "(7236)"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(3916_3927)del?"), "?"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1705_?del?"), "?"
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assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-?_421+?del"), "c.1-?_421+?"
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end
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def test_translate_prot_mutation_hgvs2rbbt
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38
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E255K"), "E255K"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E279Z"), "E279Z"
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40
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.R132?"), "R132?"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.*757?"), "*757?"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.A2216>?"), "A2216Indel"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.M552_W557>Z"), "M552Indel"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.T1151_L1152insT"), "T1151Indel"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.N771_P772ins?"), "N771Indel"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.T310_?insKAAQRGA"), "T310Indel"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.D579del"), "D579Indel"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E746_A750delELREA"), "E746Indel"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.P14fs*?"), "P14Frameshift"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.*588fs?"), "*588Frameshift"
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs*(46_47)"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(A443)fs*?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(574_1542)fs*?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.fs*?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs*?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(P1249)fs*?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.WQQSYLD25?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(449_514)?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.0?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?_?ins?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?_?insXXXX"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(A775)ins?"), nil
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assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?del"), nil
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end
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end
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: rbbt-util
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version: !ruby/object:Gem::Version
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version: 5.20.
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version: 5.20.9
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platform: ruby
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authors:
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- Miguel Vazquez
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@@ -433,6 +433,7 @@ files:
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433
433
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- test/rbbt/util/misc/test_bgzf.rb
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434
434
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- test/rbbt/util/misc/test_lock.rb
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435
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- test/rbbt/util/misc/test_multipart_payload.rb
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436
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+
- test/rbbt/util/misc/test_omics.rb
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437
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- test/rbbt/util/misc/test_pipes.rb
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437
438
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- test/rbbt/util/simpleopt/test_get.rb
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438
439
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- test/rbbt/util/simpleopt/test_parse.rb
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@@ -495,6 +496,7 @@ test_files:
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495
496
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- test/rbbt/util/misc/test_multipart_payload.rb
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- test/rbbt/util/misc/test_bgzf.rb
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498
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- test/rbbt/util/misc/test_pipes.rb
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499
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+
- test/rbbt/util/misc/test_omics.rb
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500
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- test/rbbt/util/test_concurrency.rb
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501
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- test/rbbt/util/test_R.rb
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- test/rbbt/util/log/test_progress.rb
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