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Replace varity.util/revcomp-bases with cljam.util.sequence/revcomp
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@alumi
alumi committed Aug 24, 2018
1 parent c1a2812 commit 70113dd
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Showing 7 changed files with 34 additions and 52 deletions.
16 changes: 8 additions & 8 deletions src/varity/hgvs_to_vcf/cdna.clj
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
(ns varity.hgvs-to-vcf.cdna
(:require clj-hgvs.mutation
[cljam.io.sequence :as cseq]
[varity.ref-gene :as rg]
[varity.util :refer [revcomp-bases]]))
[cljam.util.sequence :as util-seq]
[varity.ref-gene :as rg]))

;; AGT => ["AGT"]
;; AGTAGT => ["AGT" "AGTAGT"]
Expand All @@ -23,9 +23,9 @@
{:chr chr
:pos pos
:ref (cond-> (:ref mut*)
(= strand "-") (revcomp-bases))
(= strand "-") (util-seq/revcomp))
:alt (cond-> (:alt mut*)
(= strand "-") (revcomp-bases))}))
(= strand "-") (util-seq/revcomp))}))

(defmethod vcf-variant clj_hgvs.mutation.DNADeletion
[mut* seq-rdr {:keys [chr strand] :as rg}]
Expand Down Expand Up @@ -79,7 +79,7 @@
:pos start
:ref ref
:alt (str ref (cond-> (:alt mut*)
(= strand "-") (revcomp-bases)))})))
(= strand "-") (util-seq/revcomp)))})))

(defmethod vcf-variant clj_hgvs.mutation.DNAInversion
[mut* seq-rdr {:keys [chr strand] :as rg}]
Expand All @@ -96,7 +96,7 @@
{:chr chr
:pos (dec start)
:ref ref
:alt (str (first ref) (revcomp-bases (subs ref 1)))}))))
:alt (str (first ref) (util-seq/revcomp (subs ref 1)))}))))

(defmethod vcf-variant clj_hgvs.mutation.DNAIndel
[mut* seq-rdr {:keys [chr strand] :as rg}]
Expand All @@ -113,12 +113,12 @@
(let [ref (cseq/read-sequence seq-rdr {:chr chr, :start (dec start), :end end})]
(if (or (nil? (:ref mut*))
(= (subs ref 1) (cond-> (:ref mut*)
(= strand "-") (revcomp-bases))))
(= strand "-") (util-seq/revcomp))))
{:chr chr
:pos (dec start)
:ref ref
:alt (str (first ref) (cond-> (:alt mut*)
(= strand "-") (revcomp-bases)))})))))
(= strand "-") (util-seq/revcomp)))})))))

(defmethod vcf-variant clj_hgvs.mutation.DNARepeatedSeqs
[mut* seq-rdr {:keys [chr strand] :as rg}]
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16 changes: 8 additions & 8 deletions src/varity/hgvs_to_vcf/protein.clj
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Expand Up @@ -2,9 +2,9 @@
(:require [clj-hgvs.core :as hgvs]
[clj-hgvs.mutation :as mut]
[cljam.io.sequence :as cseq]
[cljam.util.sequence :as util-seq]
[varity.codon :as codon]
[varity.ref-gene :as rg]
[varity.util :refer [revcomp-bases]])
[varity.ref-gene :as rg])
(:import [clj_hgvs.mutation ProteinSubstitution]))

(defn- pos-candidates
Expand All @@ -28,7 +28,7 @@
(let [ref-codon1 (->> pos-cands
(map #(cseq/read-sequence seq-rdr {:chr chr, :start %, :end %}))
(apply str))
ref-codon (cond-> ref-codon1 (= strand "-") revcomp-bases)
ref-codon (cond-> ref-codon1 (= strand "-") util-seq/revcomp)
palt (mut/->short-amino-acid (:alt mut*))
codon-cands (codon/amino-acid->codons palt)]
(->> codon-cands
Expand All @@ -40,9 +40,9 @@
{:chr chr
:pos pos
:ref (cond-> (str (nth ref-codon idx))
(= strand "-") revcomp-bases)
(= strand "-") util-seq/revcomp)
:alt (cond-> (str (nth codon* idx))
(= strand "-") revcomp-bases)})))
(= strand "-") util-seq/revcomp)})))
(remove nil?))))
(flatten)))))
(throw (IllegalArgumentException. "Unsupported mutation"))))
Expand All @@ -59,7 +59,7 @@
(let [ref-codon1 (->> pos-cands
(map #(cseq/read-sequence seq-rdr {:chr chr, :start %, :end %}))
(apply str))
ref-codon (cond-> ref-codon1 (= strand "-") revcomp-bases)
ref-codon (cond-> ref-codon1 (= strand "-") util-seq/revcomp)
palt (mut/->short-amino-acid (:alt mut*))
codon-cands (codon/amino-acid->codons palt)
pos-cands (cond-> pos-cands (= strand "-") reverse)]
Expand All @@ -73,8 +73,8 @@
alt (str (nth codon* idx))]
{:vcf {:chr chr
:pos pos
:ref (cond-> ref (= strand "-") revcomp-bases)
:alt (cond-> alt (= strand "-") revcomp-bases)}
:ref (cond-> ref (= strand "-") util-seq/revcomp)
:alt (cond-> alt (= strand "-") util-seq/revcomp)}
:cdna (hgvs/hgvs (:name rg) :cdna (mut/dna-substitution (rg/cds-coord pos rg)
ref
(if (= ref alt) "=" ">")
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3 changes: 2 additions & 1 deletion src/varity/ref_gene.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
[clj-hgvs.coordinate :as coord]
[cljam.io.sequence :as cseq]
[cljam.util.chromosome :refer [normalize-chromosome-key]]
[cljam.util.sequence :as util-seq]
[proton.core :refer [as-long]]
[varity.util :as util]))

Expand Down Expand Up @@ -186,7 +187,7 @@
"Reads a base sequence of an `exon` from `seq-rdr`."
[seq-rdr {:keys [reverse?] :as exon}]
(cond-> (cseq/read-sequence seq-rdr exon)
reverse? util/revcomp-bases))
reverse? util-seq/revcomp))

(defn ^String read-gene-sequence
"Reads a DNA base sequence of a ref-gene record `gene` from `seq-rdr`."
Expand Down
9 changes: 1 addition & 8 deletions src/varity/util.clj
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@@ -1,17 +1,10 @@
(ns varity.util
"Utilities."
(:require [clojure.java.io :as io]
[cljam.util.sequence :as util-seq])
(:require [clojure.java.io :as io])
(:import [java.io InputStream]
[org.apache.commons.compress.compressors
CompressorStreamFactory CompressorException]))

(defn revcomp-bases
"Returns reverse complementary bases string."
[s]
{:pre [(string? s)]}
(util-seq/revcomp s))

(defn ^InputStream compressor-input-stream
"Returns an compressor input stream from f, autodetecting the compressor type
from the first few bytes of f. Returns java.io.BufferedInputStream if the
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22 changes: 11 additions & 11 deletions src/varity/vcf_to_hgvs/cdna.clj
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
(ns varity.vcf-to-hgvs.cdna
(:require [clj-hgvs.core :as hgvs]
[clj-hgvs.mutation :as mut]
[cljam.util.sequence :as util-seq]
[varity.ref-gene :as rg]
[varity.util :refer [revcomp-bases]]
[varity.vcf-to-hgvs.common :refer [diff-bases] :as common]))

(defn- repeat-info-forward
Expand Down Expand Up @@ -33,9 +33,9 @@
100)
(map (fn [seq*]
(let [nseq* (count seq*)]
(if-let [[unit ref-repeat :as ri] (common/repeat-info (revcomp-bases seq*)
(if-let [[unit ref-repeat :as ri] (common/repeat-info (util-seq/revcomp seq*)
(inc nseq*)
(revcomp-bases ins))]
(util-seq/revcomp ins))]
(let [nunit (count unit)]
(if (> (* nunit ref-repeat) (- nseq* nunit))
false
Expand All @@ -58,7 +58,7 @@
[unit ref-repeat ins-repeat] (repeat-info* seq-rdr rg (+ pos offset) alt-only)]
(cond
(and (= nrefo 1) (= nalto 1)) :substitution
(= ref-only (revcomp-bases alt-only)) :inversion
(= ref-only (util-seq/revcomp alt-only)) :inversion
(and (pos? nrefo) (zero? nalto)) :deletion
(and (pos? nrefo) (pos? nalto)) :indel
(some? unit) (cond
Expand All @@ -72,9 +72,9 @@
[rg pos ref alt]
(let [{:keys [strand]} rg]
(mut/dna-substitution (rg/cds-coord pos rg)
(cond-> ref (= strand "-") revcomp-bases)
(cond-> ref (= strand "-") util-seq/revcomp)
(if (= ref alt) "=" ">")
(cond-> alt (= strand "-") revcomp-bases))))
(cond-> alt (= strand "-") util-seq/revcomp))))

(defn- dna-deletion
[rg pos ref alt]
Expand All @@ -92,7 +92,7 @@
"+" right
"-" left)
rg))
(cond-> (subs ref offset) (= strand "-") revcomp-bases))))
(cond-> (subs ref offset) (= strand "-") util-seq/revcomp))))

(defn- dna-duplication
[rg pos ref alt]
Expand All @@ -106,7 +106,7 @@
"-" (inc (- start (count ins))))]
(mut/dna-duplication (rg/cds-coord start rg)
(rg/cds-coord end rg)
(cond-> ins (= strand "-") revcomp-bases))))
(cond-> ins (= strand "-") util-seq/revcomp))))

(defn- dna-insertion
[rg pos ref alt]
Expand All @@ -116,7 +116,7 @@
end (cond-> (+ pos offset) (= strand "-") dec)]
(mut/dna-insertion (rg/cds-coord start rg)
(rg/cds-coord end rg)
(cond-> ins (= strand "-") revcomp-bases))))
(cond-> ins (= strand "-") util-seq/revcomp))))

(defn- dna-inversion
[rg pos ref alt]
Expand Down Expand Up @@ -153,8 +153,8 @@
"+" right
"-" left)
rg))
(cond-> del (= strand "-") revcomp-bases)
(cond-> ins (= strand "-") revcomp-bases))))
(cond-> del (= strand "-") util-seq/revcomp)
(cond-> ins (= strand "-") util-seq/revcomp))))

(defn- dna-repeated-seqs
[seq-rdr rg pos ref alt]
Expand Down
8 changes: 4 additions & 4 deletions src/varity/vcf_to_hgvs/protein.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,9 @@
[clj-hgvs.core :as hgvs]
[clj-hgvs.mutation :as mut]
[cljam.io.sequence :as cseq]
[cljam.util.sequence :as util-seq]
[varity.codon :as codon]
[varity.ref-gene :as rg]
[varity.util :refer [revcomp-bases]]
[varity.vcf-to-hgvs.common :refer [diff-bases] :as common]))

(defn- split-string-at [s x]
Expand Down Expand Up @@ -107,13 +107,13 @@
alt-exon-seq1 (exon-sequence alt-seq cds-start alt-exon-ranges*)]
{:ref-exon-seq ref-exon-seq1
:ref-prot-seq (codon/amino-acid-sequence (cond-> ref-exon-seq1
(= strand "-") revcomp-bases))
(= strand "-") util-seq/revcomp))
:alt-exon-seq alt-exon-seq1
:alt-prot-seq (codon/amino-acid-sequence (cond-> alt-exon-seq1
(= strand "-") revcomp-bases))
(= strand "-") util-seq/revcomp))
:alt-tx-prot-seq (codon/amino-acid-sequence
(cond-> (str ref-up-exon-seq1 alt-exon-seq1 ref-down-exon-seq1)
(= strand "-") revcomp-bases))
(= strand "-") util-seq/revcomp))
:ini-offset (quot (:position (rg/cds-coord (case strand
"+" tx-start
"-" tx-end) rg))
Expand Down
12 changes: 0 additions & 12 deletions test/varity/util_test.clj
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