Update clj-hgvs to 0.4.0

chrovis · Aug 16, 2019 · f96d12f · f96d12f
1 parent 62f7049
commit f96d12f
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Showing 7 changed files with 9 additions and 9 deletions.
diff --git a/project.clj b/project.clj
@@ -6,7 +6,7 @@
   :min-lein-version "2.7.0"
   :dependencies [[org.clojure/clojure "1.10.1" :scope "provided"]
                  [org.clojure/tools.logging "0.4.1"]
-                 [clj-hgvs "0.3.1"]
+                 [clj-hgvs "0.4.0"]
                  [cljam "0.7.2"]
                  [org.apache.commons/commons-compress "1.18"]
                  [proton "0.1.8"]]

diff --git a/src/varity/hgvs_to_vcf.clj b/src/varity/hgvs_to_vcf.clj
@@ -54,7 +54,7 @@
   ([hgvs seq-rdr rgidx] (hgvs->vcf-variants hgvs nil seq-rdr rgidx))
   ([hgvs gene seq-rdr rgidx]
    (let [convert (case (:kind hgvs)
-                   :cdna cdna-hgvs->vcf-variants
+                   :coding-dna cdna-hgvs->vcf-variants
                    :protein protein-hgvs->vcf-variants)
          rgs (if-let [[rs] (re-find #"^(NM|NR)_\d+" (str (:transcript hgvs)))]
                (rg/ref-genes rs rgidx)
@@ -68,7 +68,7 @@
   ([hgvs seq-rdr rg] (hgvs->vcf-variants hgvs nil seq-rdr rg))
   ([hgvs _ seq-rdr rg]
    (let [convert (case (:kind hgvs)
-                   :cdna cdna/->vcf-variant
+                   :coding-dna cdna/->vcf-variant
                    :protein prot/->vcf-variants)]
      (convert hgvs seq-rdr rg))))
 

diff --git a/src/varity/hgvs_to_vcf/cdna.clj b/src/varity/hgvs_to_vcf/cdna.clj
@@ -8,7 +8,7 @@
 (defn- cds-coord->genomic-pos
   [coord rg]
   (cond
-    (instance? clj_hgvs.coordinate.CDNACoordinate coord)
+    (instance? clj_hgvs.coordinate.CodingDNACoordinate coord)
     (rg/cds-coord->genomic-pos coord rg)
 
     (or (instance? clj_hgvs.coordinate.UnknownCoordinate coord)

diff --git a/src/varity/hgvs_to_vcf/protein.clj b/src/varity/hgvs_to_vcf/protein.clj
@@ -104,7 +104,7 @@
                                  :pos ((if reverse? last first) ps),
                                  :ref (cond-> ref reverse? util-seq/revcomp),
                                  :alt (cond-> alt reverse? util-seq/revcomp)},
-                           :cdna (hgvs/hgvs (:name rg) :cdna mut)}))))))))))
+                           :cdna (hgvs/hgvs (:name rg) :coding-dna mut)}))))))))))
     (throw (IllegalArgumentException. "Unsupported mutation"))))
 
 (defn ->vcf-variants-with-cdna-hgvs

diff --git a/src/varity/ref_gene.clj b/src/varity/ref_gene.clj
@@ -285,7 +285,7 @@
                             (and tx-edge? (= region :upstream)) [(- cds-pos* offset) 0]
                             (and tx-edge? (= region :downstream)) [(+ cds-pos* offset) 0]
                             :else [cds-pos* offset])]
-    (coord/cdna-coordinate cds-pos* offset region)))
+    (coord/coding-dna-coordinate cds-pos* offset region)))
 
 ;;; Calculation of genomic coordinate
 

diff --git a/src/varity/vcf_to_hgvs/cdna.clj b/src/varity/vcf_to_hgvs/cdna.clj
@@ -194,7 +194,7 @@
 (defn ->hgvs
   [{:keys [pos ref alt]} seq-rdr rg]
   (hgvs/hgvs (:name rg)
-             :cdna
+             :coding-dna
              (mutation seq-rdr rg pos ref alt)))
 
 (defn- sequence-pstring

diff --git a/test/varity/ref_gene_test.clj b/test/varity/ref_gene_test.clj
@@ -267,7 +267,7 @@
 (deftest cds-coord->genomic-pos-test
   ;; 1 [2 3 4] 5 6 7 [8 9 10 11] 12 13 14 15
   (testing "strand +"
-    (are [c s e r] (= (rg/cds-coord->genomic-pos (coord/parse-cdna-coordinate c)
+    (are [c s e r] (= (rg/cds-coord->genomic-pos (coord/parse-coding-dna-coordinate c)
                                                  {:strand :forward
                                                   :cds-start s
                                                   :cds-end e
@@ -287,7 +287,7 @@
       "-5"   9 11 1
       "*7"   2 3  13))
   (testing "strand -"
-    (are [c s e r] (= (rg/cds-coord->genomic-pos (coord/parse-cdna-coordinate c)
+    (are [c s e r] (= (rg/cds-coord->genomic-pos (coord/parse-coding-dna-coordinate c)
                                                  {:strand :reverse
                                                   :cds-start s
                                                   :cds-end e