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Tweak GENCODE loading performance #55

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merged 2 commits into from
Jul 26, 2022
Merged

Tweak GENCODE loading performance #55

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00961b6
perf: tweak gencode's gtf and gff3 loading performance with pmap, etc.
federkasten Jul 24, 2022
aad6305
chore: specify chunk size of gtf and gff3 paralell loading
federkasten Jul 26, 2022
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38 changes: 23 additions & 15 deletions src/varity/ref_gene.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -107,15 +107,22 @@
(when (= (count row) 9)
{:attribute (->gencode-attr (nth row 8) attr-kv-sep)})))))

(defn- ->feature-map
(def ^:private ens-t-pattern #"ENST\d+\.\d+")
(def ^:private ens-g-pattern #"ENSG\d+\.\d+")

(def find-ens-t-id (memoize #(re-find ens-t-pattern %)))
(def find-ens-g-id (memoize #(re-find ens-g-pattern %)))

(defn- build-feature-map
([features]
(->feature-map features (zipmap [:transcript :exon :cds] (repeat {}))))
([gtf-lines data]
(reduce (fn [data {:keys [seqname feature attribute] :as gtf}]
(let [base (merge (select-keys gtf [:start :end])
{:chr seqname})]
(build-feature-map features (zipmap [:transcript :exon :cds] (repeat {}))))
([features data]
(reduce (fn [data {:keys [start end seqname feature attribute] :as gtf}]
(let [base {:start start
:end end
:chr seqname}]
(if-let [t-id (get attribute "transcript_id")]
(let [t-id (re-find #"ENST\d+\.\d+" t-id)]
(let [t-id (find-ens-t-id t-id)]
(case feature
"transcript"
(assoc-in data
Expand All @@ -124,7 +131,7 @@
{:name t-id
:name2 (get attribute "gene_name")
:gene-id (when-let [g-id (get attribute "gene_id")]
(re-find #"ENSG\d+\.\d+" g-id))
(find-ens-g-id g-id))
:strand (:strand gtf)
:score (:score gtf)}))

Expand All @@ -136,6 +143,7 @@
{:exon-number (as-long (get attribute "exon_number"))
:frame (:frame gtf)
:strand (:strand gtf)}))

"CDS"
(update-in data [:cds t-id] conj base)

Expand All @@ -145,7 +153,7 @@
data))
data)))
data
gtf-lines)))
features)))

(defn- extend-cds
"Extend 3'-most cds's `:end` or `:start` depending on the `strand` value
Expand Down Expand Up @@ -193,14 +201,14 @@
:strand strand))))

(defn load-gencode
[f parse-line]
[f parse-line & {:keys [chunk-size] :or {chunk-size 10000}}]
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It might be better to add this optional arg to both load-gtf and load-gff because currently these functions are easier to use. Or reimplement load-gencode to pick up an appropriate function based on f's extension (sorry my first implementation is not well designed).

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Thanks. I had missed it.

BTW, I think the GTF/GFF3 loader should use cljam's implementation (https://github.com/chrovis/cljam/blob/master/src/cljam/io/gff.clj). I am willing to do a complete rewrite on that.

(with-open [rdr (io/reader (util/compressor-input-stream f))]
(let [feature-map (->> (line-seq rdr)
(keep parse-line)
->feature-map)]
(->> (:transcript feature-map)
(map #(->region feature-map %))
doall))))
(partition-all chunk-size)
(pmap #(doall (keep parse-line %)))
(apply concat)
build-feature-map)]
(doall (map (partial ->region feature-map) (:transcript feature-map))))))

(defn load-gtf
[f]
Expand Down