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Copy pathstrain-ows-jsdctpt-calc.clj
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strain-ows-jsdctpt-calc.clj
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(ns )
(->> "/home/jsa/Bio/ribosomal-proteins-all.csv" slurp
csv/read-csv rest
(mapv #(let [name (first %)
[s e st] (->> % (drop 2) (take 3))
len (Math/abs (- (Integer. e) (Integer. s)))
rp (last %)]
[name len s e st rp]))
(sort-by second >)
(coll/takev 21))
(->> "/home/jsa/Bio/S1-proteins.csv" slurp
csv/read-csv rest
(mapv #(let [name (first %)
[s e st] (->> % (drop 2) (take 3))
len (Math/abs (- (Integer. e) (Integer. s)))
rp (last %)]
[name s e st]))
(sort-by first)
(mapv #(apply bufiles/make-entry %)))
(->> "/home/jsa/Bio/S1-proteins.csv" slurp
csv/read-csv rest
(mapv #(let [name (first %)
[s e st] (->> % (drop 2) (take 3))
len (Math/abs (- (Integer. e) (Integer. s)))
rp (last %)]
[name s e st]))
(sort-by first)
(mapv #(apply bufiles/make-entry %))
bufiles/gen-name-seq-pairs
(#(opt-wz % :alpha "AUGC"))
#_(mapv (fn[[n s]] [n (aerial.bio.utils.seqxform/ntseq->aaseq s)]))
#_(#(opt-wz % :alpha "ACDEFGHIKLMNPQRSSETVWY"))
first)
;; => 10
(->> "/home/jsa/Bio/S1-proteins.csv" slurp
csv/read-csv rest
(mapv #(let [name (first %)
[s e st] (->> % (drop 2) (take 3))
len (Math/abs (- (Integer. e) (Integer. s)))
rp (last %)]
[name s e st]))
(sort-by first)
(mapv #(apply bufiles/make-entry %))
bufiles/gen-name-seq-pairs
#_(mapv (fn[[n s]] [n (aerial.bio.utils.seqxform/ntseq->aaseq s)]))
(aerial.utils.math.combinatorics/combins 2)
#_shuffle
#_(take 10)
(mapv (fn[[nsq1 nsq2]]
(let [[n1 sq1] nsq1
[n2 sq2] nsq2
k 10
d1 (p/probs k sq1)
d2 (p/probs k sq2)]
[n1 n2 (it/jensen-shannon d1 d2)])))
(mapv last)
(apply max))
;; => 0.035
(->> jsds second (sort-by second)
(coll/dropv-until #(-> % second (> 0.4)))
(coll/takev-until #(-> % second (> 0.5)))
(mapv (fn[[nm & _]] [nm (mmc2Hmap nm)])))
(mapv (fn[x] (->> x (sort-by second)
#_(coll/dropv-until #(-> % second (> 0.4)))
(coll/takev-until #(-> % second (> 0.3)))
(mapv (fn[[nm & _]] [nm (mmc2Hmap nm)])) count))
jsds)
#_(->> :????
(filter (fn[[k v]] (not= 3 (count v))))
(filter (fn[[nm recs]] (not (some #(->> % second (= "NC_003028")) recs))))
(mapv first))
;;; "NC_018630"
(def Strains ["NC_003028" "NC_012469" "NC_008533"])
(def mmc2 (->> "/home/jsa/Bio/mmc2.csv" slurp csv/read-csv rest))
(def mmc2H (->> mmc2 rest
(filter (fn[[t4 t19f d39 & _]]
(reduce (fn[all x] (and all (not= x "n.p.")))
true [t4 t19f d39])))))
(def mmc2Hmap (reduce (fn[M [t4 t19 d39]]
(assoc M t4 [t19 d39]
t19 [t4 d39]
d39 [t4 t19]))
{} mmc2H))
(def mmc2T4Hmap (reduce (fn[M [t4 t19 d39]]
(assoc M t4 t4
t19 t4
d39 t4))
{} mmc2H))
(def homologs
(->> Strains ;; only works for t4, 19f, d39 - only xref table
(mapcat (fn[nc]
(let [base "/store/data/SPStrains/RefSeq77/CSV/"]
(->> (str nc ".csv") (fs/join base) slurp
csv/read-csv rest (mapv #(coll/takev 6 %))
(filter (fn[[nm s e st g ol]]
(or (not= g "NA") ; gene or known xref locus
(mmc2T4Hmap ol))))))))
(map (fn[[nm s e st g ol]]
(let [len (Math/abs (- (Integer. e) (Integer. s)))]
[len nm s e st g ol])))
(group-by (fn[[len nm s e st g ol]]
(if (not= g "NA") g (mmc2T4Hmap ol))))
(filter (fn[[k v]] (= 3 (count v)))) #_(take 10)))
(def OWS
[(->> homologs (sort-by (fn[[k recs]] (ffirst recs))) (random-sample 0.05)
(mapv (fn[[k recs]]
[k (ffirst recs)
(->> recs (map #(->> % rest (take 4)
(apply bufiles/make-entry)))
bufiles/gen-name-seq-pairs
(#(opt-wz % :alpha "AUGC"))
first)])))
(->> homologs (sort-by (fn[[k recs]] (ffirst recs))) (random-sample 0.05)
(mapv (fn[[k recs]]
[k (ffirst recs)
(->> recs (map #(->> % rest (take 4)
(apply bufiles/make-entry)))
bufiles/gen-name-seq-pairs
(mapv (fn[[n s]]
[n (sqx/ntseq->aaseq s)]))
(#(opt-wz % :alpha "ACDEFGHIKLMNPQRSSETVWY"))
first)])))])
;;=> NT: [["gyrB" 10] ["cbiO" 9]]
;;=> AA: [["gyrB" 6] ["cbiO" 5]]
(def jsds
(let [samps (->> homologs (sort-by (fn[[k recs]] (ffirst recs)))
#_(random-sample 0.20))]
[(->> samps
(vfold (fn[[k recs]]
(let [x (->> recs (map #(->> % rest (take 4)
(apply bufiles/make-entry)))
bufiles/gen-name-seq-pairs
(cmb/combins 2)
(mapv (fn[[nsq1 nsq2]]
(let [[n1 sq1] nsq1
[n2 sq2] nsq2
k 9
d1 (p/probs k sq1)
d2 (p/probs k sq2)]
[n1 n2 (it/jensen-shannon d1 d2)])))
(sort-by last))]
[k x])))
(sort-by (comp last first second) >))
(->> samps
(vfold (fn[[k recs]]
(let [x (->> recs (map #(->> % rest (take 4)
(apply bufiles/make-entry)))
bufiles/gen-name-seq-pairs
(mapv (fn[[n s]]
[n (ntseq2aaseq s)]))
(cmb/combins 2)
(mapv (fn[[nsq1 nsq2]]
(let [[n1 sq1] nsq1
[n2 sq2] nsq2
k 6
d1 (p/probs k sq1)
d2 (p/probs k sq2)]
[n1 n2 (it/jensen-shannon d1 d2)])))
(sort-by last))]
[k x])))
(sort-by (comp last first second) >))]))
;;; Just the _named_ (well known) genes
(->> jsds second (sort-by (comp last first second))
(coll/takev-until #(-> % ((comp last first second)) (> 0.42)))
(filter (fn[[n & _]] (not= "SP" (str/take 2 n)))) count)
(def ntjsds-m
(->> jsds first
(vfold (fn[[n v]]
(let [v (sort-by last > v)
sq-pairs
(mapv (fn[x] (->> x butlast
(mapv #(->> % bufiles/gen-name-seq
second))))
v)
hms-lens (mapv (fn[[s1 s2]]
(let [hm (it/levenshtein s1 s2)
len (max (count s1) (count s2))]
[(-> hm (/ len) double) [hm len]]))
sq-pairs)
v2 (->> v (interleave hms-lens)
(partition-all 2)
(mapv (fn[[x y]] (conj x y))))]
[n v2])))
(into {})))
(def aajsds-m
(->> jsds second
(vfold (fn[[n v]]
(let [v (sort-by last > v)
sq-pairs
(mapv (fn[x] (->> x butlast
(mapv #(->> % bufiles/gen-name-seq
second))
(mapv ntseq2aaseq)))
v)
hms-lens (mapv (fn[[s1 s2]]
(let [hm (it/levenshtein s1 s2)
len (max (count s1) (count s2))]
[(-> hm (/ len) double) [hm len]]))
sq-pairs)
v2 (->> v (interleave hms-lens)
(partition-all 2)
(mapv (fn[[x y]] (conj x y))))]
[n v2])))
(into {})))
(aajsds-m "engB")
(ntjsds-m "recX")
(->> ["NC_012469/1519593-1522385/-1" "NC_018630/1506925-1509717/-1"]
bufiles/gen-name-seq-pairs (map second) (map count))
(->> ["NC_003028/1475387-1475974/-1" "NC_012469/1439232-1439819/-1" ]
bufiles/gen-name-seq-pairs (map second) (map count))
(->> jsds second (sort-by (comp first second))
(coll/takev-until #(-> % ((comp first second)) (> 0.42)))
#_(filter (fn[[n & _]] (not= "SP" (str/take 2 n))))
(filter (fn[[_ [mn mx av] & _]] (> mx 0.99))) last)
(def gene2jsds
(->> ntjsds-m keys
(mapv #(vector % {:nt (ntjsds-m %) :aa (aajsds-m %)}))
(into {})))
(def nm-xref {"NC_003028" "T4", "NC_012469" "19F", "NC_008533" "D39"})
(def vgl-maps
(coll/concatv
(->> gene2jsds
(mapcat (fn[[k m]]
(map (fn[[hm% [hm len] [e1 e2 jsd]]]
(let [n1 (->> e1 (str/split #"/") first nm-xref)
n2 (->> e2 (str/split #"/") first nm-xref)
hm% (roundit hm%)
jsd (roundit jsd)]
{:name k :hm hm% :len len
:kind "NT" :nt jsd
:tt (format "[%s %s] %s: %s,%s %s"
hm% jsd k n1 n2 [hm len])}))
(m :nt)))))
(->> gene2jsds
(mapcat (fn[[k m]]
(map (fn[[hm% [hm len] [e1 e2 jsd]]]
(let [n1 (->> e1 (str/split #"/") first nm-xref)
n2 (->> e2 (str/split #"/") first nm-xref)
hm% (roundit hm%)
jsd (roundit jsd)]
{:name k :hm hm% :len len
:kind "AA" :aa jsd
:tt (format "[%s %s] %s: %s,%s %s"
hm% jsd k n1 n2 [hm len])}))
(m :aa)))))))
(io/with-out-writer "/home/jsa/Bio/panclus-vgl-maps.clj"
(prn vgl-maps))