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/genomics/sequencing/exome/analyses/candidate-snps.clj

https://github.com/jandot/bavs
Clojure | 49 lines | 44 code | 4 blank | 1 comment | 3 complexity | 6a0438f706e19075ef6a2f74795dff46 MD5 | raw file
    

  1. (require '[exome core])
    2. 

  2. (in-ns 'exome.core)
    3. 

    4. 

  4. (defn in-any-candidate-gene?
    5. 

  5.   [snp gene-list]
    6. 

  6.   (contains? (set gene-list) (:gene snp))) 
    7. 

  7. 

  8. (defn overview-causative-snps
    9. 

  9.   [ind]
    10. 

  10.   (let [vnnlh (variants-nsssi-novel-lof-highqual ind)
    11. 

  11.         vnnlh-for-homnonref (filter #(homnonref? % ind) vnnlh)
    12. 

  12.         genes-w-homnonref (map #(:gene %) vnnlh-for-homnonref)
    13. 

  13.         g-homnonref genes-w-homnonref
    14. 

  14.         causative-snps-homnonref
    15. 

  15.           (reduce conj []
    16. 

  16.             (map #(assoc {}
    17. 

  17.                          :group "homnonref"
    18. 

  18.                          :gene (:gene %)
    19. 

  19.                          :locus (:locus %)
    20. 

  20.                          :vartype (:vartype %)
    21. 

  21.                          :consequence (:consequence %))
    22. 

  22.                  (filter #(in-any-candidate-gene? % g-homnonref) vnnlh-for-homnonref)))
    23. 

  23.         vnnlh-for-het (filter #(het? % ind) vnnlh)
    24. 

  24.         genes-w-hets (map #(:gene %) (filter #(het? % ind) vnnlh))
    25. 

  25.         m-het (group-by (set genes-w-hets) genes-w-hets)
    26. 

  26.         c-het (zipmap (keys m-het) (map #(count %) (vals m-het)))
    27. 

  27.         g-het (keys (filter #(> (val %) 1) c-het))
    28. 

  28.         causative-snps-comphet
    29. 

  29.           (reduce conj []
    30. 

  30.             (map #(assoc {}
    31. 

  31.                          :group "comphet"
    32. 

  32.                          :gene (:gene %)
    33. 

  33.                          :locus (:locus %)
    34. 

  34.                          :vartype (:vartype %)
    35. 

  35.                          :consequence (:consequence %))
    36. 

  36.                  (filter #(in-any-candidate-gene? % g-het) vnnlh-for-het)))]
    37. 

  37.     (flatten (conj causative-snps-homnonref causative-snps-comphet))))
    38. 

  38. 

  39. ;; diseaseA
    40. 

  40. (clojure.contrib.duck-streams/with-out-writer "analyses/candidate-snps-diseaseA.txt"
    41. 

  41.   (doseq [ind diseaseA-individuals] 
    42. 

  42.     (println "==========") 
    43. 

  43.     (println ind)
    44. 

  44.     (doseq [gene (group-by :gene (overview-causative-snps ind))]
    45. 

  45.       (println "---")
    46. 

  46.       (println (first gene))
    47. 

  47.       (doseq [snp (sort-by :gene (second gene))]
    48. 

  48.         (println (clojure.string/join "\t" ["" (:group snp) (:vartype snp) (:locus snp) (:consequence snp)]))))))
    49. 

  49. 

  50.