fastq.grammar

file : (not-qual sanger <'\n'>)+ | (not-qual illumina-1-0 <'\n'>)+ | (not-qual illumina-1-3 <'\n'>)+
sanger: ('!' | '\"' | '#' | '$' | '%' | '&' | '\'' | '(' | ')' | '*' | '+' | ',' | '-' | '.' | '/' | '0' | '1' | '2' | '3' | '4' | '5' | '6' | '7' | '8' | '9' | ':' | ';' | '<' | '=' | '>' | '?' | '@' | 'A' | 'B' | 'C' | 'D' | 'E' | 'F' | 'G' | 'H' | 'I' | 'J' | 'K' | 'L' | 'M' | 'N' | 'O' | 'P' | 'Q' | 'R' | 'S' | 'T' | 'U' | 'V' | 'W' | 'X' | 'Y' | 'Z' | '[' | '\\' | ']' | '^' | '_' | '`' | 'a' | 'b' | 'c' | 'd' | 'e' | 'f' | 'g' | 'h' | 'i' | 'j' | 'k' | 'l' | 'm' | 'n' | 'o' | 'p' | 'q' | 'r' | 's' | 't' | 'u' | 'v' | 'w' | 'x' | 'y' | 'z' | '{' | '|' | '}')+
illumina-1-0: (';' | '<' | '=' | '>' | '?' | '@' | 'A' | 'B' | 'C' | 'D' | 'E' | 'F' | 'G' | 'H' | 'I' | 'J' | 'K' | 'L' | 'M' | 'N' | 'O' | 'P' | 'Q' | 'R' | 'S' | 'T' | 'U' | 'V' | 'W' | 'X' | 'Y' | 'Z' | '[' | '\\' | ']' | '^' | '_' | '`' | 'a' | 'b' | 'c' | 'd' | 'e' | 'f' | 'g' | 'h' | 'i' | 'j' | 'k' | 'l' | 'm' | 'n' | 'o' | 'p' | 'q' | 'r' | 's' | 't' | 'u' | 'v' | 'w' | 'x' | 'y' | 'z' | '{' | '|' | '}')+
illumina-1-3: ('@' | 'A' | 'B' | 'C' | 'D' | 'E' | 'F' | 'G' | 'H' | 'I' | 'J' | 'K' | 'L' | 'M' | 'N' | 'O' | 'P' | 'Q' | 'R' | 'S' | 'T' | 'U' | 'V' | 'W' | 'X' | 'Y' | 'Z' | '[' | '\\' | ']' | '^' | '_' | '`' | 'a' | 'b' | 'c' | 'd' | 'e' | 'f' | 'g' | 'h' | 'i' | 'j' | 'k' | 'l' | 'm' | 'n' | 'o' | 'p' | 'q' | 'r' | 's' | 't' | 'u' | 'v' | 'w' | 'x' | 'y' | 'z' | '{' | '|' | '}')+
<not-qual> : header <'\n'> sequence <'\n'>  desc <'\n'> 
desc : <'+'> not-newline?
header : <'@'>  not-newline  
<not-newline> : #'[^\n]+'
sequence : ('A' | 'G' | 'C' | 'T')+ 

insta-fastq.clj

(require ['clojure.zip :as 'z])
(require '[clojure.test :refer :all])

(def fq-parse (insta/parser (clojure.java.io/file "fastq.grammar")))
 
(def tr1
(fq-parse
"@M02261:12:000000000-A6FJ2:1:1101:15914:1452 1:N:0:12
CTTATCTCCTGTTCCACTTCAAACAGCAGTTGTAATGCTTGCATGAATGTTATTTGTTCAAAGCTATTTTCAGTTGTTCTTAATCTGTGTCTCACTTCTTCAATTAGCCATCTTATCTCTTCAAACTTCTGACCTAGCTGTTCTCGCCATTTCCCGTTTCTGTTTTGGAGTAAGTGGAGGTCCCCCATTTTCATTACTGCTTCTCCTAGCGAATCTCTGTAGATTTTTAGAGACTCGAACTGTGTT
+
1>AA1FD3DFFFG3BBF11FGGGGHHGFHGFGGHHFGBHHFHHHFFFFF1DFGHHHGF1FFH10G1HHBHFHEHHGGHHHHH2FFGHABGAGHFHHHFHHBGFHF1GBFFHHHFEGGHBGB1B@EGGHFHFEHGGFFHFFGH2EGGGCFGFHHFBE/FBGEDEBFCB?10FFHDDDHDC//@@FGE?CG2<FGGGHEHBGFHHHHH1<>C--@>CHFHDDDBD000DG./<DDGGB..:.GFHHHH
"))

(def tr2
(fq-parse
"@EAS54_6_R1_2_1_443_348
GTTGCTTCTGGCGTGGGTGGGGGGG
+
ZZZZZZZZZZZXZVZZMVZRXRRRR
"))

(defn get-encoding [t] (-> (z/vector-zip t) z/down z/right z/right z/right z/right z/node first)) 

(is
  (= :sanger (get-encoding tr1)))

(is
  (= :illumina-1-3 (get-encoding tr2)))