Sometimes you just want to make a quick FASTQ file for testing.

Usage:

1. Write your FASTQ spec in a foo.lisp file (see below for the syntax).
2. quick-fastq foo.lisp (or cat foo.lisp | quick-fastq if you prefer) to dump a random FASTQ on stdout.

Syntax

quick-fastq will read two Common Lisp forms (using the standard reader for now, so don't run it on untrusted data). The format of the input is:

bindings
expr

expr is an expression describing how to generate a random read.

• A literal string like "ATCG" generates those bases with random quality scores.
• An integer like 123 generates that many random bases with random quality scores.
• A vector like #(expr1 expr2 …) evaluates each expression and concatenates the results.
• A symbol like x looks up the value in the bindings (see below).
• A list performs some operation on the form inside, depending on the symbol at the head of the list:
  • (qN expr) where N is 0-90 evaluates expr and sets its quality scores to N, e.g. (q12 500) will generate 500 random bases with a qscore of 12.
  • (rev expr) reverses expr (you can also use (r expr) as a shortcut).
  • (comp expr) complements expr (you can also use (c expr) as a shortcut).
  • (revcomp expr) is equivalent to (rev (comp expr)) (you can also use (rc expr) as a shortcut)
  • (first n expr) takes the first n bases of expr (you can also use (f n expr) as a shortcut).
  • (last n expr) takes the last n bases of expr (you can also use (l n expr) as a shortcut).
  • (rep n expr) concatenates n copies of expr (you can also use (tr n expr) as a shortcut).
  • (snp freq expr) modifies expr to add SNPs at a rate of freq (freq must be between 0 and 1).
  • (ins freq expr) modifies expr to insert bases at a rate of freq (freq must be between 0 and 1).
  • (del freq expr) modifies expr to delete bases at a rate of freq (freq must be between 0 and 1).
  • (err freq expr) is equivalent to (ins freq (del freq (snp freq expr))) (freq must be between 0 and 1).

Bindings must be a (possibly empty) list of bindings, each of the form (symbol expr). expr will be evaluated and bound to symbol. Bindings are performed in order as if by let*. Several keyword symbols have special meanings:

• Binding :entries to an integer n will generate that many FASTQ entries instead of just a single one.
• Binding :seed to an integer will seed the RNG with a specific seed, to make runs reproducible.

Examples

Generate a random 1000bp read:

()
1000

Generate a read with the same 100bp beginning and end, with 500bp of random bases in the middle:

((x 100))
#(x 500 x)

Generate a gapped foldback chimeric read, with the second half having a lower quality than the first:

((x (q40 1000))
 (f (q20 (revcomp x))))
#(x 25 f)

Generate a read with a tandem repeat in the middle:

()
#(1000 (rep 200 "ATTT") 1000)

Generate a foldback chimeric read with a double tandem duplication in the foldback strand, with simulated sequencing error, and small chunks of low-quality bases to make the transitions between sections as a hack:

((x 1000)
 (lq (q1 10))
 (a (first 800 x))
 (b (last 200 x))
 (dup (last 150 a))
 (f (revcomp #(lq a lq dup lq (rc dup) lq dup lq b))))

(err 0.01 #(x f))