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#![deny(warnings, missing_docs)]
use nom::{
branch::alt,
bytes::complete::{tag, take_until},
character::complete::{alpha1, char, digit1, line_ending, multispace1, not_line_ending},
error::Error,
multi::{many0, many1},
sequence::{pair, tuple},
Err, IResult,
};
#[derive(Debug, PartialEq)]
pub struct RepeatSpacer<'a> {
pub repeat: &'a str,
pub spacer: &'a str,
pub start: usize,
pub end: usize,
pub spacer_start: usize,
pub spacer_end: usize,
pub repeat_start: usize,
pub repeat_end: usize,
}
#[derive(Debug, PartialEq)]
pub struct RepeatOnly<'a> {
pub repeat: &'a str,
pub start: usize,
pub end: usize,
}
#[derive(Debug, PartialEq)]
pub enum Repeat<'a> {
WithSpacer(RepeatSpacer<'a>),
WithoutSpacer(RepeatOnly<'a>),
}
#[derive(Debug, PartialEq)]
pub struct Array<'a> {
pub order: usize,
pub start: usize,
pub end: usize,
pub repeat_spacers: Vec<Repeat<'a>>,
}
#[derive(Debug)]
pub struct Contig<'a> {
pub accession: &'a str,
pub bp: usize,
pub arrays: Vec<Array<'a>>,
}
pub fn parse(input: &str) -> Result<Vec<Contig>, Err<Error<&str>>> {
let result = many0(parse_contig_arrays)(input);
match result {
Ok((_, contigs)) => Ok(contigs),
Err(e) => Err(e),
}
}
fn parse_contig_arrays(input: &str) -> IResult<&str, Contig> {
let result = tuple((
parse_accession_line,
skip_empty_line,
many1(parse_array),
parse_footer,
))(input);
match result {
Ok((remainder, ((accession, bp), _, arrays, _))) => Ok((
remainder,
Contig {
accession,
bp,
arrays,
},
)),
Err(e) => Err(e),
}
}
fn parse_array(input: &str) -> IResult<&str, Array> {
let result = tuple((
skip_empty_line,
parse_crispr_order_and_coordinates,
skip_empty_line,
skip_one_line,
skip_one_line,
many1(parse_repeat_spacer_line),
skip_one_line,
skip_one_line,
))(input);
match result {
Ok((remainder, (_, (order, start, end), _, _, _, repeat_spacers, _, _))) => Ok((
remainder,
Array {
order,
start,
end,
repeat_spacers,
},
)),
Err(e) => Err(e),
}
}
fn skip_one_line(input: &str) -> IResult<&str, ()> {
let result = pair(not_line_ending, line_ending)(input);
match result {
Ok((remaining, _)) => Ok((remaining, ())),
Err(e) => Err(e),
}
}
fn skip_empty_line(input: &str) -> IResult<&str, ()> {
let result = line_ending(input);
match result {
Ok((remaining, _)) => Ok((remaining, ())),
Err(e) => Err(e),
}
}
fn parse_footer(input: &str) -> IResult<&str, ()> {
let result = tuple((
skip_empty_line,
skip_one_line,
skip_empty_line,
skip_empty_line,
))(input);
match result {
Ok((remainder, _)) => Ok((remainder, ())),
Err(e) => Err(e),
}
}
fn parse_crispr_order_and_coordinates(input: &str) -> IResult<&str, (usize, usize, usize)> {
let result = tuple((
tag("CRISPR"),
char(' '),
digit1,
multispace1,
tag("Range:"),
char(' '),
digit1,
tag(" - "),
digit1,
))(input);
match result {
Ok((remaining, (_, _, raw_order, _, _, _, start, _, end))) => Ok((
remaining,
(
raw_order.parse::<usize>().unwrap() - 1,
start.parse::<usize>().unwrap() - 1,
end.parse::<usize>().unwrap(),
),
)),
Err(e) => Err(e),
}
}
fn parse_accession_line(input: &str) -> IResult<&str, (&str, usize)> {
let result = tuple((
tag("Sequence '"),
take_until("'"),
tag("'"),
char(' '),
tag("("),
take_until(" "),
tag(" bp)"),
))(input);
match result {
Ok((remainder, (_, accession, _, _, _, bp, _))) => {
Ok((remainder, (accession, bp.parse::<usize>().unwrap())))
}
Err(e) => Err(e),
}
}
fn parse_repeat_spacer_line(input: &str) -> IResult<&str, Repeat> {
alt((parse_repeat_with_spacer, parse_repeat_only))(input)
}
fn parse_repeat_only(input: &str) -> IResult<&str, Repeat> {
let result = tuple((digit1, multispace1, alpha1, multispace1))(input);
match result {
Ok((remaining, (raw_start, _, repeat, _))) => {
let start = raw_start.parse::<usize>().unwrap() - 1;
Ok((
remaining,
Repeat::WithoutSpacer(RepeatOnly {
repeat,
start,
end: start + repeat.len(),
}),
))
}
Err(e) => Err(e),
}
}
fn parse_repeat_with_spacer(input: &str) -> IResult<&str, Repeat> {
let result = tuple((
digit1,
multispace1,
alpha1,
multispace1,
alpha1,
not_line_ending,
line_ending,
))(input);
match result {
Ok((remaining, (raw_start, _, repeat, _, spacer, _, _))) => {
let start = raw_start.parse::<usize>().unwrap() - 1;
Ok((
remaining,
Repeat::WithSpacer(RepeatSpacer {
repeat,
spacer,
start,
end: start + repeat.len() + spacer.len(),
repeat_start: start,
repeat_end: start + repeat.len(),
spacer_start: start + repeat.len(),
spacer_end: start + repeat.len() + spacer.len(),
}),
))
}
Err(e) => Err(e),
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_parse_array() {
let input = "\nCRISPR 1 Range: 10648 - 10814
POSITION REPEAT SPACER
-------- ----------------------------- ----------------------------------------
10648 CAAGTGCACCAACCAATCTCACCACCTCA GGGGGTGCACTTAAAGGGGGTGCACTTGTCTCAAGTGCACCAAGAA [ 29, 46 ]
10723 CAAGTGCACCAACCAATCTCACCACCTCA CCATCTCACCACCTCTCAGGGGGTGCAGTTGTCT [ 29, 34 ]
10786 CAAGTGCACCAACCAATCTCACCACCTCA
-------- ----------------------------- ----------------------------------------
Repeats: 3 Average Length: 29 Average Length: 40\n";
let expected = Array {
order: 0,
start: 10647,
end: 10814,
repeat_spacers: vec![
Repeat::WithSpacer(RepeatSpacer {
start: 10647,
end: 10722,
repeat_start: 10647,
repeat_end: 10676,
spacer_start: 10676,
spacer_end: 10722,
repeat: "CAAGTGCACCAACCAATCTCACCACCTCA",
spacer: "GGGGGTGCACTTAAAGGGGGTGCACTTGTCTCAAGTGCACCAAGAA",
}),
Repeat::WithSpacer(RepeatSpacer {
start: 10722,
end: 10785,
repeat_start: 10722,
repeat_end: 10751,
spacer_start: 10751,
spacer_end: 10785,
repeat: "CAAGTGCACCAACCAATCTCACCACCTCA",
spacer: "CCATCTCACCACCTCTCAGGGGGTGCAGTTGTCT",
}),
Repeat::WithoutSpacer(RepeatOnly {
start: 10785,
end: 10814,
repeat: "CAAGTGCACCAACCAATCTCACCACCTCA",
}),
],
};
let (_, actual) = parse_array(input).unwrap();
assert_eq!(expected, actual);
}
#[test]
fn test_parse_crispr_order_and_coordinates() {
let input = r"CRISPR 1 Range: 1214 - 1776";
let expected = (0, 1213, 1776);
let (_, actual) = parse_crispr_order_and_coordinates(input).unwrap();
assert_eq!(expected, actual);
}
#[test]
fn test_parse_accession_line() {
let input = "Sequence 'MGYG000166779_38' (12280 bp)";
let expected = ("MGYG000166779_38", 12280);
let (_, actual) = parse_accession_line(input).unwrap();
assert_eq!(expected, actual);
}
#[test]
fn test_parse_repeat_spacer() {
let input = "10723 CAAGTGCACCAACCAATCTCACCACCTCA CCATCTCACCACCTCTCAGGGGGTGCAGTTGTCT [ 29, 34 ]\n";
let expected = RepeatSpacer {
repeat: "CAAGTGCACCAACCAATCTCACCACCTCA",
spacer: "CCATCTCACCACCTCTCAGGGGGTGCAGTTGTCT",
start: 10722,
end: 10785,
repeat_start: 10722,
repeat_end: 10751,
spacer_start: 10751,
spacer_end: 10785,
};
let (_, actual) = parse_repeat_spacer_line(input).unwrap();
match actual {
Repeat::WithSpacer(act) => {
assert_eq!(expected, act);
}
_ => {
unreachable!()
}
}
}
#[test]
fn test_parse_repeat_only_line() {
let input = "10786 CAAGTGCACCAACCAATCTCACCACCTCA\n";
let expected = RepeatOnly {
repeat: "CAAGTGCACCAACCAATCTCACCACCTCA",
start: 10785,
end: 10814,
};
let (_, actual) = parse_repeat_spacer_line(input).unwrap();
match actual {
Repeat::WithoutSpacer(act) => {
assert_eq!(expected, act);
}
_ => {
unreachable!()
}
}
}
#[test]
fn test_parse_contig_arrays() {
let input = "Sequence 'MGYG000242676_4' (164254 bp)
CRISPR 3 Range: 60487 - 61025
POSITION REPEAT SPACER
-------- ------------------------------------ --------------------------
60487 TTTAATAACCCTATATAATTTCTACTATTGTAGATA TCTCCTTTGTAACTTCTTTGATTCGG [ 36, 26 ]
60549 TTTAATAACCCTATATAATTTCTACTGTCGTAGATA TTGTTCTTTTATATGTGTACATAGCTAGA [ 36, 29 ]
60990 TTTAATAACCCTATATAATTTCTACTTTTTTGATTA
-------- ------------------------------------ --------------------------
Repeats: 9 Average Length: 36 Average Length: 26
CRISPR 4 Range: 157550 - 157915
POSITION REPEAT SPACER
-------- ------------------------------------ ------------------------------
157550 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC GAGGGGTTGTCCTTCATGTACTCTTTACCT [ 36, 30 ]
157748 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC GGGCTTATACTCTGACTTTCAACAAGTTAG [ 36, 30 ]
157814 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC CCGATTTTTTCATTGCCAAAACGATATTTT [ 36, 30 ]
157880 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC
-------- ------------------------------------ ------------------------------
Repeats: 6 Average Length: 36 Average Length: 30
Time to find repeats: 22 ms
";
let (_, contig) = parse_contig_arrays(input).unwrap();
assert_eq!(contig.accession, "MGYG000242676_4");
assert_eq!(contig.bp, 164254);
assert_eq!(contig.arrays.len(), 2);
}
#[test]
fn test_parse() {
let input = "Sequence 'MGYG000166779_38' (12280 bp)
CRISPR 1 Range: 10648 - 10814
POSITION REPEAT SPACER
-------- ----------------------------- ----------------------------------------
10648 CAAGTGCACCAACCAATCTCACCACCTCA GGGGGTGCACTTAAAGGGGGTGCACTTGTCTCAAGTGCACCAAGAA [ 29, 46 ]
10723 CAAGTGCACCAACCAATCTCACCACCTCA CCATCTCACCACCTCTCAGGGGGTGCAGTTGTCT [ 29, 34 ]
10786 CAAGTGCACCAACCAATCTCACCACCTCA
-------- ----------------------------- ----------------------------------------
Repeats: 3 Average Length: 29 Average Length: 40
Time to find repeats: 3 ms
Sequence 'MGYG000166779_43' (11302 bp)
CRISPR 2 Range: 4 - 1413
POSITION REPEAT SPACER
-------- ------------------------------------ -----------------------------
4 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC ACGGGTGCACTTTCGATGTCGCACTTTTTG [ 36, 30 ]
70 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC TATACATCATCGTACATATAAGCATACAG [ 36, 29 ]
135 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC GAAAAATCAGAGCCCAAAGTACGAGTAAC [ 36, 29 ]
200 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC CCAGTTCCCGAATTTGATGCTCTTGGCAT [ 36, 29 ]
265 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC ACTTACAACAACAACAATAACAATAAATG [ 36, 29 ]
330 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC ATACGTGTGCTCTATATACGCACCCATTGG [ 36, 30 ]
396 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC GGAGCTCTTTCGATGTCGCACTTTCTGAAG [ 36, 30 ]
462 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC CGTGCTCGCTTTGAATTTGTAGAACCCGA [ 36, 29 ]
527 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC TCTCGACACTATTTCTAACGAGGAAATTAA [ 36, 30 ]
593 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC GCGCTGAGAAGTTACCACCGACCGCTTGA [ 36, 29 ]
658 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC AATACTAAACCAAGATTGCCAAAGGTCCA [ 36, 29 ]
723 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC AGATGATCTACGCTCAATATTAGAAAAAC [ 36, 29 ]
788 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC GTATCTGCGGAACAAGTACAGAGAACATGA [ 36, 30 ]
854 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC CGAACCTAATACGGCTTTAGCCTTTTTGCA [ 36, 30 ]
920 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC AATGAGTACCAAAAGCAAAGAACAAATCGA [ 36, 30 ]
986 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC TATATTTTTGTGCGTTACCCGTCCGTGAGG [ 36, 30 ]
1052 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC TTACTTACGACTATTACGACCAGGTGAAC [ 36, 29 ]
1117 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC ATAATTATAATCGGAAATCAAGCGGATAA [ 36, 29 ]
1182 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC TTTGAATTAGATTCGGCAACCTTAGCATT [ 36, 29 ]
1247 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC TTTTCATCATATTCATAAGAATAGCGACC [ 36, 29 ]
1312 GTTGTGGTTTGATGTAGGAATCAAAAGATATACAAC CCATACGCTCCTTGGTGGTCTTGGTAAGGA [ 36, 30 ]
1378 GTTGTGGTTTGATGTAGAAATCAAAAGACATACAAC
-------- ------------------------------------ -----------------------------
Repeats: 22 Average Length: 36 Average Length: 29
Time to find repeats: 3 ms
Sequence 'MGYG000242676_4' (164254 bp)
CRISPR 3 Range: 60487 - 61025
POSITION REPEAT SPACER
-------- ------------------------------------ --------------------------
60487 TTTAATAACCCTATATAATTTCTACTATTGTAGATA TCTCCTTTGTAACTTCTTTGATTCGG [ 36, 26 ]
60549 TTTAATAACCCTATATAATTTCTACTGTCGTAGATA TTGTTCTTTTATATGTGTACATAGCTAGA [ 36, 29 ]
60614 TTTAATAACCCTATATAATTTCTACTATTGTAGATA ACCTCCTTTGGATTTTCAGCAAATCAGG [ 36, 28 ]
60678 TTTAATAACCCTATATAATTTCTACTATTTTAGATA ATACTGCTTGTTCTGTAAAAATTTTG [ 36, 26 ]
60740 TTTAATAACTCTATATAATTTCTACTATTGTAGATG GAGTTCTCCAACCGTTTGCGGCAATA [ 36, 26 ]
60802 TTTAATAACCCTATATAATTTCTACTATTGTAGATA ACGGTTGAATCAATGAGAAATGTTGTG [ 36, 27 ]
60865 TTTAATAACCCTATATAATTTCTACTATTGTAGATA TGATATTGACGGTGACCTGATTAACCG [ 36, 27 ]
60928 TTTAATAACCCTATATAATTTCTACTATTGTAGATA TGTCAATCACATCTGTGACCGCAAGG [ 36, 26 ]
60990 TTTAATAACCCTATATAATTTCTACTTTTTTGATTA
-------- ------------------------------------ --------------------------
Repeats: 9 Average Length: 36 Average Length: 26
CRISPR 4 Range: 157550 - 157915
POSITION REPEAT SPACER
-------- ------------------------------------ ------------------------------
157550 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC GAGGGGTTGTCCTTCATGTACTCTTTACCT [ 36, 30 ]
157616 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC ATACAAATGCATTGCCGAGGACAGTGTTTT [ 36, 30 ]
157682 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC TATACGGTTTGCCCGTGCAGTCTTGTACAA [ 36, 30 ]
157748 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC GGGCTTATACTCTGACTTTCAACAAGTTAG [ 36, 30 ]
157814 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC CCGATTTTTTCATTGCCAAAACGATATTTT [ 36, 30 ]
157880 GTTTTACTACCTTATAGATTTACACTATTCTCAAAC
-------- ------------------------------------ ------------------------------
Repeats: 6 Average Length: 36 Average Length: 30
Time to find repeats: 22 ms
Sequence 'MGYG000273829_14' (62198 bp)
CRISPR 5 Range: 15191 - 17205
POSITION REPEAT SPACER
-------- ------------------------------------ -----------------------------
15191 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT ATCGCTGAACCTACAACAGACGCAAGAACA [ 36, 30 ]
15257 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT GATATTGTCATACCTAAGTAAATAGGTGCG [ 36, 30 ]
15323 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT TACAATCAGTCTATAACATTTGCAACTACG [ 36, 30 ]
15389 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT TATTATAGACAGCAAGCAACTTGATGTAT [ 36, 29 ]
15454 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT CTTGAATTTGGGGAGATGTTCTCAGCTGGT [ 36, 30 ]
15520 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT AAAGTTTGCTGACAGGGACATTCAAAGCCG [ 36, 30 ]
15586 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT AAACCTGTCTGTCCGATCTGCACCATATAT [ 36, 30 ]
15652 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT ACCGCTATTGCGCTGCAGCATCCACAAGGA [ 36, 30 ]
15718 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT GCATCTTCCTGCGCTCTCTCTGAAAACATG [ 36, 30 ]
15784 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT CGAAGCCTAAAGCTCATTTCGCTTAGGCTT [ 36, 30 ]
15850 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT AAACATGGTGTTGATGTCAAAGAGCTGTAT [ 36, 30 ]
15916 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT TGGGCGAATATAAATTCCATCGGTGGCAAG [ 36, 30 ]
15982 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT AATATTGGATGATGTGTATGGCATTTTACT [ 36, 30 ]
16048 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT AGTGTATATGTGAACCCTGCTCCCAGTGCT [ 36, 30 ]
16114 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT AAAGACCGGAGCAAAGATGTCCGGGAGCCG [ 36, 30 ]
16180 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT TGAAAGTGGTGTAATTGTTATAACTCATTG [ 36, 30 ]
16246 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT AGACAACAGGTGTGGAAGCATATGTCTTTA [ 36, 30 ]
16312 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT TGCTGCATAGGTGTGTATTTTCTCATGTCG [ 36, 30 ]
16378 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT GGTAATGGTGGTGGCGGTTATACCGCAACT [ 36, 30 ]
16444 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT ATGGTCGGGGCTACATATTACGCCGCAGTA [ 36, 30 ]
16510 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT CGTGAGGTCTCCGACCGTGAAAACAGTTCT [ 36, 30 ]
16576 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT ACGAACTTAGTACCCTTTTCTGGGCGGCAT [ 36, 30 ]
16642 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT CCGCAGGTGCTACCGCTGTTATACTCTGTT [ 36, 30 ]
16708 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT CGTAAATCGTTGGCGAAACGCTACCAACTG [ 36, 30 ]
16774 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT CCTCGGTCTGCTCTAACAGATCCCCCAAGT [ 36, 30 ]
16840 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT ACAGAGAAAGAAAGAGAGATTAACGACTAC [ 36, 30 ]
16906 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT TGAAACGGAGTGGACAGGTAAAGGAATGGG [ 36, 30 ]
16972 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT TGCGGTCCCTTGGTTCCGTCAACAACATCA [ 36, 30 ]
17038 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT TGTCCTATTCCCTTTTATGCTGCGTGTATA [ 36, 30 ]
17104 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT AATACAAGCATAAAGAACGAACCGCAACGG [ 36, 30 ]
17170 GCTGTAGTTCCCGGTTATTACTTGGTATGTTATAAT
-------- ------------------------------------ -----------------------------
Repeats: 31 Average Length: 36 Average Length: 29
Time to find repeats: 9 ms
";
let contigs = parse(input).unwrap();
assert_eq!(contigs.len(), 4);
let array_count: usize = contigs.iter().map(|c| c.arrays.len()).sum();
assert_eq!(array_count, 5);
}
}