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asd-2024
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Antonio De Lucreziis 7 months ago
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5
.gitignore vendored
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# Cargo
/target
# Local files
*.local*

96
Cargo.lock generated
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# This file is automatically @generated by Cargo.
# It is not intended for manual editing.
version = 3
[[package]]
name = "argh"
version = "0.1.12"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "7af5ba06967ff7214ce4c7419c7d185be7ecd6cc4965a8f6e1d8ce0398aad219"
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7
Cargo.toml
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[package]
name = "asd-2024-gfa"
version = "0.1.0"
edition = "2021"
[dependencies]
argh = "0.1.12"

48
README.md
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# Progetto ASD 2023/2024
## Example GFA
```
H VN:Z:1.0
S 11 G
S 12 A
S 13 T
S 14 T
S 15 A
S 16 C
S 17 A
S 21 G
S 22 A
S 23 T
S 24 T
S 25 A
L 11 + 12 + *
L 11 + 13 + *
L 12 + 14 + *
L 13 + 14 + *
L 14 + 15 + *
L 14 + 16 + *
L 15 + 17 + *
L 16 + 17 + *
L 21 + 22 + *
L 21 + 23 + *
L 22 + 24 + *
L 23 + 24 - *
L 24 + 25 + *
P A 11+,12+,14+,15+,17+ *,*,*,*
P B 21+,22+,24+,25+ *,*,*
W sample 1 A 0 5 >11>12>14>15>17
W sample 2 A 0 5 >11>13>14>16>17
W sample 1 B 0 5 >21>22>24<23<21
W sample 2 B 0 4 >21>22>24>25
```
## Note
- Documentazione del formato GFA: http://gfa-spec.github.io/GFA-spec/GFA1.html
- Data set:
- [example.gfa](https://github.com/jltsiren/gbwt-rs/blob/main/test-data/example.gfa)
- [drb1.gfa](https://github.com/pangenome/odgi/blob/master/test/DRB1-3123_unsorted.gfa)
- [chrY.gfa](https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/pggb/chroms/chrY.hprc-v1.0-pggb.gfa.gz)
- [chrX.gfa](https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/pggb/chroms/chrX.hprc-v1.0-pggb.gfa.gz)

32
examples/example.gfa
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H VN:Z:1.0
S 11 G
S 12 A
S 13 T
S 14 T
S 15 A
S 16 C
S 17 A
S 21 G
S 22 A
S 23 T
S 24 T
S 25 A
L 11 + 12 + *
L 11 + 13 + *
L 12 + 14 + *
L 13 + 14 + *
L 14 + 15 + *
L 14 + 16 + *
L 15 + 17 + *
L 16 + 17 + *
L 21 + 22 + *
L 21 + 23 + *
L 22 + 24 + *
L 23 + 24 - *
L 24 + 25 + *
P A 11+,12+,14+,15+,17+ *,*,*,*
P B 21+,22+,24+,25+ *,*,*
W sample 1 A 0 5 >11>12>14>15>17
W sample 2 A 0 5 >11>13>14>16>17
W sample 1 B 0 5 >21>22>24<23<21
W sample 2 B 0 4 >21>22>24>25

40
src/main.rs
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use argh::FromArgs;
mod parser;
#[derive(FromArgs, PartialEq, Debug)]
/// Strumento CLI per il progetto di Algoritmi e Strutture Dati 2024
struct CliTool {
#[argh(subcommand)]
nested: MySubCommandEnum,
}
#[derive(FromArgs, PartialEq, Debug)]
#[argh(subcommand)]
enum MySubCommandEnum {
Show(CommandShow),
}
#[derive(FromArgs, PartialEq, Debug)]
/// Parse and show the content of a file
#[argh(subcommand, name = "show")]
struct CommandShow {
#[argh(option, short = 'i')]
/// file to read
input: String,
}
fn main() {
let opts = argh::from_env::<CliTool>();
match opts.nested {
MySubCommandEnum::Show(show) => {
let file = std::fs::read_to_string(show.input).expect("cannot read file");
let entries = parser::parse_source(file.as_str());
for entry in entries {
println!("{:?}", entry);
}
}
}
}

184
src/parser.rs
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use std::str::FromStr;
#[derive(Debug)]
pub enum Orientation {
Forward,
Reverse,
}
impl From<&str> for Orientation {
fn from(s: &str) -> Self {
match s {
"+" => Orientation::Forward,
">" => Orientation::Forward,
"-" => Orientation::Reverse,
"<" => Orientation::Reverse,
_ => panic!("Invalid orientation: {}", s),
}
}
}
#[derive(Debug)]
pub enum Entry {
Header {
version: String,
},
Segment {
id: String,
sequence: String,
},
Link {
from: String,
from_orient: Orientation,
to: String,
to_orient: Orientation,
},
Path {
name: String,
segments: Vec<(String, Orientation)>,
},
Walk {
sample: String,
haplotype_index: usize,
seq_id: String,
seq_start: usize,
seq_end: usize,
segments: Vec<(String, Orientation)>,
},
}
/// Parse a line of the source file into a Header struct
///
/// ```txt
/// H VN:Z:1.0
/// ```
///
fn parse_header(line: &str) -> Entry {
let columns: Vec<&str> = line.split(':').collect();
Entry::Header {
version: columns[2].to_string(),
}
}
/// Parse a line of the source file into a Segment struct
///
/// ```txt
/// S 1 ACGT
/// ```
fn parse_segment(line: &str) -> Entry {
let columns: Vec<&str> = line.split('\t').collect();
Entry::Segment {
id: columns[1].to_string(),
sequence: columns[2].to_string(),
}
}
/// Parse a line of the source file into a Link struct
///
/// ```txt
/// L 1 + 2 - 3M
/// ```
fn parse_link(line: &str) -> Entry {
let columns: Vec<&str> = line.split('\t').collect();
Entry::Link {
from: columns[1].to_string(),
from_orient: columns[2].into(),
to: columns[3].to_string(),
to_orient: columns[4].into(),
}
}
/// Parse a line of the source file into a Path struct
///
/// ```txt
/// P A 11+,12+,14+,15-,17+ *,*,*,*
/// ```
fn parse_path(line: &str) -> Entry {
let columns: Vec<&str> = line.split('\t').collect();
Entry::Path {
name: columns[1].to_string(),
segments: columns[2]
.split(',')
.map(|s| {
let (name, orient) = s.split_at(s.len() - 1);
(name.to_string(), orient.into())
})
.collect(),
}
}
fn parse_path_segments(s: &str) -> Vec<(String, Orientation)> {
let mut result = Vec::new();
let mut rest = s;
loop {
println!("Rest: {}", rest);
let r = rest;
let (orient, r) = r.split_at(1);
let (name, r) = r.split_at(r.find(['<', '>']).unwrap_or(r.len()));
rest = r;
result.push((name.to_string(), orient.into()));
if rest.is_empty() {
break;
}
}
result
}
/// Parse a line of the source file into a Walk struct
///
/// ```txt
/// W sample 1 A 0 5 >11>12>14>15>17
/// ```
fn parse_walk(line: &str) -> Entry {
let columns: Vec<&str> = line.split('\t').collect();
Entry::Walk {
sample: columns[1].to_string(),
haplotype_index: usize::from_str(columns[2]).unwrap(),
seq_id: columns[3].to_string(),
seq_start: usize::from_str(columns[4]).unwrap(),
seq_end: usize::from_str(columns[5]).unwrap(),
segments: parse_path_segments(columns[6]),
}
}
pub fn parse_source(source: &str) -> Vec<Entry> {
let mut entries = Vec::new();
for line in source.lines() {
let line = line.trim();
if line.is_empty() || line.starts_with('#') {
continue;
}
println!("Parsing: {}", line);
let first_char = line.chars().next().unwrap();
let entry = match first_char {
'H' => parse_header(line),
'S' => parse_segment(line),
'L' => parse_link(line),
'P' => parse_path(line),
'W' => parse_walk(line),
_ => {
eprintln!("Unknown line type: {}", line);
continue;
}
};
entries.push(entry);
}
entries
}
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