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Merge branch 'main' of https://github.com/LCrossman/microBioRust
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merge with main
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@LCrossman
LCrossman committed Dec 4, 2024
2 parents 36e9d39 + 3420927 commit 089b2f6
Showing 1 changed file with 34 additions and 25 deletions.
59 changes: 34 additions & 25 deletions microSeqIO/src/gbk.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -456,7 +456,7 @@ where
//initialise variables
let mut sequences = String::new();
let mut source_map = SourceAttributeBuilder::new();
let mut cds = FeatureAttributeBuilder::new();
let mut cds = FeatureAttributeBuilder::new();
let mut seq_features = SequenceAttributeBuilder::new();
let mut cds_counter: i32 = 0;
let mut source_counter: i32 = 0;
Expand Down Expand Up @@ -485,22 +485,26 @@ where
let mut header_fields: Vec<&str> = self.line_buffer.split_whitespace().collect();
let mut header_iter = header_fields.iter();
header_iter.next();
record.id = header_iter.next().map(|s| s.to_string()).unwrap();
let lens = header_iter.next().map(|s| s.to_string()).unwrap();
record.length = lens.trim().parse::<u32>().unwrap();
record.id = header_iter.next()
.ok_or_else(|| anyhow::anyhow!("missing record id"))? // Get &str or error
.to_string();
let lens = header_iter.next()
.ok_or_else(|| anyhow::anyhow!("missing record length"))? // Get &str or error
.to_string();
record.length = lens.trim().parse::<u32>()?;
self.line_buffer.clear();
}
//collect the source fields and populate the source_map and source_attributes
if self.line_buffer.starts_with(" source") {
let re = Regex::new(r"([0-9]+)[[:punct:]]+([0-9]+)").unwrap();
let location = re.captures(&self.line_buffer).unwrap();
let re = Regex::new(r"([0-9]+)[[:punct:]]+([0-9]+)")?;
let location = re.captures(&self.line_buffer).ok_or_else(|| anyhow::anyhow!("missing location"))?;
let start = &location[1];
let end = &location[2];
thestart = start.trim().parse::<u32>().unwrap();
thestart = start.trim().parse::<u32>()?;
source_counter+=1;
source_name = format!("source_{}_{}",record.id,source_counter).to_string();
thestart += prev_end;
theend = end.trim().parse::<u32>().unwrap() + prev_end;
theend = end.trim().parse::<u32>()? + prev_end;
//println!("so the start and end are {:?} {:?}", &thestart, &theend);
loop {
self.line_buffer.clear();
Expand Down Expand Up @@ -554,7 +558,7 @@ where
let mut joined: bool = false;
//gather the feature coordinates
let joined = if self.line_buffer.contains("join") { true } else { false };
let re = Regex::new(r"([0-9]+)[[:punct:]]+([0-9]+)").unwrap();
let re = Regex::new(r"([0-9]+)[[:punct:]]+([0-9]+)")?;
//let matches: Vec<&regex::Captures> = re.captures_iter(&self.line_buffer).collect();
for cap in re.captures_iter(&self.line_buffer) {
cds_counter+=1;
Expand All @@ -579,7 +583,7 @@ where
}
if self.line_buffer.contains("/codon_start") {
let codstart: Vec<&str> = self.line_buffer.split('=').collect();
let valstart = codstart[1].trim().parse::<u8>().unwrap();
let valstart = codstart[1].trim().parse::<u8>()?;
codon_start = valstart;
//println!("designated codon start {:?} {:?}", &codon_start, &locus_tag);
}
Expand All @@ -590,7 +594,7 @@ where
}
if self.line_buffer.contains("/product") {
let prod: Vec<&str> = self.line_buffer.split('\"').collect();
product = substitute_odd_punctuation(prod[1].to_string());
product = substitute_odd_punctuation(prod[1].to_string())?;
//println!("designated product {:?} {:?}", &product, &locus_tag);
}
if self.line_buffer.starts_with(" CDS") || self.line_buffer.starts_with("ORIGIN") || self.line_buffer.starts_with(" gene") || self.line_buffer.starts_with(" misc_feature") {
Expand Down Expand Up @@ -668,13 +672,18 @@ where
_ => (),
}
}
let sta = a.map(|o| o as usize).ok_or_else(|| { println!("No value for start") }).unwrap();
let sto = b.map(|t| t as usize).ok_or_else(|| { println!("No value for stop") }).unwrap() - 1;
let stra = c.map(|u| u as i8).ok_or_else(|| { println!("No value for strand") }).unwrap();
let cod = d.map(|v| v as usize - 1).ok_or_else(|| { println!("No value for strand") }).unwrap();
let star = sta.try_into().unwrap();
let stow = sto.try_into().unwrap();
let codd = cod.try_into().unwrap();
let sta = a.map(|o| o as usize)
.ok_or(anyhow!("No value for start"))?;
let sto = b.map(|t| t as usize)
.ok_or(anyhow!("No value for stop"))? - 1;
let stra = c.map(|u| u as i8)
.ok_or(anyhow!("No value for strand"))?;
let cod = d.map(|v| v as usize - 1)
.ok_or(anyhow!("No value for strand"))?;

let star = sta.try_into()?;
let stow = sto.try_into()?;
let codd = cod.try_into()?;
let mut sliced_sequence: &str = "";
//collects the DNA sequence and translations on the correct strand
if stra == -1 {
Expand Down Expand Up @@ -928,13 +937,13 @@ create_builder!(

///product lines can contain difficult to parse punctuation such as biochemical symbols like unclosed single quotes, superscripts, single and double brackets etc.
///here we substitute these for an underscore
pub fn substitute_odd_punctuation(input: String) -> String {
let re = Regex::new(r"[/?()',`]|[α-ωΑ-Ω]").unwrap();
let suf = &input
.strip_suffix("\r\n")
.or(input.strip_suffix("\n"))
.unwrap_or(&input);
re.replace_all(suf, "_").to_string()
pub fn substitute_odd_punctuation(input: String) -> Result<String, anyhow::Error> {
let re = Regex::new(r"[/?()',`]|[α-ωΑ-Ω]")?;

// Strip either \r\n or \n more elegantly
let cleaned = input.trim_end_matches(&['\r', '\n'][..]);

Ok(re.replace_all(cleaned, "_").to_string())
}

///GFF3 field9 construct
Expand Down

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