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improving error handling
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@jeffersonfparil
jeffersonfparil committed May 11, 2024
1 parent 8afe356 commit 61e0e5b
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Showing 4 changed files with 346 additions and 152 deletions.
71 changes: 46 additions & 25 deletions src/aldknni.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -554,7 +554,13 @@ impl GenotypesAndPhenotypes {
// - Input vcf file will have all alleles per locus extracted.
// - Similarly, input sync file will have all alleles per locus extracted.
// - Finally, input allele frequency table file which can be represented by all alleles or one less allele per locus will be appended with the alternative allele if the sum of allele frequencies per locus do not add up to one.
self.check();
match self.check() {
Ok(x) => x,
Err(e) => return Err(ImputefError{
code: 108,
message: "Error checking GenotypesAndPhenotypes type in method adaptive_ld_knn_imputation() | ".to_owned() + &e.message
})
};
// Parse arguments
let min_loci_corr: &f64 = optimisation_arguments.0;
let max_pool_dist: &f64 = optimisation_arguments.1;
Expand Down Expand Up @@ -591,7 +597,7 @@ impl GenotypesAndPhenotypes {
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 108,
code: 109,
message: "Error defining chunks of the file for parallel imputation."
.to_owned(),
})
Expand Down Expand Up @@ -619,7 +625,7 @@ impl GenotypesAndPhenotypes {
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 109,
code: 110,
message: "Error executing per_chunk_aldknni() method on self_clone."
.to_owned(),
})
Expand All @@ -632,7 +638,7 @@ impl GenotypesAndPhenotypes {
.duration_since(UNIX_EPOCH) {
Ok(x) => x.as_secs_f64(),
Err(_) => return Err(ImputefError{
code: 110,
code: 111,
message: "Error extracting time in UNIX_EPOCH within write_tsv() method for GenotypesAndPhenotypes struct.".to_owned()
})
};
Expand All @@ -642,7 +648,7 @@ impl GenotypesAndPhenotypes {
Some(x) => x.to_owned().to_string().len(),
None => {
return Err(ImputefError {
code: 111,
code: 112,
message: "Error extracting the last element of loci_idx. Probably empty."
.to_owned(),
})
Expand Down Expand Up @@ -672,15 +678,23 @@ impl GenotypesAndPhenotypes {
match chromosome.len() == p {
true => (),
false => return Err(ImputefError{
code: 112,
code: 113,
message: "Error, the number of chromosome names and the total number of loci are not equal.".to_owned()
})
};
// Instantiate output file
let mae_intermediate = match sensible_round(sum_mae / n_missing, 4) {
Ok(x) => x,
Err(e) => return Err(ImputefError {
code: 114,
message: "Error printing the MAE for the intermediate file: ".to_owned() +
&fname_intermediate_file
})
};
println!(
"--> {}: Writing out intermediate file with expected MAE of {}: {}",
i,
sensible_round(sum_mae / n_missing, 4),
mae_intermediate,
&fname_intermediate_file
);
let mut file_out = match OpenOptions::new()
Expand All @@ -692,7 +706,7 @@ impl GenotypesAndPhenotypes {
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 113,
code: 115,
message: "Unable to create file: ".to_owned() + &fname_intermediate_file,
})
}
Expand All @@ -705,7 +719,7 @@ impl GenotypesAndPhenotypes {
) {
Ok(x) => x,
Err(_) => return Err(ImputefError{
code: 114,
code: 116,
message: "Error calling write_all() within the write_tsv() method for GenotypesAndPhenotypes struct. Unable to create file: ".to_owned() + &fname_intermediate_file
})
};
Expand All @@ -722,7 +736,7 @@ impl GenotypesAndPhenotypes {
allele_frequencies
.column(j)
.iter()
.map(|&x| parse_f64_roundup_and_own(x, 6))
.map(|&x| parse_f64_roundup_and_own(x, 6).expect("Error in rounding and converting the allele frequencies into String."))
.collect::<Vec<String>>()
.join("\t"),
]
Expand All @@ -731,7 +745,7 @@ impl GenotypesAndPhenotypes {
match file_out.write_all(line.as_bytes()) {
Ok(x) => x,
Err(_) => return Err(ImputefError{
code: 115,
code: 117,
message: "Error calling write_all() per line of the output file within the write_tsv() method for GenotypesAndPhenotypes struct. Unable to create file: ".to_owned() + &fname_intermediate_file
})
};
Expand Down Expand Up @@ -760,7 +774,7 @@ impl GenotypesAndPhenotypes {
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 116,
code: 118,
message: "Error opening the intermediate file of the first chunk: ".to_owned()
+ &vec_fname_intermediate_files_and_mae[0].0,
})
Expand All @@ -773,7 +787,7 @@ impl GenotypesAndPhenotypes {
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 117,
code: 119,
message: "Error opening the intermediate file of a chunk: ".to_owned()
+ &name_and_mae.0,
})
Expand All @@ -783,7 +797,7 @@ impl GenotypesAndPhenotypes {
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 118,
code: 120,
message: "Error concatenating intermediate output files: ".to_owned()
+ &vec_fname_intermediate_files_and_mae[0].0
+ " and "
Expand All @@ -795,7 +809,7 @@ impl GenotypesAndPhenotypes {
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 119,
code: 121,
message: "Error removing the intermediate file of a chunk: ".to_owned()
+ &name_and_mae.0,
})
Expand All @@ -804,7 +818,14 @@ impl GenotypesAndPhenotypes {
sum_mae += name_and_mae.1;
n_missing += name_and_mae.2;
}
let mae = sensible_round(sum_mae / n_missing, 4);
let mae = match sensible_round(sum_mae / n_missing, 4) {
Ok(x) => x,
Err(e) => return Err(ImputefError {
code: 122,
message: "Error in adaptive_ld_knn_imputation() method | ".to_owned() +
&e.message
})
};
Ok((vec_fname_intermediate_files_and_mae[0].0.to_owned(), mae))
}
}
Expand Down Expand Up @@ -865,7 +886,7 @@ pub fn impute_aldknni(
Ok(x) => x,
Err(e) => {
return Err(ImputefError {
code: 120,
code: 121,
message: e.message,
})
}
Expand Down Expand Up @@ -900,7 +921,7 @@ pub fn impute_aldknni(
Ok(x) => x,
Err(e) => {
return Err(ImputefError {
code: 121,
code: 122,
message: e.message,
})
}
Expand All @@ -909,7 +930,7 @@ pub fn impute_aldknni(
let duration = match end.duration_since(start) {
Ok(x) => x,
Err(e) => return Err(ImputefError{
code: 122,
code: 123,
message: "Error measuring the duration of running adaptive_ld_knn_imputation() within impute_aldknni().".to_owned()
})
};
Expand All @@ -928,7 +949,7 @@ pub fn impute_aldknni(
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 123,
code: 124,
message: "Error loading the imputed genotype file: ".to_owned() + &fname_imputed,
})
}
Expand All @@ -937,7 +958,7 @@ pub fn impute_aldknni(
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 124,
code: 125,
message: "Error removing concatenated intermediate file: ".to_owned()
+ &fname_imputed,
})
Expand All @@ -950,7 +971,7 @@ pub fn impute_aldknni(
match genotypes_and_phenotypes.missing_rate() {
Ok(x) => x,
Err(_) => return Err(ImputefError{
code: 125,
code: 126,
message: "Error measuring sparsity of the data using missing_rate() method within impute_aldknni().".to_owned()
})
},
Expand All @@ -962,7 +983,7 @@ pub fn impute_aldknni(
Ok(x) => x,
Err(_) => {
return Err(ImputefError {
code: 126,
code: 127,
message:
"Error calling filter_out_top_missing_loci() method within impute_aldknni()."
.to_owned(),
Expand All @@ -978,7 +999,7 @@ pub fn impute_aldknni(
match genotypes_and_phenotypes.missing_rate() {
Ok(x) => x,
Err(_) => return Err(ImputefError{
code: 127,
code: 128,
message: "Error measuring sparsity of the data using missing_rate() method after filtering for missing top loci within impute_aldknni().".to_owned()
})
},
Expand All @@ -989,7 +1010,7 @@ pub fn impute_aldknni(
.write_tsv(filter_stats, false, out, n_threads) {
Ok(x) => x,
Err(_) => return Err(ImputefError{
code: 127,
code: 129,
message: "Error writing the output file using the write_tsv() method within impute_aldknni(): ".to_owned() + &out
})
};
Expand Down
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