blul_proc/
execute_blast.rs

1use blul_core::domain::{
2    dtos::blast_builder::BlastBuilder,
3    entities::execute_blastn::{ExecuteBlastn, ExecutionResponse},
4};
5use mycelium_base::utils::errors::{execution_err, MappedErrors};
6use subprocess::{Exec, Redirection};
7
8#[derive(Debug)]
9pub struct ExecuteBlastnProcRepository {}
10
11impl ExecuteBlastn for ExecuteBlastnProcRepository {
12    fn run(
13        &self,
14        query_sequences: String,
15        blast_config: BlastBuilder,
16        threads: usize,
17    ) -> Result<ExecutionResponse, MappedErrors> {
18        let blast_response = match Exec::cmd("blastn")
19            .stdin(&*query_sequences)
20            .arg("-db")
21            .arg(&blast_config.subject_reads)
22            .arg("-outfmt")
23            .arg(&blast_config.out_format.to_string())
24            .arg("-max_target_seqs")
25            .arg(&blast_config.max_target_seqs.to_string())
26            .arg("-perc_identity")
27            .arg(&blast_config.perc_identity.to_string())
28            .arg("-qcov_hsp_perc")
29            .arg(&blast_config.query_cov.to_string())
30            .arg("-strand")
31            .arg(&blast_config.strand.to_string())
32            .arg("-evalue")
33            .arg(&blast_config.e_value.to_string())
34            .arg("-word_size")
35            .arg(&blast_config.word_size.to_string())
36            .arg("-num_threads")
37            .arg(threads.to_string())
38            .stdout(Redirection::Pipe)
39            .stderr(Redirection::Pipe)
40            .capture()
41        {
42            Err(err) => {
43                return execution_err(format!(
44                    "Unexpected error detected on execute blast: {err}"
45                ))
46                .as_error()
47            }
48            Ok(res) => res,
49        };
50
51        if !blast_response.success() {
52            return Ok(ExecutionResponse::Fail(blast_response.stderr_str()));
53        }
54
55        Ok(ExecutionResponse::Success(blast_response.stdout_str()))
56    }
57}
blul_proc/execute_blast.rs

blul_proc/
execute_blast.rs
