Merge pull request #115 from neherlab/suggestion-2

Author: ivan-aksamentov

packages/pangraph/src/align/mmseqs/align_with_mmseqs.rs

@@ -6,7 +6,10 @@ use crate::io::file::open_file_or_stdin;
 use crate::io::fs::path_to_str;
 use crate::pangraph::pangraph_block::{BlockId, PangraphBlock};
 use crate::utils::subprocess::create_arg_optional;
+use crate::{make_error, vec_of_owned};
+use color_eyre::{Section, SectionExt};
 use eyre::{Report, WrapErr};
+use itertools::Itertools;
 use std::collections::BTreeMap;
 use std::io::Read;
 use std::process::Command;
@@ -32,33 +35,32 @@ pub fn align_with_mmseqs(
   }
 
   let output_column_names = PafTsvRecord::fields_names().join(",");
-  let k = create_arg_optional("-k", &params.kmer_length);
 
-  let cmd_outcome = Command::new("mmseqs")
-    .arg("easy-search")
-    .arg(&input_path)
-    .arg(&input_path)
-    .arg(&output_path)
-    .arg(&tmp_path)
-    .arg("--threads")
-    .arg("1")
-    .arg("--max-seq-len")
-    .arg("10000")
-    .arg("-a")
-    .arg("--search-type")
-    .arg("3")
-    .arg("--format-output")
-    .arg(&output_column_names)
-    .args(&k)
-    .output()
-    .wrap_err("When trying to align sequences using mmseqs")?;
+  let mut args = vec_of_owned![
+    "easy-search",
+    &input_path,
+    &input_path,
+    &output_path,
+    &tmp_path,
+    "--thread",
+    "1",
+    "--max-seq-len",
+    "10000",
+    "-a",
+    "--search-type",
+    "3",
+    "--format-output",
+    &output_column_names,
+  ];
 
-  if !cmd_outcome.status.success() {
-    return Err(Report::msg(format!(
-      "mmseqs command {}\nfailed with stderr:\n{}",
-      cmd_outcome.status,
-      String::from_utf8_lossy(&cmd_outcome.stderr).trim()
-    )));
+  args.extend(create_arg_optional("-k", &params.kmer_length));
+
+  let cmd = Command::new("mmseqs").args(&args).output()?;
+
+  if !cmd.status.success() {
+    return make_error!("{}", String::from_utf8(cmd.stderr)?.trim())
+      .wrap_err_with(|| format!("mmseqs failed with exit code {}", cmd.status.code().unwrap()))
+      .with_section(|| format!("mmseqs {}", args.join(" ")).header("Full command line was:"));
   }
 
   let mut paf_str = String::new();

packages/pangraph/src/pangraph/graph_merging.rs

@@ -176,6 +176,7 @@ pub fn find_matches(
     AlignmentBackend::Minimap2 => align_with_minimap2_lib(blocks, &args.aln_args),
     AlignmentBackend::Mmseqs => align_with_mmseqs(blocks, &args.aln_args),
   }
+  .wrap_err_with(|| format!("When trying to align sequences using {}", &args.alignment_kernel))
 }
 
 pub fn filter_matches(alns: &[Alignment], args: &AlignmentArgs) -> Vec<Alignment> {

packages/pangraph/src/utils/subprocess.rs

@@ -64,6 +64,6 @@ where
 pub fn create_arg_optional(name: impl AsRef<str>, value: &Option<impl ToString>) -> Vec<String> {
   value
     .as_ref()
-    .map(|kmer_len| vec![name.as_ref().to_owned(), kmer_len.to_string()])
+    .map(|value| vec![name.as_ref().to_owned(), value.to_string()])
     .unwrap_or_default()
 }