replace m8 with tsv

src/modules/profile.rs

@@ -8,7 +8,7 @@ use std::fs::File;
 use std::io::{self, BufRead, BufReader, BufWriter, Write};
 use std::path::Path;
 
-fn profile(m8_file: &str, mapping: &str, output_dir: &str, threshold: usize, print_copiness: bool) -> io::Result<()> {
+fn profile(tsv_file: &str, mapping: &str, output_dir: &str, threshold: usize, print_copiness: bool) -> io::Result<()> {
     let mut gene_to_spe: HashMap<String, HashSet<String>> = HashMap::new();
     let mut species_set: HashSet<String> = HashSet::new();
 
@@ -32,7 +32,7 @@ fn profile(m8_file: &str, mapping: &str, output_dir: &str, threshold: usize, pri
     if let Some(output) = output.as_mut() {
         writeln!(output, "Query\tMultipleCopyPercent\tSingleCopyPercent")?;
     }
-    let file = File::open(m8_file)?;
+    let file = File::open(tsv_file)?;
     let reader = BufReader::new(file);
     let mut curr_query: Option<String> = None;
     let mut spe_cnt: HashMap<String, i32> = HashMap::new();
@@ -99,7 +99,7 @@ fn output_statistics_and_genes<W: Write>(output: &mut Option<W>, query: &str, sp
 pub fn run(args: &Args, _: &var::BinaryPaths) -> Result<(), Box<dyn std::error::Error>> {
     // Retrieve arguments
     let input_db = args.profile_input_db.clone().unwrap_or_else(|| { crate::envs::error_handler::error(crate::envs::error_handler::ERR_ARGPARSE, Some("profile - input".to_string())); });
-    let input_m8 = args.profile_input_m8.clone().unwrap_or_else(|| { crate::envs::error_handler::error(crate::envs::error_handler::ERR_ARGPARSE, Some("profile - mapping".to_string())); });
+    let input_tsv = args.profile_input_tsv.clone().unwrap_or_else(|| { crate::envs::error_handler::error(crate::envs::error_handler::ERR_ARGPARSE, Some("profile - mapping".to_string())); });
     let output = args.profile_output.clone().unwrap_or_else(|| { crate::envs::error_handler::error(crate::envs::error_handler::ERR_ARGPARSE, Some("profile - output".to_string())); });
     let threshold = args.profile_threshold.unwrap_or_else(|| { crate::envs::error_handler::error(crate::envs::error_handler::ERR_ARGPARSE, Some("profile - threshold".to_string())); });
     let print_copiness = args.profile_print_copiness.unwrap_or_else(|| { crate::envs::error_handler::error(crate::envs::error_handler::ERR_ARGPARSE, Some("profile - print_copiness".to_string())); });
@@ -113,7 +113,7 @@ pub fn run(args: &Args, _: &var::BinaryPaths) -> Result<(), Box<dyn std::error::
     chkpnt::write_checkpoint(&format!("{}/profile.chk", output), "0")?;
 
     let mapping = format!("{}.map", input_db);
-    profile(&input_m8, &mapping, &output, threshold, print_copiness)?;
+    profile(&input_tsv, &mapping, &output, threshold, print_copiness)?;
 
     // Write the checkpoint file
     chkpnt::write_checkpoint(&format!("{}/profile.chk", output), "1")?;

src/util/arg_parser.rs

@@ -131,8 +131,8 @@ pub enum Commands {
     Profile {
         /// Input database (createdb output)
         input_db: PathBuf,
-        /// Input m8 file (cluster or search output)
-        input_m8: PathBuf,
+        /// Input tsv file (cluster or search output)
+        input_tsv: PathBuf,
         /// Output directory
         output: PathBuf,
         /// Coverage threshold for core structures. [0 - 100]
@@ -335,7 +335,7 @@ pub struct Args {
     pub createdb_afdb_local: Option<Option<String>>,
 
     pub profile_input_db: Option<String>,
-    pub profile_input_m8: Option<String>,
+    pub profile_input_tsv: Option<String>,
     pub profile_output: Option<String>,
     pub profile_threshold: Option<usize>,
     pub profile_print_copiness: Option<bool>,
@@ -448,8 +448,8 @@ impl Args {
             Some(EasyCore { output, .. }) => Some(format!("{}/proteome/proteome_db", own(output))),
             Some(EasySearch { output, .. }) => Some(format!("{}/proteome/proteome_db", own(output))), _ => None,
         };
-        let profile_input_m8 = match &args.command {
-            Some(Profile { input_m8, .. }) => Some(own(input_m8)),
+        let profile_input_tsv = match &args.command {
+            Some(Profile { input_tsv, .. }) => Some(own(input_tsv)),
             Some(EasyCore { output, .. }) => Some(format!("{}/cluster/clust.tsv", own(output))),
             Some(EasySearch { output, .. }) => Some(format!("{}/search/search.m8", own(output))), _ => None,
         };
@@ -559,7 +559,7 @@ impl Args {
         Args {
             command: args.command, version: args.version, threads, verbosity,
             createdb_input, createdb_output, createdb_model, createdb_keep, createdb_overwrite, createdb_max_len, createdb_gpu, createdb_use_python, createdb_use_foldseek, createdb_afdb_lookup, createdb_afdb_local,
-            profile_input_db, profile_input_m8, profile_output, profile_threshold, profile_print_copiness,
+            profile_input_db, profile_input_tsv, profile_output, profile_threshold, profile_print_copiness,
             search_input, search_target, search_output, search_tmp, search_keep_aln_db, search_search_options,
             cluster_input, cluster_output, cluster_tmp, cluster_keep_cluster_db, cluster_cluster_options,
             tree_db, tree_input, tree_output, tree_aligner, tree_tree_builder, tree_aligner_options, tree_tree_options, tree_threshold,