pretty examples

steineggerlab · Jan 21, 2025 · dee32f2 · dee32f2
1 parent acce174
commit dee32f2
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Showing 2 changed files with 17 additions and 46 deletions.
diff --git a/Cargo.toml b/Cargo.toml
@@ -9,4 +9,5 @@ edition = "2021"
 clap = { version = "4.5.4", features = ["derive"] }
 md5 = { version = "0.7.0" }
 reqwest = { version = "0.12.9", features = ["blocking"] }
-num_cpus = "1.16.0"
+num_cpus = "1.16.0"
+color-print = "0.3.7"
diff --git a/src/util/arg_parser.rs b/src/util/arg_parser.rs
@@ -1,6 +1,8 @@
 use std::path::PathBuf;
 use clap::{Parser, Subcommand};
+use color_print::cstr;
 use crate::util::arg_parser::Commands::*;
+
 #[derive(Parser)]
 #[clap(disable_version_flag = true, arg_required_else_help = true)]
 pub struct ClapArgs {
@@ -29,18 +31,21 @@ fn _threshold_in_range_f64(s: &str) -> Result<f64, String> {
     }
 }
 
+// Extra help messages
+const PROFILE_HELP: &str = cstr!(r#"<bold><underline>Example:</underline></bold>
+  # Define core genes above 85% coverage threshold
+  <bold>unicore profile -t 85 example/db/proteome_db example/out/clu.tsv result</bold>
+"#);
+const GENETREE_HELP: &str = cstr!(r#"<bold><underline>Example:</underline></bold>
+  # Create a list of hashed gene names
+  <bold>awk -F'\t' 'NR==FNR {a[$1];next} ($3 in a) {print $1}' /path/to/original/gene/names db/proteome_db.map > /path/to/hashed/gene/names</bold>
+  # Run gene-tree with the list of hashed gene names; use --realign option to recompute the alignment with custom --threshold option for MSA gap threshold
+  <bold>unicore gene-tree --realign --threshold 30 --name /path/to/hashed/gene/names example/tree</bold>
+"#);
 #[derive(Subcommand)]
 pub enum Commands {
     /// Create Foldseek database from amino acid sequences
     #[clap(arg_required_else_help = true, allow_hyphen_values = true, verbatim_doc_comment)]
-    #[command(
-        after_help=
-        "
-        Example:
-        // Download ProstT5 weights as below if you haven't already
-        // foldseek databases ProstT5 /path/to/prostt5/weights tmp
-        unicore createdb example/data example/db/proteome_db example/model
-        ")]
     Createdb {
         /// Input directory with fasta files or a single fasta file
         input: PathBuf,
@@ -89,12 +94,6 @@ pub enum Commands {
     },
     /// Cluster Foldseek database
     #[clap(arg_required_else_help = true, allow_hyphen_values = true)]
-    #[command(
-        after_help=
-        "
-        Example:
-        unicore cluster example/db/proteome_db example/out/clu tmp
-        ")]
     Cluster {
         /// Input database (createdb output)
         input: PathBuf,
@@ -141,13 +140,7 @@ pub enum Commands {
     },
     /// Create core structures from Foldseek database
     #[clap(arg_required_else_help = true)]
-    #[command(
-        after_help=
-        "
-        Example:
-        // 85% coverage
-        unicore profile -t 85 example/db/proteome_db example/out/clu.tsv result
-        ")]
+    #[command(after_help=PROFILE_HELP)]
     Profile {
         /// Input database (createdb output)
         input_db: PathBuf,
@@ -170,12 +163,6 @@ pub enum Commands {
     },
     /// Infer phylogenetic tree from core structures
     #[clap(arg_required_else_help = true, allow_hyphen_values = true)]
-    #[command(
-        after_help=
-        "
-        Example: 
-        unicore tree example/db/proteome_db example/result example/tree
-        ")]
     Tree {
         /// Input database (createdb output)
         db: PathBuf,
@@ -207,18 +194,7 @@ pub enum Commands {
     },
     // Infer phylogenetic tree of each core structures
     #[clap(arg_required_else_help = true, allow_hyphen_values = true)]
-    #[command(
-        after_help=
-        "
-        Examples: 
-        unicore gene-tree example/tree
-
-        // Create a list of hashed gene names
-        awk -F'\t' 'NR==FNR {a[$1];next} ($3 in a) {print $1}' /path/to/original/gene/names db/proteome_db.map > /path/to/hashed/gene/names
-        // Run gene-tree with the list of hashed gene names
-        // Also optionally use --realign option to recompute the alignment and --threshold option to filter the MSA
-        unicore gene-tree --realign --threshold 30 --name /path/to/hashed/gene/names example/tree
-        ")]
+    #[command(after_help=GENETREE_HELP)]
     GeneTree {
         /// Input directory containing species phylogenetic tree (Output of the Tree module)
         input: PathBuf,
@@ -252,12 +228,6 @@ pub enum Commands {
     },
     /// Easy core gene phylogeny workflow, from fasta files to phylogenetic tree
     #[clap(arg_required_else_help = true, allow_hyphen_values = true)]
-    #[command(
-        after_help=
-        "
-        Example: 
-        unicore easy-core --use-foldseek --gpu example/data example/results example/model example/tmp
-        ")]
     EasyCore {
         /// Input directory with fasta files or a single fasta file
         input: PathBuf,