v0.20.0

fraterenz · Dec 11, 2023 · 6386dc8 · 6386dc8
1 parent ae1bbbe
commit 6386dc8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,10 @@
 # Changelog
 
 
+## 0.20.0
+change files and dir names after saving the data.
+Now: `{SAMPLE}samples{CELLS}population/{MEASUREMENT}/{B0}b0_{B1}b1_{D0}d0_{D1}d1_0idx.json`.
+
 ## 0.19.0
 remove bin `abc`.
 

diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "ecdna-evo"
-version = "0.19.0"
+version = "0.20.0"
 edition = "2021"
 repository = "https://github.com/fraterenz/ecdna-evo"
 description = "Evolutionary models of extra-chromosomal DNA (ecDNA)"

diff --git a/src/app.rs b/src/app.rs
@@ -38,7 +38,7 @@ impl Dynamics {
         P: AdvanceStep<NB_REACTIONS, Reaction = REACTION>
             + Clone
             + Debug
-            + ToFile
+            + ToFile<NB_REACTIONS>
             + RandomSampling,
         REACTION: std::fmt::Debug,
     {
@@ -101,7 +101,7 @@ impl Dynamics {
                         println!("subsample with {} cells", sampling.0);
                     }
                     process
-                        .save(&path2dir.join("before_subsampling"), idx)
+                        .save(&path2dir.join("before_subsampling"), rates, idx)
                         .with_context(|| {
                             format!(
                                 "Cannot save run {} before subsampling",
@@ -139,7 +139,7 @@ impl Dynamics {
                     initial_state.population.iter().sum::<u64>() == 0u64;
                 if last_sample || no_individuals_left {
                     process
-                        .save(&path2dir.join("after_subsampling"), idx)
+                        .save(&path2dir.join("after_subsampling"), rates, idx)
                         .with_context(|| {
                             format!(
                                 "Cannot save run {} for timepoint {}",
@@ -161,7 +161,7 @@ impl Dynamics {
             }
             run_helper(None, &self.path2dir, initial_state, &mut process);
             process
-                .save(&self.path2dir, idx)
+                .save(&self.path2dir, rates, idx)
                 .with_context(|| format!("Cannot save run {}", idx))
                 .unwrap();
         };

diff --git a/src/clap_app.rs b/src/clap_app.rs
@@ -175,24 +175,14 @@ impl Cli {
                 let samples_str: Vec<String> =
                     samples.iter().map(|ele| ele.to_string()).collect();
                 cli.path.join(format!(
-                    "{}samples{}population_{}b0_{}b1_{}d0_{}d1",
+                    "{}samples{}population",
                     samples_str.join("_"),
                     cells,
-                    cli.b0.to_string().replace('.', ""),
-                    cli.b1.to_string().replace('.', ""),
-                    d0.to_string().replace('.', ""),
-                    d1.to_string().replace('.', ""),
                 ))
             }
-            None => cli.path.join(format!(
-                "{}samples{}population_{}b0_{}b1_{}d0_{}d1",
-                cells,
-                cells,
-                cli.b0.to_string().replace('.', ""),
-                cli.b1.to_string().replace('.', ""),
-                d0.to_string().replace('.', ""),
-                d1.to_string().replace('.', ""),
-            )),
+            None => {
+                cli.path.join(format!("{}samples{}population", cells, cells,))
+            }
         };
 
         let process_type = {

diff --git a/src/lib.rs b/src/lib.rs
@@ -14,11 +14,16 @@ use std::path::Path;
 use ecdna_lib::distribution::SamplingStrategy;
 pub use ecdna_lib::{abc, distribution, DNACopy};
 use rand::Rng;
-use sosa::NbIndividuals;
+use sosa::{NbIndividuals, ReactionRates};
 
 /// Save the results of the simulations.
-pub trait ToFile {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()>;
+pub trait ToFile<const NB_REACTIONS: usize> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<NB_REACTIONS>,
+        id: usize,
+    ) -> anyhow::Result<()>;
 }
 
 /// Undersample a process by randomly reducing the number of individuals.

diff --git a/src/process.rs b/src/process.rs
@@ -5,6 +5,7 @@ use ecdna_lib::distribution::SamplingStrategy;
 use rand::Rng;
 use sosa::{
     write2file, AdvanceStep, CurrentState, NbIndividuals, NextReaction,
+    ReactionRates,
 };
 
 use crate::{
@@ -18,6 +19,26 @@ use super::{
     segregation::IsUneven,
 };
 
+fn create_filename_birth_death(rates: &[f32; 4], id: usize) -> String {
+    format!(
+        "{}b0_{}b1_{}d0_{}d1_{}idx",
+        rates[0].to_string().replace('.', ""),
+        rates[1].to_string().replace('.', ""),
+        rates[2].to_string().replace('.', ""),
+        rates[3].to_string().replace('.', ""),
+        id,
+    )
+}
+
+fn create_filename_pure_birth(rates: &[f32; 2], id: usize) -> String {
+    format!(
+        "{}b0_{}b1_0d0_0d1_{}idx",
+        rates[0].to_string().replace('.', "dot"),
+        rates[1].to_string().replace('.', "dot"),
+        id,
+    )
+}
+
 #[derive(Debug, Clone, Copy)]
 pub enum EcDNAEvent {
     ProliferateNPlus,
@@ -85,16 +106,22 @@ where
     }
 }
 
-impl<P, S> ToFile for PureBirth<P, S>
+impl<P, S> ToFile<2> for PureBirth<P, S>
 where
     P: EcDNAProliferation,
     S: Segregate,
 {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<2>,
+        id: usize,
+    ) -> anyhow::Result<()> {
         //! Save the ecDNA distribution
         let path2ecdna = path2dir.join("ecdna");
         fs::create_dir_all(&path2ecdna).expect("Cannot create dir");
-        let path2file = path2ecdna.join(id.to_string()).with_extension("json");
+        let filename = create_filename_pure_birth(&rates.0, id);
+        let path2file = path2ecdna.join(filename).with_extension("json");
         self.distribution.save(&path2file, self.verbosity)?;
         Ok(())
     }
@@ -238,14 +265,19 @@ where
     }
 }
 
-impl<P, S> ToFile for PureBirthNMinusNPlus<P, S>
+impl<P, S> ToFile<2> for PureBirthNMinusNPlus<P, S>
 where
     P: EcDNAProliferation,
     S: Segregate,
 {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<2>,
+        id: usize,
+    ) -> anyhow::Result<()> {
         fs::create_dir_all(path2dir).expect("Cannot create dir");
-        let filename = id.to_string();
+        let filename = create_filename_pure_birth(&rates.0, id);
         self.data.save(path2dir, &filename, self.verbosity)?;
         Ok(())
     }
@@ -386,15 +418,20 @@ where
     }
 }
 
-impl<P, S> ToFile for PureBirthMean<P, S>
+impl<P, S> ToFile<2> for PureBirthMean<P, S>
 where
     P: EcDNAProliferation,
     S: Segregate,
 {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<2>,
+        id: usize,
+    ) -> anyhow::Result<()> {
         fs::create_dir_all(path2dir).expect("Cannot create dir");
 
-        let filename = id.to_string();
+        let filename = create_filename_pure_birth(&rates.0, id);
         if self.verbosity > 1 {
             println!("Saving data in {:#?}", path2dir)
         }
@@ -597,12 +634,18 @@ impl<P: EcDNAProliferation, S: Segregate> AdvanceStep<4> for BirthDeath<P, S> {
     }
 }
 
-impl<P: EcDNAProliferation, S: Segregate> ToFile for BirthDeath<P, S> {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()> {
+impl<P: EcDNAProliferation, S: Segregate> ToFile<4> for BirthDeath<P, S> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<4>,
+        id: usize,
+    ) -> anyhow::Result<()> {
         //! Save the ecDNA distribution
         let path2ecdna = path2dir.join("ecdna");
+        let filename = create_filename_birth_death(&rates.0, id);
         fs::create_dir_all(&path2ecdna).expect("Cannot create dir");
-        let path2file = path2ecdna.join(id.to_string()).with_extension("json");
+        let path2file = path2ecdna.join(filename).with_extension("json");
         self.distribution.save(&path2file, self.verbosity)?;
         Ok(())
     }
@@ -675,15 +718,20 @@ where
     }
 }
 
-impl<P, S> ToFile for BirthDeathNMinusNPlus<P, S>
+impl<P, S> ToFile<4> for BirthDeathNMinusNPlus<P, S>
 where
     P: EcDNAProliferation,
     S: Segregate,
 {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<4>,
+        id: usize,
+    ) -> anyhow::Result<()> {
         fs::create_dir_all(path2dir).expect("Cannot create dir");
 
-        let filename = id.to_string();
+        let filename = create_filename_birth_death(&rates.0, id);
         if self.verbosity > 1 {
             println!("Saving data in {:#?}", path2dir)
         }
@@ -842,15 +890,20 @@ where
     }
 }
 
-impl<P, S> ToFile for BirthDeathMean<P, S>
+impl<P, S> ToFile<4> for BirthDeathMean<P, S>
 where
     P: EcDNAProliferation,
     S: Segregate,
 {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<4>,
+        id: usize,
+    ) -> anyhow::Result<()> {
         fs::create_dir_all(path2dir).expect("Cannot create dir");
 
-        let filename = id.to_string();
+        let filename = create_filename_birth_death(&rates.0, id);
         if self.verbosity > 1 {
             println!("Saving data in {:#?}", path2dir)
         }
@@ -1046,15 +1099,20 @@ where
     }
 }
 
-impl<P, S> ToFile for BirthDeathMeanVariance<P, S>
+impl<P, S> ToFile<4> for BirthDeathMeanVariance<P, S>
 where
     P: EcDNAProliferation,
     S: Segregate,
 {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<4>,
+        id: usize,
+    ) -> anyhow::Result<()> {
         fs::create_dir_all(path2dir).expect("Cannot create dir");
 
-        let filename = id.to_string();
+        let filename = create_filename_birth_death(&rates.0, id);
         if self.verbosity > 1 {
             println!("Saving data in {:#?}", path2dir)
         }
@@ -1265,15 +1323,20 @@ where
     }
 }
 
-impl<P, S> ToFile for BirthDeathMeanVarianceEntropy<P, S>
+impl<P, S> ToFile<4> for BirthDeathMeanVarianceEntropy<P, S>
 where
     P: EcDNAProliferation,
     S: Segregate,
 {
-    fn save(&self, path2dir: &Path, id: usize) -> anyhow::Result<()> {
+    fn save(
+        &self,
+        path2dir: &Path,
+        rates: &ReactionRates<4>,
+        id: usize,
+    ) -> anyhow::Result<()> {
         fs::create_dir_all(path2dir).expect("Cannot create dir");
 
-        let filename = id.to_string();
+        let filename = create_filename_birth_death(&rates.0, id);
         if self.verbosity > 1 {
             println!("Saving data in {:#?}", path2dir)
         }