feat: rework summary json (#37)

total_taxon_count has been replaced with a more useful  taxons_identified.

reads_extracted_per_taxon now include any taxons at 0 due to parent/child behaviour

Author: Sam-Sims

README.md

@@ -157,10 +157,13 @@ Use `--summary` to get summary statistics (output to stdout on completion)
 
 ```json
 {
-  "total_taxon_count": 2,
+  "taxons_identified": [
+    0,
+    1
+  ],
   "missing_taxon_ids": [
     999999999
-  ]
+  ],
   "reads_extracted_per_taxon": {
     "0": 745591,
     "1": 1646
@@ -174,6 +177,20 @@ Use `--summary` to get summary statistics (output to stdout on completion)
 }
 ```
 
+Fields:
+
+- `taxons_identified`: Taxon IDs found in the Kraken report/output based on the requested taxids (includes
+  parents/children if used).
+- `missing_taxon_ids`: Requested taxon IDs that were not found in the Kraken report.
+- `reads_extracted_per_taxon`: Number of reads extracted per identified taxon ID (0 indicates no direct assignments, but
+  present due to children/parents).
+- `total_reads_in`: Total reads parsed from the input file(s).
+- `total_reads_out`: Total reads written to the output file(s).
+- `proportion_extracted`: `total_reads_out / total_reads_in`.
+- `input_format`: `single` or `paired` input mode.
+- `output_format`: `fastq` or `fasta`, depending on `--output-fasta`.
+- `kractor_version`: Version of kractor that produced the summary.
+
 ### Arguments:
 
 ### Required:

src/kractor.rs

@@ -9,7 +9,7 @@ use serde::{Deserialize, Serialize};
 
 #[derive(Serialize, Deserialize)]
 struct Summary {
-    total_taxon_count: usize,
+    taxons_identified: Vec<i32>,
     reads_extracted_per_taxon: FxHashMap<i32, usize>,
     total_reads_in: usize,
     total_reads_out: usize,
@@ -88,6 +88,7 @@ impl Kractor {
     fn process_reads(&mut self) -> Result<()> {
         let paired = self.args.input.len() == 2;
         let input_format = if paired { "paired" } else { "single" };
+        let reads_extracted_per_taxon = self.get_reads_extracted_per_taxon();
 
         if paired {
             let ((reads_parsed1, reads_output1), (reads_parsed2, reads_output2)) =
@@ -105,8 +106,8 @@ impl Kractor {
             let reads_out = reads_output1 + reads_output2;
 
             self.summary = Some(Summary {
-                total_taxon_count: self.taxon_ids.len(),
-                reads_extracted_per_taxon: self.reads_per_taxon.clone(),
+                taxons_identified: self.taxon_ids.clone(),
+                reads_extracted_per_taxon: reads_extracted_per_taxon.clone(),
                 total_reads_in: reads_in,
                 total_reads_out: reads_out,
                 proportion_extracted: reads_out as f64 / reads_in as f64,
@@ -133,8 +134,8 @@ impl Kractor {
             let reads_out = reads_output1;
 
             self.summary = Some(Summary {
-                total_taxon_count: self.taxon_ids.len(),
-                reads_extracted_per_taxon: self.reads_per_taxon.clone(),
+                taxons_identified: self.taxon_ids.clone(),
+                reads_extracted_per_taxon,
                 missing_taxon_ids: self.missing_taxon_ids.clone(),
                 total_reads_in: reads_in,
                 total_reads_out: reads_out,
@@ -162,6 +163,14 @@ impl Kractor {
         Ok(())
     }
 
+    fn get_reads_extracted_per_taxon(&self) -> FxHashMap<i32, usize> {
+        let mut reads_extracted_per_taxon = self.reads_per_taxon.clone();
+        for taxon_id in &self.taxon_ids {
+            reads_extracted_per_taxon.entry(*taxon_id).or_insert(0);
+        }
+        reads_extracted_per_taxon
+    }
+
     pub fn run(&mut self) -> Result<()> {
         info!(
             "Starting kractor at {}",
@@ -236,4 +245,33 @@ mod tests {
         let kractor = Kractor::new(args);
         assert!(kractor.validate_outputs().is_err());
     }
+
+    #[test]
+    fn test_get_reads_extracted_per_taxon() {
+        let input_files = vec![PathBuf::from("input.fastq")];
+        let args = Cli {
+            input: input_files,
+            output: vec![PathBuf::from("output.fastq")],
+            kraken: PathBuf::from("kraken_output.txt"),
+            report: None,
+            taxid: vec![2901879, 227984],
+            output_type: None,
+            compression_level: niffler::Level::One,
+            parents: false,
+            children: false,
+            exclude: false,
+            output_fasta: false,
+            summary: false,
+            no_report_header_detect: false,
+            verbose: false,
+        };
+        let mut kractor = Kractor::new(args);
+        kractor.taxon_ids = vec![2901879, 227984];
+        kractor.reads_per_taxon.insert(227984, 257);
+
+        let reads_extracted_per_taxon = kractor.get_reads_extracted_per_taxon();
+
+        assert_eq!(reads_extracted_per_taxon.get(&2901879), Some(&0));
+        assert_eq!(reads_extracted_per_taxon.get(&227984), Some(&257));
+    }
 }