Add start and end positions in output matrix

crates/sage-cli/src/output.rs

@@ -30,6 +30,8 @@ impl Runner {
                 .format(peptide.proteins.len())
                 .as_bytes(),
         );
+        record.push_field(peptide.start_position.iter().map(|&x| x.to_string()).collect::<Vec<String>>().join(";").as_bytes());
+        record.push_field(peptide.end_position.iter().map(|&x| x.to_string()).collect::<Vec<String>>().join(";").as_bytes());
         record.push_field(filenames[feature.file_id].as_bytes());
         record.push_field(feature.spec_id.as_bytes());
         record.push_field(itoa::Buffer::new().format(feature.rank).as_bytes());
@@ -161,12 +163,14 @@ impl Runner {
             "peptide",
             "proteins",
             "num_proteins",
+            "start_positions",
+            "end_positions",
             "filename",
-            "scannr",
+            "scan",
             "rank",
             "label",
-            "expmass",
-            "calcmass",
+            "measured_mass",
+            "calculated_mass",
             "charge",
             "peptide_len",
             "missed_cleavages",

crates/sage-cli/tests/integration.rs

@@ -1,7 +1,5 @@
 use sage_core::database::Builder;
-use sage_core::enzyme::Digest;
 use sage_core::mass::Tolerance;
-use sage_core::peptide::Peptide;
 use sage_core::scoring::Scorer;
 use sage_core::spectrum::SpectrumProcessor;
 

crates/sage/src/enzyme.rs

@@ -18,11 +18,22 @@ pub struct Digest {
     /// Cleaved peptide sequence
     pub sequence: String,
     /// Protein accession
-    pub protein: Arc<String>,
+    pub protein: ProteinAssignment,
     /// Missed cleavages
     pub missed_cleavages: u8,
     /// Is this an N-terminal peptide of the protein?
     pub position: Position,
+    /// What residue position does this start at (1-based inclusive)?
+    pub start_position: u32,
+    /// What residue position does this end at (1-based inclusive)?
+    pub end_position: u32
+}
+
+#[derive(Clone, PartialOrd, Ord, Debug, Default)]
+pub struct ProteinAssignment {
+    identifier: Arc<String>,
+    start_position: u32,
+    end_position: u32    
 }
 
 #[derive(Copy, Clone, PartialEq, Eq, PartialOrd, Ord, Debug, Hash)]
@@ -58,6 +69,8 @@ impl Digest {
             sequence: sequence.into_iter().collect(),
             missed_cleavages: self.missed_cleavages,
             position: self.position,
+            start_position: self.start_position,
+            end_position: self.end_position
         }
     }
 }
@@ -306,6 +319,8 @@ impl EnzymeParameters {
                     semi_enzymatic: site.semi_enzymatic,
                     position,
                     protein: protein.clone(),
+                    start_position: (start + 1) as u32,
+                    end_position: end as u32
                 });
             }
         }
@@ -330,6 +345,8 @@ mod test {
                 missed_cleavages: 0,
                 position: Position::Nterm,
                 protein: Arc::new(String::default()),
+                start_position: 1,
+                end_position: 6
             },
             Digest {
                 decoy: false,
@@ -338,6 +355,8 @@ mod test {
                 missed_cleavages: 0,
                 position: Position::Nterm,
                 protein: Arc::new(String::default()),
+                start_position: 1,
+                end_position: 6
             },
         ];
 
@@ -353,6 +372,8 @@ mod test {
                 missed_cleavages: 0,
                 position: Position::Nterm,
                 protein: Arc::new(String::default()),
+                start_position: 1,
+                end_position: 6
             },
             Digest {
                 decoy: false,
@@ -361,6 +382,8 @@ mod test {
                 missed_cleavages: 0,
                 position: Position::Internal,
                 protein: Arc::new(String::default()),
+                start_position: 7,
+                end_position: 12
             },
         ];
 
@@ -373,11 +396,11 @@ mod test {
     fn trypsin() {
         let sequence = "MADEEKLPPGWEKRMSRSSGRVYYFNHITNASQWERPSGN";
         let expected = vec![
-            ("MADEEK".into(), Position::Nterm),
-            ("LPPGWEK".into(), Position::Internal),
-            ("MSR".into(), Position::Internal),
-            ("SSGR".into(), Position::Internal),
-            ("VYYFNHITNASQWERPSGN".into(), Position::Cterm),
+            ("MADEEK".into(), Position::Nterm, 1, 6),
+            ("LPPGWEK".into(), Position::Internal, 7, 13),
+            ("MSR".into(), Position::Internal, 14, 16),
+            ("SSGR".into(), Position::Internal, 17, 20),
+            ("VYYFNHITNASQWERPSGN".into(), Position::Cterm, 21, 40),
         ];
 
         let tryp = EnzymeParameters {
@@ -391,7 +414,7 @@ mod test {
             expected,
             tryp.digest(sequence, Arc::default())
                 .into_iter()
-                .map(|d| (d.sequence, d.position))
+                .map(|d| (d.sequence, d.position, d.start_position, d.end_position))
                 .collect::<Vec<_>>()
         );
     }

crates/sage/src/peptide.rs

@@ -28,6 +28,10 @@ pub struct Peptide {
     pub position: Position,
 
     pub proteins: Vec<Arc<String>>,
+    /// What residue does this peptide start at in the protein (1-based inclusive)?
+    pub start_position: Vec<u32>,
+    /// What residue does this peptide end at in the protein (1-based inclusive)?
+    pub end_position: Vec<u32>,
 }
 
 impl Peptide {
@@ -66,6 +70,8 @@ impl Debug for Peptide {
             .field("monoisotopic", &self.monoisotopic)
             .field("missed_cleavages", &self.missed_cleavages)
             .field("position", &self.position)
+            .field("start_position", &self.start_position)
+            .field("end_position", &self.end_position)
             .finish()
     }
 }
@@ -313,6 +319,8 @@ impl Peptide {
             s[1..n].reverse();
             pep.sequence = Arc::from(s.into_boxed_slice());
             pep.modifications[1..n].reverse();
+            pep.start_position = pep.start_position; // TODO: calculate start/end in reversed protein sequences?
+            pep.end_position = pep.end_position;
         }
         pep
     }
@@ -373,6 +381,8 @@ impl TryFrom<Digest> for Peptide {
             missed_cleavages: value.missed_cleavages,
             semi_enzymatic: value.semi_enzymatic,
             proteins: vec![value.protein],
+            start_position: vec![value.start_position],
+            end_position: vec![value.end_position],
         })
     }
 }