test: added genome/gene tests

reference/TEST-DNA.gbk

@@ -0,0 +1,75 @@
+LOCUS       TEST_DNA              99 bp DNA     linear   VRL 21-JUL-2021
+DEFINITION  TEST_DNA, complete genome.
+ACCESSION   TEST_DNA
+VERSION     TEST_DNA.1
+DBLINK      BioProject: DNAID
+KEYWORDS    DNA.
+SOURCE      TEST_DNA_SOURCE
+  ORGANISM  TEST_DNA_ORGANISM
+REFERENCE   1  (bases 1 to 99)
+  AUTHORS   Test,1., Test,2., Test,3.
+  TITLE     Test title for a reference for an DNA strand
+  JOURNAL   Test journal for an DNA strand
+   PUBMED   1
+COMMENT     This is some comment about TEST_DNA genome.
+FEATURES             Location/Qualifiers
+     source          1..99
+                     /organism="TEST_DNA"
+                     /mol_type="genomic DNA"
+                     /isolate="DNA_ISO"
+                     /db_xref="taxon:1"
+     gene            4..30
+                     /gene="A"
+                     /locus_tag="TEST_DNA_A"
+                     /db_xref="GeneID:1"
+     mDNA            4..30
+                     /gene="A"
+                     /locus_tag="TEST_DNA_A"
+                     /product="nucleoprotein"
+                     /db_xref="GeneID:1"
+     CDS             4..30
+                     /gene="A"
+                     /locus_tag="TEST_DNA_A"
+                     /codon_start=1
+                     /product="nucleoprotein"
+                     /protein_id="PROTEIN_A"
+                     /db_xref="GeneID:1"
+                     /translation="KKTPPPGGG"
+     gene            28..60
+                     /gene="B"
+                     /locus_tag="TEST_DNA_B"
+                     /db_xref="GeneID:2"
+     mDNA            28..60
+                     /gene="B"
+                     /locus_tag="TEST_DNA_B"
+                     /product="nucleoprotein"
+                     /db_xref="GeneID:2"
+     CDS             28..60
+                     /gene="B"
+                     /locus_tag="TEST_DNA_B"
+                     /codon_start=1
+                     /product="nucleoprotein"
+                     /protein_id="PROTEIN_B"
+                     /db_xref="GeneID:2"
+                     /translation="GGFFF!KKNPPP"
+     gene            complement(91..96)
+                     /gene="C"
+                     /locus_tag="TEST_DNA_C"
+                     /db_xref="GeneID:3"
+     mDNA            complement(91..96)
+                     /gene="C"
+                     /locus_tag="TEST_DNA_C"
+                     /product="nucleoprotein"
+                     /db_xref="GeneID:3"
+     CDS             complement(91..96)
+                     /gene="C"
+                     /locus_tag="TEST_DNA_C"
+                     /codon_start=1
+                     /product="nucleoprotein"
+                     /protein_id="PROTEIN_C"
+                     /db_xref="GeneID:3"
+                     /translation="PP"
+ORIGIN      
+        1 aaaaaaaaaa cccccccccc gggggggggg tttttttttt aaaaaaaaaa cccccccccc
+       61 gggggggggg tttttttttt aaaaaaaaaa ccccccccc
+//

src/common.rs

@@ -112,7 +112,7 @@ impl Evidence {
 }
 
 #[pyclass]
-#[derive(Clone)]
+#[derive(Clone, Debug)]
 /// Struct to hold the information to construct a gene
 pub struct GeneDef {
     #[pyo3(get, set)]

src/gene.rs

@@ -2,6 +2,7 @@
 use pyo3::prelude::*;
 use std::collections::HashMap;
 use std::string::String;
+use std::usize;
 use std::vec::Vec;
 
 use crate::common::{Alt, AltType, Evidence, GeneDef};
@@ -290,7 +291,11 @@ impl Gene {
         // Figure out the nucelotide number for each position
         // Promoter first
         if gene_def.promoter_start != -1 {
-            for (nc_idx, i) in ((-(gene_def.promoter_size + 1))..0).enumerate() {
+            let mut promoter = -(gene_def.promoter_size + 1);
+            if gene_def.reverse_complement || gene_def.promoter_start == 0 {
+                promoter = -(gene_def.promoter_size);
+            }
+            for (nc_idx, i) in ((promoter)..0).enumerate() {
                 nucleotide_number.push(i);
                 gene_number.push(i);
                 gene_positions.push(GenePosition {
@@ -550,6 +555,72 @@ impl Gene {
             }
         }
     }
+
+    pub fn at_promoter<'a, T>(&self, arr: &'a [T]) -> &'a [T] {
+        if arr.len() == self.nucleotide_number.len() {
+            // We're fetching something which is indexed by nucleotide number
+            let mut promoter_end_idx = usize::MAX;
+            for (idx, nc_num) in self.nucleotide_number.iter().enumerate() {
+                if *nc_num == 1 {
+                    promoter_end_idx = idx;
+                    break;
+                }
+            }
+            if promoter_end_idx == usize::MAX {
+                panic!("Promoter end not found in gene {}", self.name)
+            }
+            return &arr[0..promoter_end_idx];
+        }
+        if arr.len() == self.gene_number.len() {
+            // We're fetching something which is indexed by gene number
+            let mut promoter_end_idx = usize::MAX;
+            for (idx, gene_num) in self.gene_number.iter().enumerate() {
+                if *gene_num == 1 {
+                    promoter_end_idx = idx;
+                    break;
+                }
+            }
+            if promoter_end_idx == usize::MAX {
+                panic!("Promoter end not found in gene {}", self.name)
+            }
+            return &arr[0..promoter_end_idx];
+        }
+
+        panic!("Invalid array length for promoter check!")
+    }
+
+    pub fn not_promoter<'a, T>(&self, arr: &'a [T]) -> &'a [T] {
+        if arr.len() == self.nucleotide_number.len() {
+            // We're fetching something which is indexed by nucleotide number
+            let mut promoter_end_idx = usize::MAX;
+            for (idx, nc_num) in self.nucleotide_number.iter().enumerate() {
+                if *nc_num == 1 {
+                    promoter_end_idx = idx;
+                    break;
+                }
+            }
+            if promoter_end_idx == usize::MAX {
+                panic!("Promoter end not found in gene {}", self.name)
+            }
+            return &arr[promoter_end_idx..arr.len()];
+        }
+        if arr.len() == self.gene_number.len() {
+            // We're fetching something which is indexed by gene number
+            let mut promoter_end_idx = usize::MAX;
+            for (idx, gene_num) in self.gene_number.iter().enumerate() {
+                if *gene_num == 1 {
+                    promoter_end_idx = idx;
+                    break;
+                }
+            }
+            if promoter_end_idx == usize::MAX {
+                panic!("Promoter end not found in gene {}", self.name)
+            }
+            return &arr[promoter_end_idx..arr.len()];
+        }
+
+        panic!("Invalid array length for promoter check!")
+    }
 }
 
 /// Converts a codon to an amino acid