to lib

src/main.rs → src/lib.rs

@@ -1,57 +1,5 @@
 use duct::cmd;
 
-fn main() {
-    let ref_path = "/home/thomas/NGS/ref/hg19.fa";
-    // let sequence = "
-    // CATTATATTCTTTTTTACAGTGCCACGGGTATATTTAGTAAACATTGAAATGTGTGGTTG
-    // GAATTGTTCATCACTGATGTTTTTGGTGATATTTGTTTATGTTCTGAAGCTATTGCTGTA
-    // GACCAACATGGAGTAAACAGAAAATAATTGGGACACAGGGGCAATAAAACTCATATATTA
-    // TTTTCCCATGACACTCAGAGGACTCTTCCCAATGCTGAGACATACATAGCGGGTCACGGC
-    // TGGGTGTTTTTGGACAAAGGCTTAATGCACTCCAACCTAGGTCCAAGAACTACAACGGCT
-    // GCTGCCGGCCGGGCCCGCTCCCTGGCCTACCTTGCACAAGAAGTCGACATCGTAGAAGGC
-    // GGACAGAAGTGTGGTCGACATGTTTCTGGAA"
-    // .replace("\n", "")
-    // .replace(" ", "");
-
-    // let sequence = "
-    // CGTTATTCGTCGTGGCTCAAGCCCGGCCACGCCGCCCCAAGGGCTCCTCCCGACCTCCCG
-    // GCCTGCCGCTCCGGCCACTGCGGGATCCAGAAACATGTCGACCACACTTCTGTCCGCCTT
-    // CTACGATGTCGACTTCTTGTGCAAGGTAGGCCAGGGAGCGGGCCCGGCCGGCAGCAGCCG
-    // TTGTAGTTCTTGGACCTAGGTTGGAGTGCATTAAGCCTTTGTCCAAAAACACCCAGCCGT
-    // GACCCGCTATGTATGTCTCAGCATTGGGAAGAGTCCTCTGAGTGTCATGGGAAAATAATA
-    // TATGAGTTT"
-    // .replace("\n", "")
-    // .replace(" ", "");
-
-    //2011N160703-HAOAA 1
-    let sequence = "
-    CCTCCCGCCCTGCCTTTCAGGTCGGGAAAGTCCCGGGGTTTGCAAAAGAGTGTCCGAGCG
-    CCCTGGAGGCGGGGAGGGCGGCAAGGAGGGCGCCGGTGTCGCGGTTGAGTTTCTCCACTG
-    CCGACCGCGGCCACGCTGCCCGGGGCTTCCCGGACAGGCTTCGCGCCGCCCACCTCGGCA
-    GCCGGGGCGGA
-    TGG
-    CCACACAGGTTGGAGTGCATTAAGCCTTTGTCCAAAAACACCCAGC
-    CGTGACCCGCTATGTATGTCTCAGCATTGGGAAGAGTCCTCTGAGTGTCATGGGAAAATA
-    ATATATGAGTT"
-    .replace("\n", "")
-    .replace(" ", "");
-    //2011N160703-HAOAA 2
-    // let sequence = "
-    // TGGAATTGTTCATCACTGATGTTTTTGGTGATATTTGTTTATGTTCTGAAGCTATTGCTG
-    // TAGACCAACATGGAGTAAACAGAAAATAATTGGGACACAGGGGCAATAAAACTCATATAT
-    // TATTTTCCCATGACACTCAGAGGACTCTTCCCAATGCTGAGACATACATAGCGGGTCACG
-    // GCTGGGTGTTTTTGGACAAAGGCTTAATGCACTCCAACCTGTGTGGCCATCCGCCCCGGC
-    // TGCCGAGGTGGGCGGCGCGAAGCCTGTCCGGGAAGCCCCGGGCAGCGTGGCCGCGGTCGG
-    // CAGTGGAGAAACTCAACCGCGACACC"
-    // .replace("\n", "")
-    // .replace(" ", "");
-    
-    let alns = Alignments::to_reference(&sequence, ref_path);
-
-    alns.ranges.iter().for_each(|r| println!("{:?}", r));
-
-}
-
 pub fn bwa_aln(ref_path: &str, query_sequence: &str) -> Vec<Sam> {
     let stdout = cmd!("echo", "-e", format!("\">sequence_to_query\n{}\"", query_sequence))
     .pipe(cmd!("bwa", "mem", ref_path, "-"))
@@ -290,19 +238,52 @@ pub fn format_seq(name: &str, sequence: &str, line_size: usize) -> String {
     format!(">{name}\n{res}")
 }
 
-// pub fn compose_seq(ref_path: &str, ranges: Vec<(String, i32, i32)>) -> String {
-//     let fa = IndexedFasta::from_file(ref_path).expect("Error opening fa");
+#[cfg(test)]
+mod tests {
+    use super::*;
 
-//     let mut sequence = String::new();
-//     for (contig, start, stop) in ranges {
-//         let chr_index = fa.fai().tid(&contig).expect("Cannot find chr in index");
-//         if start < stop {
-//             let v = fa.view(chr_index, start as usize,stop as usize).expect("Cannot get .fa view");
-//             sequence = format!("{}{}", sequence, v.to_string());
-//         } else {
-//             let v = fa.view(chr_index, stop as usize, start as usize).expect("Cannot get .fa view");
-//             sequence = format!("{}{}", sequence, revcomp(&v.to_string()));
-//         }
-//     }
-//     sequence
-// }
+    #[test]
+    fn test_1() {
+        let ref_path = "/home/thomas/NGS/ref/hg19.fa";
+
+        //2011N160703-HAOAA 1
+        let sequence = "
+        CCTCCCGCCCTGCCTTTCAGGTCGGGAAAGTCCCGGGGTTTGCAAAAGAGTGTCCGAGCG
+        CCCTGGAGGCGGGGAGGGCGGCAAGGAGGGCGCCGGTGTCGCGGTTGAGTTTCTCCACTG
+        CCGACCGCGGCCACGCTGCCCGGGGCTTCCCGGACAGGCTTCGCGCCGCCCACCTCGGCA
+        GCCGGGGCGGA
+        TGG
+        CCACACAGGTTGGAGTGCATTAAGCCTTTGTCCAAAAACACCCAGC
+        CGTGACCCGCTATGTATGTCTCAGCATTGGGAAGAGTCCTCTGAGTGTCATGGGAAAATA
+        ATATATGAGTT"
+        .replace("\n", "")
+        .replace(" ", "");
+
+        let alns = Alignments::to_reference(&sequence, ref_path);
+        assert_eq!(
+            alns.ranges,
+            vec![vec![((43453321, 43453131), (1, 191))], vec![((22908007, 22908123), (195, 311))]]
+        );
+    }
+    #[test]
+    fn test_2() {
+        let ref_path = "/home/thomas/NGS/ref/hg19.fa";
+        //2011N160703-HAOAA 2
+        let sequence = "
+        TGGAATTGTTCATCACTGATGTTTTTGGTGATATTTGTTTATGTTCTGAAGCTATTGCTG
+        TAGACCAACATGGAGTAAACAGAAAATAATTGGGACACAGGGGCAATAAAACTCATATAT
+        TATTTTCCCATGACACTCAGAGGACTCTTCCCAATGCTGAGACATACATAGCGGGTCACG
+        GCTGGGTGTTTTTGGACAAAGGCTTAATGCACTCCAACCTGTGTGGCCATCCGCCCCGGC
+        TGCCGAGGTGGGCGGCGCGAAGCCTGTCCGGGAAGCCCCGGGCAGCGTGGCCGCGGTCGG
+        CAGTGGAGAAACTCAACCGCGACACC"
+        .replace("\n", "")
+        .replace(" ", "");
+
+        let alns = Alignments::to_reference(&sequence, ref_path);
+        
+        assert_eq!(
+            alns.ranges,
+            vec![vec![((22908232, 22908007), (1, 226))], vec![((43453131, 43453227), (230, 326))]]
+        );
+    }
+}