2024/10/28-15:30:52 (Linux VDI0092.zit.bam.de x86_64)

pbenner · Oct 28, 2024 · d797171 · d797171
1 parent 8838a3e
commit d797171
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Showing 5 changed files with 61 additions and 13 deletions.
diff --git a/src/granges_bed.rs b/src/granges_bed.rs
@@ -73,7 +73,7 @@ impl GRanges {
             Some(v) => v.clone(),
             None    => comp![ self.ranges[i].from as i64 for i in 0..self.num_rows() ]
         };
-        let thick_end   = match self.meta.get_column_int("thickStart") {
+        let thick_end   = match self.meta.get_column_int("thickEnd") {
             Some(v) => v.clone(),
             None    => comp![ self.ranges[i].to   as i64 for i in 0..self.num_rows() ]
         };
@@ -157,7 +157,7 @@ impl GRanges {
     pub fn bufread_bed3<R: Read + BufRead>(&mut self, reader: &mut R) -> Result<(), Box<dyn Error>> {
         let mut line = String::new();
         while reader.read_line(&mut line)? > 0 {
-            let fields: Vec<&str> = line.trim().split('\t').collect();
+            let fields: Vec<&str> = line.split_whitespace().collect();
             if fields.len() < 3 {
                 return Err(Box::new(io::Error::new(io::ErrorKind::InvalidInput, "Bed file must have at least 3 columns".to_string())));
             }
@@ -177,7 +177,7 @@ impl GRanges {
         let mut name  = Vec::new();
         let mut score = Vec::new();
         while reader.read_line(&mut line)? > 0 {
-            let fields: Vec<&str> = line.trim().split('\t').collect();
+            let fields: Vec<&str> = line.split_whitespace().collect();
             if fields.len() < 6 {
                 return Err(Box::new(io::Error::new(io::ErrorKind::InvalidInput, "Bed file must have at least 6 columns".to_string())));
             }
@@ -205,7 +205,11 @@ impl GRanges {
         let mut thick_end   = Vec::new();
         let mut item_rgb    = Vec::new();
         while reader.read_line(&mut line)? > 0 {
-            let fields: Vec<&str> = line.trim().split('\t').collect();
+            let fields: Vec<&str> = line.split_whitespace().collect();
+            if fields.len() > 0 && (fields[0] == "track" || fields[0] == "browser") {
+                line.clear();
+                continue;
+            }
             if fields.len() < 9 {
                 return Err(Box::new(io::Error::new(io::ErrorKind::InvalidInput, "Bed file must have at least 9 columns".to_string())));
             }
@@ -226,7 +230,7 @@ impl GRanges {
         self.meta.add("score"     , MetaData::IntArray   (score))?;
         self.meta.add("thickStart", MetaData::IntArray   (thick_start))?;
         self.meta.add("thickEnd"  , MetaData::IntArray   (thick_end  ))?;
-        self.meta.add("item_rgb"  , MetaData::StringArray(item_rgb   ))?;
+        self.meta.add("itemRgb"   , MetaData::StringArray(item_rgb   ))?;
         Ok(())
     }
 

diff --git a/src/granges_gtf.rs b/src/granges_gtf.rs
@@ -513,8 +513,6 @@ mod tests {
         assert!(frame.is_none());
         assert!(gene_id.is_some());
 
-        println!("{:?}", gene_id.unwrap());
-
         assert_eq!(source.unwrap()[0], "transcribed_unprocessed_pseudogene");
         assert_eq!(source.unwrap()[1], "processed_transcript");
 

diff --git a/tests/test_granges.rs b/tests/test_granges.rs
@@ -38,13 +38,47 @@ mod tests {
 
         // Import given granges
         assert!(
-            granges1.import_bed("tests/test_granges.bed", 3, false).is_ok());
+            granges1.import_bed("tests/test_granges_1.bed", 3, false).is_ok());
+
+        assert_eq!(
+            granges1.num_rows(), 20);
+
+        // Export to new file and import again
+        assert!(
+            granges1.export_bed3("tests/test_granges_1.bed.tmp", false).is_ok());
+        assert!(
+            granges2.import_bed3("tests/test_granges_1.bed.tmp", false).is_ok());
+        assert!(
+            granges1 == granges2);
+
+        // Modify granges and test for inequality
+        granges2.seqnames[2] = String::from("test");
+        assert!(
+            granges1 != granges2);
+
+        assert!(
+            remove_file("tests/test_granges_1.bed.tmp").is_ok());
+
+    }
+
+    #[test]
+    fn test_granges_bed9() {
+
+        let mut granges1 = GRanges::default();
+        let mut granges2 = GRanges::default();
+
+        // Import given granges
+        assert!(
+            granges1.import_bed("tests/test_granges_2.bed", 9, false).is_ok());
+
+        assert_eq!(
+            granges1.num_rows(), 9);
 
         // Export to new file and import again
         assert!(
-            granges1.export_bed3("tests/test_granges.bed.tmp", false).is_ok());
+            granges1.export_bed9("tests/test_granges_2.bed.tmp", false).is_ok());
         assert!(
-            granges2.import_bed3("tests/test_granges.bed.tmp", false).is_ok());
+            granges2.import_bed9("tests/test_granges_2.bed.tmp", false).is_ok());
         assert!(
             granges1 == granges2);
 
@@ -54,7 +88,7 @@ mod tests {
             granges1 != granges2);
 
         assert!(
-            remove_file("tests/test_granges.bed.tmp").is_ok());
+            remove_file("tests/test_granges_2.bed.tmp").is_ok());
 
     }
 
@@ -66,10 +100,10 @@ mod tests {
 
         // Import given granges
         assert!(
-            granges1.import_bed("tests/test_granges.bed", 3, false).is_ok()
+            granges1.import_bed("tests/test_granges_1.bed", 3, false).is_ok()
         );
         assert!(
-            granges2.import_bed("tests/test_granges.bed", 3, false).is_ok()
+            granges2.import_bed("tests/test_granges_1.bed", 3, false).is_ok()
         );
         granges1 = granges1.subset(&[0,1]);
         granges2 = granges1.subset(&[0,1]);

diff --git a/tests/test_granges.bed → tests/test_granges_1.bed b/tests/test_granges.bed → tests/test_granges_1.bed
diff --git a/tests/test_granges_2.bed b/tests/test_granges_2.bed
@@ -0,0 +1,12 @@
+browser position chr7:127471196-127495720
+browser hide all
+track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On"
+chr7    127471196    127472363    Pos1    0    +    127471196    127472363    255,0,0
+chr7    127472363    127473530    Pos2    0    +    127472363    127473530    255,0,0
+chr7    127473530    127474697    Pos3    0    +    127473530    127474697    255,0,0
+chr7    127474697    127475864    Pos4    0    +    127474697    127475864    255,0,0
+chr7    127475864    127477031    Neg1    0    -    127475864    127477031    0,0,255
+chr7    127477031    127478198    Neg2    0    -    127477031    127478198    0,0,255
+chr7    127478198    127479365    Neg3    0    -    127478198    127479365    0,0,255
+chr7    127479365    127480532    Pos5    0    +    127479365    127480532    255,0,0
+chr7    127480532    127481699    Neg4    0    -    127480532    127481699    0,0,255