update manuscript demo code to use rust, keep all fields in the lifto…

…ver output
comprna · Apr 11, 2024 · 1c4e079 · 1c4e079
1 parent ed3826d
commit 1c4e079
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/manuscript_demo/process_data.sh b/manuscript_demo/process_data.sh
@@ -17,10 +17,10 @@ export wd="/g/data/lf10/as7425/R2DTool_demo/"; mkdir -p ${wd}
 bash ~/R2Dtool/scripts/cheui_to_bed.sh ${methylation_calls} "${wd}/methylation_calls.bed"
 
 # annotate the methylation calls against gencode v38 
-r2d annotate -i "${wd}/methylation_calls.bed" -g ${annotation} -H > "${wd}/methylation_calls_annotated.bed"
+time r2d annotate -i "${wd}/methylation_calls.bed" -g ${annotation} -H > "${wd}/methylation_calls_annotated.bed"
 
 # liftover the annotated called to genomic coordinates 
-r2d liftover -i "${wd}/methylation_calls.bed" -g ${annotation} -H > "${wd}/methylation_calls_annotated.bed"
+time r2d liftover -i "${wd}/methylation_calls_annotated.bed" -g ${annotation} -H > "${wd}/methylation_calls_annotated_lifted.bed"
 
 # annotate methylation calls using Gencode v38
 time Rscript ~/R2Dtool/scripts/R2_annotate.R "${wd}/methylationCalls.bed" "${annotation}" "${wd}/methylationCalls_annotated.bed"

diff --git a/src/liftover.rs b/src/liftover.rs
@@ -58,8 +58,8 @@ pub fn convert_transcriptomic_to_genomic_coordinates(
                 // Get the genomic strand
                 let genomic_strand = &transcript.strand;
 
-                // Join the additional columns (fields after the second one) using a tab character
-                let additional_columns = site_fields[2..].join("\t");
+                // Keep all original columns in the output of the liftover 
+                let additional_columns = site_fields.join("\t");
 
                 // Return the formatted output string
                 return Some(format!(

diff --git a/src/parse_gtf.rs b/src/parse_gtf.rs
@@ -368,22 +368,22 @@ pub fn read_annotation_file(file_path: &str, is_gtf: bool) -> Result<HashMap<Str
                             if feature.end < cds_start {
                                 // 5'UTR for positive strand
                                 transcript.utr5_len = Some(transcript.utr5_len.unwrap_or(0) + feature.length);
-                                println!("5'UTR detected with length {}", feature.length);
+                                // println!("5'UTR detected with length {}", feature.length);
                             } else if feature.start > cds_end {
                                 // 3'UTR for positive strand
                                 transcript.utr3_len = Some(transcript.utr3_len.unwrap_or(0) + feature.length);
-                                println!("3'UTR detected with length {}", feature.length);
+                                // println!("3'UTR detected with length {}", feature.length);
                             }
                         },
                         "-" => {
                             if feature.start > cds_end {
                                 // 5'UTR for negative strand (logic is reversed)
                                 transcript.utr5_len = Some(transcript.utr5_len.unwrap_or(0) + feature.length);
-                                println!("5'UTR (neg strand) detected with length {}", feature.length);
+                                // println!("5'UTR (neg strand) detected with length {}", feature.length);
                             } else if feature.end < cds_start {
                                 // 3'UTR for negative strand (logic is reversed)
                                 transcript.utr3_len = Some(transcript.utr3_len.unwrap_or(0) + feature.length);
-                                println!("3'UTR (neg strand) detected with length {}", feature.length);
+                                // println!("3'UTR (neg strand) detected with length {}", feature.length);
                             }
                         },
                         _ => {}
@@ -487,7 +487,7 @@ mod tests {
         init(); // Initialize logging if necessary
 
         // file path 
-        let gtf_file_path = "/home/150/as7425/R2Dtool/test/gencode_v38.gtf";
+        let gtf_file_path = "./test/gencode_v38.gtf";
 
         // Read the GTF file
         let transcripts = read_annotation_file(gtf_file_path, true).expect("Failed to read GTF file");