From 5bd44abad1415c5c27dccd07c1901bfb43115749 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Thu, 12 Dec 2024 13:20:09 -0500
Subject: [PATCH] Attempt fix for #43
---
gtars/src/uniwig/counting.rs | 10 +-
gtars/src/uniwig/mod.rs | 280 +++++++++++++++++++++++++-------
gtars/tests/data/out/_core.wig | 5 +-
gtars/tests/data/out/_end.wig | 3 +-
gtars/tests/data/out/_start.wig | 3 +-
gtars/tests/test.rs | 2 +
6 files changed, 231 insertions(+), 72 deletions(-)
diff --git a/gtars/src/uniwig/counting.rs b/gtars/src/uniwig/counting.rs
index aa08cfa7..e97b74c9 100644
--- a/gtars/src/uniwig/counting.rs
+++ b/gtars/src/uniwig/counting.rs
@@ -34,6 +34,7 @@ pub fn start_end_counts(
chrom_size: i32,
smoothsize: i32,
stepsize: i32,
+ shift: i32,
) -> (Vec<u32>, Vec<i32>) {
//let vin_iter = starts_vector.iter();
@@ -54,7 +55,7 @@ pub fn start_end_counts(
adjusted_start_site = starts_vector[0]; // get first coordinate position
- adjusted_start_site.0 = adjusted_start_site.0 - smoothsize;
+ adjusted_start_site.0 = adjusted_start_site.0 - smoothsize + shift;
current_end_site = adjusted_start_site;
current_end_site.0 = adjusted_start_site.0 + 1 + smoothsize * 2;
@@ -73,7 +74,7 @@ pub fn start_end_counts(
coordinate_value = *coord;
adjusted_start_site = coordinate_value;
- adjusted_start_site.0 = coordinate_value.0 - smoothsize;
+ adjusted_start_site.0 = coordinate_value.0 - smoothsize + shift;
let current_score = adjusted_start_site.1;
@@ -163,6 +164,7 @@ pub fn core_counts(
ends_vector: &[(i32, i32)],
chrom_size: i32,
stepsize: i32,
+ shift: i32,
) -> (Vec<u32>, Vec<i32>) {
let mut v_coordinate_positions: Vec<i32> = Vec::new(); // these are the final coordinates after any adjustments
let mut v_coord_counts: Vec<u32> = Vec::new(); // u8 stores 0:255 This may be insufficient. u16 max is 65535
@@ -182,6 +184,8 @@ pub fn core_counts(
current_start_site = starts_vector[0]; // get first coordinate position
current_end_site = ends_vector[0];
+ current_start_site.0 = current_start_site.0 + shift;
+
if current_start_site.0 < 1 {
current_start_site.0 = 1;
}
@@ -197,6 +201,8 @@ pub fn core_counts(
current_start_site = coordinate_value;
+ current_start_site.0 = current_start_site.0 + shift;
+
let current_score = current_start_site.1;
count += current_score;
diff --git a/gtars/src/uniwig/mod.rs b/gtars/src/uniwig/mod.rs
index 44beac0f..9fd75801 100644
--- a/gtars/src/uniwig/mod.rs
+++ b/gtars/src/uniwig/mod.rs
@@ -272,33 +272,36 @@ pub fn uniwig_main(
if smoothsize != 0 {
match j {
0 => {
- let mut count_result = match ft {
- Ok(FileType::BED) => start_end_counts(
- &chromosome.starts,
- current_chrom_size,
- smoothsize,
- stepsize,
- ),
- _ => start_end_counts(
- &chromosome.starts,
- current_chrom_size,
- smoothsize,
- stepsize,
- ),
- };
match output_type {
"file" => {
+ panic!("Writing to file currently not supported");
//print!("Writing to CLI");
- let handle = &std::io::stdout();
- let mut buf = BufWriter::new(handle);
- for count in &count_result.0 {
- writeln!(buf, "{}", count)
- .expect("failed to write line");
- }
- buf.flush().unwrap();
+ // let handle = &std::io::stdout();
+ // let mut buf = BufWriter::new(handle);
+ // for count in &count_result.0 {
+ // writeln!(buf, "{}", count)
+ // .expect("failed to write line");
+ // }
+ // buf.flush().unwrap();
}
"wig" => {
+ let count_result = match ft {
+ Ok(FileType::BED) => start_end_counts(
+ &chromosome.starts,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 1,
+ ),
+ _ => start_end_counts(
+ &chromosome.starts,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 1,
+ ),
+ };
//println!("Writing to wig file!");
let file_name = format!(
"{}{}_{}.{}",
@@ -316,6 +319,22 @@ pub fn uniwig_main(
);
}
"bedGraph" => {
+ let mut count_result = match ft {
+ Ok(FileType::BED) => start_end_counts(
+ &chromosome.starts,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0,
+ ),
+ _ => start_end_counts(
+ &chromosome.starts,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0,
+ ),
+ };
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "start", output_type
@@ -339,6 +358,22 @@ pub fn uniwig_main(
panic!("Write to CSV. Not Implemented");
}
"npy" => {
+ let count_result = match ft {
+ Ok(FileType::BED) => start_end_counts(
+ &chromosome.starts,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0,
+ ),
+ _ => start_end_counts(
+ &chromosome.starts,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0,
+ ),
+ };
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "start", output_type
@@ -357,6 +392,22 @@ pub fn uniwig_main(
}
_ => {
println!("Defaulting to npy file...");
+ let count_result = match ft {
+ Ok(FileType::BED) => start_end_counts(
+ &chromosome.starts,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0,
+ ),
+ _ => start_end_counts(
+ &chromosome.starts,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0,
+ ),
+ };
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "start", output_type
@@ -376,32 +427,36 @@ pub fn uniwig_main(
}
}
1 => {
- let mut count_result = match ft {
- Ok(FileType::BED) => start_end_counts(
- &chromosome.ends,
- current_chrom_size,
- smoothsize,
- stepsize,
- ),
- _ => start_end_counts(
- &chromosome.ends,
- current_chrom_size,
- smoothsize,
- stepsize,
- ),
- };
match output_type {
"file" => {
- let handle = &std::io::stdout();
- let mut buf = BufWriter::new(handle);
- for count in &count_result.0 {
- writeln!(buf, "{}", count)
- .expect("failed to write line");
- }
- buf.flush().unwrap();
+ panic!("Writing to file not currently supported.")
+ // let handle = &std::io::stdout();
+ // let mut buf = BufWriter::new(handle);
+ // for count in &count_result.0 {
+ // writeln!(buf, "{}", count)
+ // .expect("failed to write line");
+ // }
+ // buf.flush().unwrap();
}
"bedGraph" => {
+ let mut count_result = match ft {
+ Ok(FileType::BED) => start_end_counts(
+ &chromosome.ends,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0
+ ),
+ _ => start_end_counts(
+ &chromosome.ends,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0
+ ),
+ };
+
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "end", output_type
@@ -423,6 +478,22 @@ pub fn uniwig_main(
);
}
"wig" => {
+ let count_result = match ft {
+ Ok(FileType::BED) => start_end_counts(
+ &chromosome.ends,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 1
+ ),
+ _ => start_end_counts(
+ &chromosome.ends,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 1
+ ),
+ };
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "end", output_type
@@ -442,6 +513,22 @@ pub fn uniwig_main(
panic!("Write to CSV. Not Implemented");
}
"npy" => {
+ let count_result = match ft {
+ Ok(FileType::BED) => start_end_counts(
+ &chromosome.ends,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0
+ ),
+ _ => start_end_counts(
+ &chromosome.ends,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0
+ ),
+ };
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "end", output_type
@@ -459,6 +546,22 @@ pub fn uniwig_main(
);
}
_ => {
+ let count_result = match ft {
+ Ok(FileType::BED) => start_end_counts(
+ &chromosome.ends,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0
+ ),
+ _ => start_end_counts(
+ &chromosome.ends,
+ current_chrom_size,
+ smoothsize,
+ stepsize,
+ 0
+ ),
+ };
println!("Defaulting to npy file...");
let file_name = format!(
"{}{}_{}.{}",
@@ -479,32 +582,35 @@ pub fn uniwig_main(
}
}
2 => {
- let mut core_results = match ft {
- Ok(FileType::BED) => core_counts(
- &chromosome.starts,
- &chromosome.ends,
- current_chrom_size,
- stepsize,
- ),
- _ => core_counts(
- &chromosome.starts,
- &chromosome.ends,
- current_chrom_size,
- stepsize,
- ),
- };
match output_type {
"file" => {
- let handle = &std::io::stdout();
- let mut buf = BufWriter::new(handle);
- for count in &core_results.0 {
- writeln!(buf, "{}", count)
- .expect("failed to write line");
- }
- buf.flush().unwrap();
+ panic!("Writing to file not supported.")
+ // let handle = &std::io::stdout();
+ // let mut buf = BufWriter::new(handle);
+ // for count in &core_results.0 {
+ // writeln!(buf, "{}", count)
+ // .expect("failed to write line");
+ // }
+ // buf.flush().unwrap();
}
"bedGraph" => {
+ let mut core_results = match ft {
+ Ok(FileType::BED) => core_counts(
+ &chromosome.starts,
+ &chromosome.ends,
+ current_chrom_size,
+ stepsize,
+ 0
+ ),
+ _ => core_counts(
+ &chromosome.starts,
+ &chromosome.ends,
+ current_chrom_size,
+ stepsize,
+ 0
+ ),
+ };
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "core", output_type
@@ -523,6 +629,22 @@ pub fn uniwig_main(
);
}
"wig" => {
+ let core_results = match ft {
+ Ok(FileType::BED) => core_counts(
+ &chromosome.starts,
+ &chromosome.ends,
+ current_chrom_size,
+ stepsize,
+ 1
+ ),
+ _ => core_counts(
+ &chromosome.starts,
+ &chromosome.ends,
+ current_chrom_size,
+ stepsize,
+ 1
+ ),
+ };
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "core", output_type
@@ -539,6 +661,22 @@ pub fn uniwig_main(
panic!("Write to CSV. Not Implemented");
}
"npy" => {
+ let core_results = match ft {
+ Ok(FileType::BED) => core_counts(
+ &chromosome.starts,
+ &chromosome.ends,
+ current_chrom_size,
+ stepsize,
+ 0
+ ),
+ _ => core_counts(
+ &chromosome.starts,
+ &chromosome.ends,
+ current_chrom_size,
+ stepsize,
+ 0
+ ),
+ };
let file_name = format!(
"{}{}_{}.{}",
bwfileheader, chrom_name, "core", output_type
@@ -553,6 +691,22 @@ pub fn uniwig_main(
);
}
_ => {
+ let core_results = match ft {
+ Ok(FileType::BED) => core_counts(
+ &chromosome.starts,
+ &chromosome.ends,
+ current_chrom_size,
+ stepsize,
+ 0
+ ),
+ _ => core_counts(
+ &chromosome.starts,
+ &chromosome.ends,
+ current_chrom_size,
+ stepsize,
+ 0
+ ),
+ };
println!("Defaulting to npy file...");
let file_name = format!(
"{}{}_{}.{}",
diff --git a/gtars/tests/data/out/_core.wig b/gtars/tests/data/out/_core.wig
index bce79299..81ae5e9f 100644
--- a/gtars/tests/data/out/_core.wig
+++ b/gtars/tests/data/out/_core.wig
@@ -2,9 +2,8 @@ fixedStep chrom=chr1 start=2 step=1
2
2
3
-4
-2
2
+1
2
1
1
@@ -16,4 +15,4 @@ fixedStep chrom=chr1 start=2 step=1
0
0
0
-0
+0
\ No newline at end of file
diff --git a/gtars/tests/data/out/_end.wig b/gtars/tests/data/out/_end.wig
index e89bdc32..f3119c10 100644
--- a/gtars/tests/data/out/_end.wig
+++ b/gtars/tests/data/out/_end.wig
@@ -12,5 +12,4 @@ fixedStep chrom=chr1 start=5 step=1
0
0
0
-0
-0
+0
\ No newline at end of file
diff --git a/gtars/tests/data/out/_start.wig b/gtars/tests/data/out/_start.wig
index 361beb36..b08c334f 100644
--- a/gtars/tests/data/out/_start.wig
+++ b/gtars/tests/data/out/_start.wig
@@ -16,5 +16,4 @@ fixedStep chrom=chr1 start=1 step=1
0
0
0
-0
-0
+0
\ No newline at end of file
diff --git a/gtars/tests/test.rs b/gtars/tests/test.rs
index 0e538082..b41a9ca0 100644
--- a/gtars/tests/test.rs
+++ b/gtars/tests/test.rs
@@ -315,6 +315,7 @@ mod tests {
&chromosome.ends,
current_chrom_size,
stepsize,
+ 0
);
}
}
@@ -335,6 +336,7 @@ mod tests {
current_chrom_size,
smooth_size,
stepsize,
+ 0
);
}
}