Merge branch 'COMBINE-lab:dev' into dev

src/atac/commands.rs

@@ -244,6 +244,10 @@ pub struct ProcessOpts {
     #[arg(short, long, default_value_t = 16, display_order = 5)]
     pub threads: u32,
 
+    /// do peak calling after generating the bed file
+    #[arg(long)]
+    pub call_peaks: bool,
+
     /// Use the provided file as the unfiltered permit list (i.e. whitelist).
     /// This argument only needs to be provided if you are providing the permit list explicitly,
     /// overriding the default permit list for the provided chemistry.

src/atac/process.rs

@@ -127,7 +127,10 @@ fn add_read_args(map_cmd: &mut std::process::Command, opts: &ProcessOpts) -> any
     Ok(())
 }
 
-pub(crate) fn check_progs<P: AsRef<Path>>(af_home_path: P) -> anyhow::Result<()> {
+pub(crate) fn check_progs<P: AsRef<Path>>(
+    af_home_path: P,
+    opts: &ProcessOpts,
+) -> anyhow::Result<()> {
     let af_home_path = af_home_path.as_ref();
     // Read the JSON contents of the file as an instance of `User`.
     let v: Value = prog_utils::inspect_af_home(af_home_path)?;
@@ -161,6 +164,21 @@ pub(crate) fn check_progs<P: AsRef<Path>>(af_home_path: P) -> anyhow::Result<()>
         Err(e) => return Err(e),
     }
 
+    if opts.call_peaks {
+        let macs_prog_info = rp
+            .macs
+            .as_ref()
+            .expect("macs2 program should be properly set if using the `--call-peaks` option");
+        match prog_utils::check_version_constraints(
+            "macs2",
+            ">=2.2.9, <3.0.0",
+            &macs_prog_info.version,
+        ) {
+            Ok(macs_ver) => info!("found macs2 version {:#}, proceeding", macs_ver),
+            Err(e) => return Err(e),
+        }
+    }
+
     Ok(())
 }
 
@@ -380,11 +398,12 @@ fn macs_call_peaks(af_home_path: &Path, opts: &ProcessOpts) -> anyhow::Result<()
         .expect("macs program info should be properly set.");
 
     let gpl_dir = opts.output.join("af_process");
-    let bed_input = gpl_dir.join("map_sorted.bed");
+    let bed_input = gpl_dir.join("map.bed");
     let peaks_output = gpl_dir.join("peaks.narrowPeak");
     let mut macs_cmd =
         std::process::Command::new(format!("{}", &macs_prog_info.exe_path.display()));
     macs_cmd
+        .arg("callpeak")
         .arg("-f")
         .arg("BEDPE")
         .arg("--nomodel")
@@ -401,6 +420,48 @@ fn macs_call_peaks(af_home_path: &Path, opts: &ProcessOpts) -> anyhow::Result<()
         .arg("-n")
         .arg(peaks_output);
 
+    let macs_cmd_string = prog_utils::get_cmd_line_string(&macs_cmd);
+    info!("macs2 command : {}", macs_cmd_string);
+
+    let macs_start = Instant::now();
+    let macs_proc_out = prog_utils::execute_command(&mut macs_cmd, CommandVerbosityLevel::Quiet)
+        .expect("could not execute [atac::macs]");
+    let macs_duration = macs_start.elapsed();
+
+    if !macs_proc_out.status.success() {
+        bail!(
+            "atac::macs failed with exit status {:?}",
+            macs_proc_out.status
+        );
+    } else {
+        info!("macs completed successfully in {:#?}", macs_duration);
+    }
+
+    let af_process_info_file = opts.output.join("simpleaf_process_log.json");
+    let json_file = std::fs::File::open(af_process_info_file.clone())
+        .with_context(|| format!("couldn't open file {}", af_process_info_file.display()))?;
+    let json_reader = BufReader::new(json_file);
+    let mut af_process_info: serde_json::Value = serde_json::from_reader(json_reader)
+        .with_context(|| {
+            format!(
+                "couldn't parse JSON content from {}",
+                af_process_info_file.display()
+            )
+        })?;
+
+    af_process_info["time_info"]["macs_time"] = json!(macs_duration.as_secs_f64());
+    af_process_info["cmd_info"]["macs_cmd"] = json!(macs_cmd_string);
+
+    // write the relevant info about
+    // our run to file.
+    std::fs::write(
+        &af_process_info_file,
+        serde_json::to_string_pretty(&af_process_info).unwrap(),
+    )
+    .with_context(|| format!("could not write {}", af_process_info_file.display()))?;
+
+    info!("successfully called peaks using macs2.");
+
     Ok(())
 }
 

src/main.rs

@@ -107,7 +107,7 @@ fn main() -> anyhow::Result<()> {
         // processing for ATAC-seq data
         Commands::Atac(AtacCommand::Process(process_opts)) => {
             // validate versions
-            atac::process::check_progs(&af_home_path)?;
+            atac::process::check_progs(&af_home_path, &process_opts)?;
             // first we map the reads
             atac::process::map_reads(af_home_path.as_path(), &process_opts)?;
             // then we generate the permit list and sort the file

src/utils/prog_utils.rs

@@ -242,15 +242,26 @@ pub fn check_version_constraints_from_output<S1: AsRef<str>>(
         Ok(vs) => {
             let x = vs.split_whitespace();
             if let Some(version) = x.last() {
-                let parsed_version = Version::parse(version).unwrap();
+                let ver = if version.split(".").count() > 3 {
+                    warn!("version info {} is not a valid semver (more than 3 dotted version parts; looking only at the major, minor & patch versions).", version);
+                    version
+                        .split(".")
+                        .take(3)
+                        .collect::<Vec<&str>>()
+                        .join(".")
+                        .to_string()
+                } else {
+                    version.to_string()
+                };
+                let parsed_version = Version::parse(&ver).unwrap();
                 let req = VersionReq::parse(req_string.as_ref()).unwrap();
                 if req.matches(&parsed_version) {
                     return Ok(parsed_version);
                 } else {
                     return Err(anyhow!(
                         "Parsed version of {} ({:?}) does not satisfy constraints {}. Please install a compatible version.",
                         prog_name,
-                        version,
+                        ver,
                         req
                     ));
                 }
@@ -395,7 +406,7 @@ pub fn get_required_progs_from_paths(
     if let Some(macs) = opt_macs {
         let st = macs.display().to_string();
         let sr = run_fun!($st --version);
-        let v = check_version_constraints_from_output("macs2", ">=2.2.9.1, <3.0.0", sr)?;
+        let v = check_version_constraints_from_output("macs2", ">=2.2.9, <3.0.0", sr)?;
         rp.macs = Some(ProgInfo {
             exe_path: macs,
             version: format!("{}", v),

src/utils/remote.rs

@@ -0,0 +1,8 @@
+/// Checks the provided URL to determine if it is a remote or local URL.
+/// The current implementation is a heuristic, and may not cover all cases.
+/// Decide if we want to pull in a crate like [url](https://crates.io/crates/url)
+/// instead to do more comprehensive testing.
+pub(crate) fn is_remote_url<T: AsRef<str>>(p: T) -> bool {
+    let pr = p.as_ref();
+    pr.starts_with("www.") || pr.starts_with("http://") || pr.starts_with("https://")
+}