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feat: attempt to infer t2g if not provided explicitly
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Rob Patro committed Jan 25, 2023
1 parent a9f4065 commit 656a84a
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Showing 2 changed files with 80 additions and 45 deletions.
123 changes: 79 additions & 44 deletions src/main.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -277,7 +277,7 @@ enum Commands {

/// transcript to gene map
#[arg(short = 'm', long, help_heading = "UMI Resolution Options")]
t2g_map: PathBuf,
t2g_map: Option<PathBuf>,

/// resolution mode
#[arg(short, long, help_heading = "UMI Resolution Options", value_parser = clap::builder::PossibleValuesParser::new(["cr-like", "cr-like-em", "parsimony", "parsimony-em", "parsimony-gene", "parsimony-gene-em"]))]
Expand Down Expand Up @@ -605,10 +605,19 @@ fn build_ref_and_index(af_home_path: PathBuf, index_args: Commands) -> anyhow::R
.expect("failed to run piscem build");
index_duration = index_start.elapsed();

// copy over the t2g file to the index
let mut t2g_out_path: Option<PathBuf> = None;
if let Some(t2g_file) = splici_t2g {
let index_t2g_path = output_index_dir.join("t2g_3col.tsv");
t2g_out_path = Some(PathBuf::from("t2g_3col.tsv"));
std::fs::copy(t2g_file, index_t2g_path)?;
}

let index_json_file = output_index_dir.join("simpleaf_index.json");
let index_json = json!({
"cmd" : format!("{:?}",piscem_index_cmd),
"index_type" : "piscem",
"t2g_file" : t2g_out_path,
"piscem_index_parameters" : {
"k" : kmer_length,
"m" : minimizer_length,
Expand Down Expand Up @@ -675,10 +684,19 @@ fn build_ref_and_index(af_home_path: PathBuf, index_args: Commands) -> anyhow::R
.expect("failed to run salmon index");
index_duration = index_start.elapsed();

// copy over the t2g file to the index
let mut t2g_out_path: Option<PathBuf> = None;
if let Some(t2g_file) = splici_t2g {
let index_t2g_path = output_index_dir.join("t2g_3col.tsv");
t2g_out_path = Some(PathBuf::from("t2g_3col.tsv"));
std::fs::copy(t2g_file, index_t2g_path)?;
}

let index_json_file = output_index_dir.join("simpleaf_index.json");
let index_json = json!({
"cmd" : format!("{:?}",salmon_index_cmd),
"index_type" : "salmon",
"t2g_file" : t2g_out_path,
"salmon_index_parameters" : {
"k" : kmer_length,
"sparse" : sparse,
Expand All @@ -694,12 +712,6 @@ fn build_ref_and_index(af_home_path: PathBuf, index_args: Commands) -> anyhow::R
.with_context(|| format!("could not write {}", index_json_file.display()))?;
}

// copy over the t2g file to the index
if let Some(t2g_file) = splici_t2g {
let index_t2g_path = output_index_dir.join("t2g_3col.tsv");
std::fs::copy(t2g_file, index_t2g_path)?;
}

let index_log_file = output.join("simpleaf_index_log.json");
let index_log_info = if let Some(pyroe_duration) = pyroe_duration {
// if we ran make-splici
Expand Down Expand Up @@ -848,7 +860,7 @@ fn map_and_quant(af_home_path: PathBuf, quant_cmd: Commands) -> anyhow::Result<(
expect_cells,
min_reads,
resolution,
t2g_map,
mut t2g_map,
chemistry,
output,
} => {
Expand All @@ -868,49 +880,72 @@ fn map_and_quant(af_home_path: PathBuf, quant_cmd: Commands) -> anyhow::Result<(

info!("prog info = {:?}", rp);

let mut had_simpleaf_index_json = false;
let mut index_type_str = String::new();
if let Some(index) = index.clone() {
let index_json_path = index.join("simpleaf_index.json");
match index_json_path.try_exists() {
Ok(true) => {
// we have the simpleaf_index.json file, so parse it.
let index_json_file =
std::fs::File::open(&index_json_path).with_context({
|| format!("Could not open file {}", index_json_path.display())
})?;

let index_json_reader = BufReader::new(&index_json_file);
let v: serde_json::Value = serde_json::from_reader(index_json_reader)?;
had_simpleaf_index_json = true;
index_type_str = serde_json::from_value(v["index_type"].clone())?;
// if the user didn't pass in a t2g_map, try and populate it
// automatically here
if t2g_map.is_none() {
let t2g_opt : Option<PathBuf> = serde_json::from_value(v["t2g_file"].clone())?;
if let Some(t2g_val) = t2g_opt {
let t2g_loc = index.join(t2g_val);
info!("found local t2g file at {}, will attempt to use this since none was provided explicitly", t2g_loc.display());
t2g_map = Some(t2g_loc);
}
}
}
Ok(false) => {
had_simpleaf_index_json = false;
}
Err(e) => {
bail!(e);
}
}
}


// at this point make sure we have a t2g value
let t2g_map_file = t2g_map.context("A transcript-to-gene map (t2g) file was not provided via `--t2g-map`|`-m` and could \
not be inferred from the index. Please provide a t2g map explicitly to the quant command.")?;
check_files_exist(&[t2g_map_file.clone()])?;

// figure out what type of index we expect
let index_type;
// only bother with this if we are mapping reads and not if we are
// starting from a RAD file
if let Some(index) = index.clone() {
// if the user said piscem explicitly, believe them
if !use_piscem {
// otherwise, see if we built the index with simpleaf and
// therefore recorded the index type
let index_json_path = index.join("simpleaf_index.json");
match index_json_path.try_exists() {
Ok(true) => {
// we have the simpleaf_index.json file, so parse it.
let index_json_file = std::fs::File::open(&index_json_path)
.with_context({
|| format!("Could not open file {}", index_json_path.display())
})?;

let index_json_reader = BufReader::new(&index_json_file);
let v: serde_json::Value = serde_json::from_reader(index_json_reader)?;
let it_str: String = serde_json::from_value(v["index_type"].clone())?;
match it_str.as_ref() {
"salmon" => {
index_type = IndexType::Salmon(index);
}
"piscem" => {
index_type = IndexType::Piscem(index.join("piscem_idx"));
}
_ => {
bail!(
"unknown index type {} present in {}",
it_str,
index_json_path.display()
);
}
if had_simpleaf_index_json {
match index_type_str.as_ref() {
"salmon" => {
index_type = IndexType::Salmon(index);
}
"piscem" => {
index_type = IndexType::Piscem(index.join("piscem_idx"));
}
_ => {
bail!(
"unknown index type {} present in simpleaf_index.json",
index_type_str,
);
}
}
Ok(false) => {
index_type = IndexType::Salmon(index);
}
Err(e) => {
bail!(e);
}
} else {
index_type = IndexType::Salmon(index);
}
} else {
index_type = IndexType::Piscem(index);
Expand Down Expand Up @@ -1301,12 +1336,12 @@ fn map_and_quant(af_home_path: PathBuf, quant_cmd: Commands) -> anyhow::Result<(
.arg("-o")
.arg(&gpl_output);
alevin_quant_cmd.arg("-t").arg(format!("{}", threads));
alevin_quant_cmd.arg("-m").arg(t2g_map.clone());
alevin_quant_cmd.arg("-m").arg(t2g_map_file.clone());
alevin_quant_cmd.arg("-r").arg(resolution);

info!("cmd : {:?}", alevin_quant_cmd);

let input_files = vec![gpl_output, t2g_map];
let input_files = vec![gpl_output, t2g_map_file];
check_files_exist(&input_files)?;

let quant_start = Instant::now();
Expand Down
2 changes: 1 addition & 1 deletion src/utils/prog_utils.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -235,7 +235,7 @@ pub fn get_required_progs() -> Result<ReqProgs> {
get_required_progs_from_paths(salmon_exe, piscem_exe, alevin_fry_exe, pyroe_exe)
}

pub fn check_files_exist(file_vec: &Vec<PathBuf>) -> Result<()> {
pub fn check_files_exist(file_vec: &[PathBuf]) -> Result<()> {
let mut all_valid = true;
for fb in file_vec {
let er = fb.as_path().try_exists();
Expand Down

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