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cluster: Add --output-representative-fasta-directory-copy.
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Fixes #3.

Suggested by: @apcamargo.
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@wwood
wwood committed May 1, 2020
1 parent ce19df7 commit bf70a16
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Showing 2 changed files with 119 additions and 43 deletions.
128 changes: 85 additions & 43 deletions src/cluster_argument_parsing.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,34 +62,10 @@ pub fn run_cluster_subcommand(matches: &clap::ArgMatches) {
.expect("Failed to open output cluster definition file")),
None => None
};
let output_representative_fasta_directory = match m.value_of("output-representative-fasta-directory") {
Some(ref d) => {
let path = std::path::Path::new(d.clone());
if path.exists() {
if path.is_dir() {
if std::fs::read_dir(path)
.expect(&format!("Error opening existing output directory {}", d))
.collect::<Vec<_>>()
.len() == 0 {

info!("Using pre-existing but empty output-representative-fasta-directory")
} else {
error!("The output-representative-fasta-directory specified ({}) exists and is not empty", d);
std::process::exit(1)
}
} else {
error!("The output-representative-fasta-directory path specified ({}) exists but is not a directory", d);
std::process::exit(1)
}
} else {
info!("Creating output-representative-fasta-directory for ..");
std::fs::create_dir_all(path)
.expect(&format!("Error creating output-representative-fasta-directory ({})", d))
}
Some(path)
},
None => None
};
let output_representative_fasta_directory = setup_representative_output_directory(&m, "output-representative-fasta-directory");
let output_representative_fasta_directory_copy = setup_representative_output_directory(&m, "output-representative-fasta-directory-copy");

let output_representative_list = match m.value_of("output-representative-list") {
Some(o) => Some(std::fs::File::create(o)
.expect("Failed to open output representative list file")),
Expand All @@ -115,10 +91,77 @@ pub fn run_cluster_subcommand(matches: &clap::ArgMatches) {
},
None => {}
}

write_cluster_reps_to_directory(&clusters,
passed_genomes,
output_representative_fasta_directory,
&|link, current_stab, rep| {
std::os::unix::fs::symlink(link, std::path::Path::new(&current_stab))
.expect(&format!("Failed to create symbolic link to representative genome {}", rep));
});
write_cluster_reps_to_directory(&clusters,
passed_genomes,
output_representative_fasta_directory_copy,
&|link, current_stab, rep| {
std::fs::copy(link, std::path::Path::new(&current_stab))
.expect(&format!("Failed to create symbolic link to representative genome {}", rep));
});

match output_representative_list {
Some(mut f) => {
for cluster in &clusters {
let rep_index = cluster[0];
writeln!(f, "{}", passed_genomes[rep_index])
.expect("Failed to write to output representative list file");
}
},
None => {}
}
info!("Finished printing genome clusters");
}

fn setup_representative_output_directory<'a>(m: &'a clap::ArgMatches,
argument: &str) -> Option<&'a std::path::Path> {

match m.value_of(argument) {
Some(ref d) => {
let path = std::path::Path::new(d.clone());
if path.exists() {
if path.is_dir() {
if std::fs::read_dir(path)
.expect(&format!("Error opening existing output directory {}", d))
.collect::<Vec<_>>()
.len() == 0 {

info!("Using pre-existing but empty {}", argument)
} else {
error!("The {} specified ({}) exists and is not empty", argument, d);
std::process::exit(1)
}
} else {
error!("The {} path specified ({}) exists but is not a directory", argument, d);
std::process::exit(1)
}
} else {
info!("Creating {} ..", argument);
std::fs::create_dir_all(path)
.expect(&format!("Error creating {} ({})", argument, d))
}
Some(path)
},
None => None
}
}

fn write_cluster_reps_to_directory(clusters: &Vec<Vec<usize>>,
passed_genomes: &Vec<&str>,
output_representative_fasta_directory: Option<&std::path::Path>,
file_creation_fn: &dyn Fn(&std::path::Path, String, &str) -> ()) {

match output_representative_fasta_directory {
Some(dir) => {
let mut some_names_clashed = false;
for cluster in &clusters {
for cluster in clusters {
let rep = passed_genomes[cluster[0]];
let link = std::fs::canonicalize(rep)
.expect(&format!("Failed to convert representative path into an absolute path: {}", rep));
Expand All @@ -136,23 +179,11 @@ pub fn run_cluster_subcommand(matches: &clap::ArgMatches) {
counter += 1;
current_stab = format!("{}.{}.fna",dir.join(basename).to_str().unwrap(),counter);
}
std::os::unix::fs::symlink(link, std::path::Path::new(&current_stab))
.expect(&format!("Failed to create symbolic link to representative genome {}", rep));
}
},
None => {}
}
match output_representative_list {
Some(mut f) => {
for cluster in &clusters {
let rep_index = cluster[0];
writeln!(f, "{}", passed_genomes[rep_index])
.expect("Failed to write to output representative list file");
file_creation_fn(&link, current_stab, rep);
}
},
None => {}
}
info!("Finished printing genome clusters");
};
}

pub fn filter_genomes_through_checkm<'a>(
Expand Down Expand Up @@ -481,20 +512,31 @@ pub fn add_cluster_subcommand<'a>(app: clap::App<'a, 'a>) -> clap::App<'a, 'a> {
.help("Output a file of representative<TAB>member lines")
.required_unless_one(&[
"output-representative-fasta-directory",
"output-representative-list"])
"output-representative-fasta-directory-copy",
"output-representative-list",])
.takes_value(true))
.arg(Arg::with_name("output-representative-fasta-directory")
.long("output-representative-fasta-directory")
.help("Symlink representative genomes into this directory")
.required_unless_one(&[
"output-cluster-definition",
"output-representative-list",
"output-representative-fasta-directory-copy",])
.takes_value(true))
.arg(Arg::with_name("output-representative-fasta-directory-copy")
.long("output-representative-fasta-directory-copy")
.help("Copy representative genomes into this directory")
.required_unless_one(&[
"output-cluster-definition",
"output-representative-fasta-directory",
"output-representative-list"])
.takes_value(true))
.arg(Arg::with_name("output-representative-list")
.long("output-representative-list")
.help("Print newline separated list of paths to representatives into this directory")
.required_unless_one(&[
"output-representative-fasta-directory",
"output-representative-fasta-directory-copy",
"output-cluster-definition"])
.takes_value(true));

Expand Down
34 changes: 34 additions & 0 deletions tests/test_cmdline.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,40 @@ mod tests {
}



#[test]
fn test_output_symlink_directory_names_clash_copy(){
let td = tempfile::TempDir::new().unwrap();
let tdp = td.path();
let extra = &format!("{}_and",tdp.to_str().unwrap());
Assert::main_binary()
.with_args(&[
"cluster",
"--quality-formula",
"Parks2020_reduced",
"--genome-fasta-files",
"tests/data/set1_name_clash/500kb.fna",
"tests/data/set1/500kb.fna",
"tests/data/set1/1mbp.fna",
"--precluster-method", // only needed temporarily
"finch",
"--output-representative-fasta-directory-copy",
extra])
.succeeds()
.stdout()
.is("")
.stderr()
.contains("One or more sequence files have the same file name")
.unwrap();
let extra_path = std::path::Path::new(extra);
let out = extra_path.join("500kb.fna");
assert!(extra_path.exists());
assert!(!std::fs::symlink_metadata(out).unwrap().file_type().is_symlink());
assert!(extra_path.join("500kb.fna.1.fna").exists());
assert!(!extra_path.join("1mbp.fna").exists());
}


#[test]
fn test_min_aligned_fraction(){
Assert::main_binary()
Expand Down

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