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DEV: additional bindings, cli for PyPI install
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,4 @@ | ||
| pub mod kmer; | ||
| pub mod kmer_minimisers; | ||
| pub mod minimiser; | ||
| pub type Kmer = u64; | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| pub mod args; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,139 +1,9 @@ | ||
| use args::CompositionCommands; | ||
| use args::Cli; | ||
| use clap::Parser; | ||
| use composition::oligo::OligoComputer; | ||
| use coverage::CovComputer; | ||
| use misc::minimisers; | ||
| mod args; | ||
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| #[cfg(not(tarpaulin_include))] | ||
| fn main() { | ||
| use composition::{cgr::CgrComputer, oligocgr::OligoCgrComputer}; | ||
| use ktio::fops::create_directory; | ||
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|
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| let cli = args::Cli::parse(); | ||
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| match cli.command { | ||
| args::Commands::Comp { command } => match command { | ||
| CompositionCommands::Oligo(command) => { | ||
| let mut com = | ||
| OligoComputer::new(command.input, command.output, command.k_size as usize); | ||
| if command.threads > 0 { | ||
| com.set_threads(command.threads); | ||
| } | ||
| com.set_norm(!command.counts); | ||
| com.set_header(command.header); | ||
|
|
||
| match command.preset { | ||
| args::VecFmtPreset::Csv => com.set_delim(",".to_owned()), | ||
| args::VecFmtPreset::Spc => com.set_delim(" ".to_owned()), | ||
| args::VecFmtPreset::Tsv => com.set_delim("\t".to_owned()), | ||
| } | ||
| if let Err(e) = com.vectorise() { | ||
| eprintln!("Error: {}", e); | ||
| } | ||
| } | ||
| CompositionCommands::Cgr(command) => { | ||
| if let Some(ksize) = command.k_size { | ||
| let vecsize = command | ||
| .vec_size | ||
| .unwrap_or((ksize as f64).powf(4.0).powf(0.5) as u64) | ||
| as usize; | ||
| let mut cgr = OligoCgrComputer::new( | ||
| command.input, | ||
| command.output, | ||
| ksize as usize, | ||
| vecsize, | ||
| ); | ||
| if command.threads > 0 { | ||
| cgr.set_threads(command.threads); | ||
| } | ||
| cgr.set_norm(!command.counts); | ||
| if let Err(e) = cgr.vectorise() { | ||
| eprintln!("Error: {}", e); | ||
| } | ||
| } else { | ||
| if command.counts { | ||
| eprintln!("Error: cannot use counts in whole sequence CGR!"); | ||
| return; | ||
| } | ||
| let vecsize = command.vec_size.unwrap_or(1) as usize; | ||
| let mut cgr = CgrComputer::new(command.input, command.output, vecsize); | ||
| if command.threads > 0 { | ||
| cgr.set_threads(command.threads); | ||
| } | ||
| if let Err(e) = cgr.vectorise() { | ||
| eprintln!("Error: {}", e); | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| args::Commands::Cov(command) => { | ||
| create_directory(&command.output).unwrap(); | ||
| let mut cov = CovComputer::new( | ||
| command.input, | ||
| command.output, | ||
| command.k_size as usize, | ||
| command.bin_size as usize, | ||
| command.bin_count as usize, | ||
| ); | ||
| if command.threads > 0 { | ||
| cov.set_threads(command.threads); | ||
| } | ||
| if let Some(path) = command.alt_input { | ||
| cov.set_kmer_path(path); | ||
| } | ||
| if command.counts { | ||
| cov.set_norm(false); | ||
| } | ||
| cov.set_max_memory(command.memory as f64); | ||
| match command.preset { | ||
| args::VecFmtPreset::Csv => cov.set_delim(",".to_owned()), | ||
| args::VecFmtPreset::Spc => cov.set_delim(" ".to_owned()), | ||
| args::VecFmtPreset::Tsv => cov.set_delim("\t".to_owned()), | ||
| } | ||
| cov.build_table().unwrap(); | ||
| cov.compute_coverages(); | ||
| } | ||
| args::Commands::Min(command) => { | ||
| if command.w_size <= command.m_size && command.w_size > 0 { | ||
| eprintln!("Window size must be longer than minimiser size!"); | ||
| return; | ||
| } | ||
| if command.m_size >= 31 { | ||
| eprintln!("Minimisers longer than 30 bases not allowed!"); | ||
| return; | ||
| } | ||
|
|
||
| match command.preset { | ||
| args::MinFmtPreset::M2s => minimisers::bin_sequences( | ||
| command.w_size as usize, | ||
| command.m_size as usize, | ||
| &command.input, | ||
| &command.output, | ||
| command.threads, | ||
| ), | ||
| args::MinFmtPreset::S2m => minimisers::seq_to_min( | ||
| command.w_size as usize, | ||
| command.m_size as usize, | ||
| &command.input, | ||
| &command.output, | ||
| command.threads, | ||
| ), | ||
| } | ||
| } | ||
| args::Commands::Ctr(command) => { | ||
| create_directory(&command.output).unwrap(); | ||
| let mut ctr = | ||
| counter::CountComputer::new(command.input, command.output, command.k_size as usize); | ||
| if command.threads > 0 { | ||
| ctr.set_threads(command.threads); | ||
| } | ||
| if command.acgt { | ||
| ctr.set_acgt_output(true); | ||
| } | ||
| ctr.set_max_memory(command.memory as f64); | ||
| ctr.count(); | ||
| ctr.merge(true); | ||
| } | ||
| } | ||
| let cli = Cli::parse(); | ||
| args::cli(cli); | ||
| } |
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