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style: improve help messages
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@DongzeHE
DongzeHE committed Jan 21, 2023
1 parent 0d5a6c0 commit 66371cc
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Showing 2 changed files with 126 additions and 103 deletions.
166 changes: 81 additions & 85 deletions src/main.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ enum Commands {
#[arg(
short,
long,
help_heading="Expanded Reference Options",
help_heading = "Expanded Reference Options",
display_order = 3,
requires = "fasta",
conflicts_with = "ref_seq"
Expand All @@ -71,7 +71,7 @@ enum Commands {
#[arg(
short,
long,
help_heading="Expanded Reference Options",
help_heading = "Expanded Reference Options",
display_order = 4,
requires = "fasta",
conflicts_with = "ref_seq"
Expand All @@ -81,7 +81,7 @@ enum Commands {
/// deduplicate identical sequences in pyroe when building an expanded reference reference
#[arg(
long = "dedup",
help_heading="Expanded Reference Options",
help_heading = "Expanded Reference Options",
display_order = 5,
requires = "fasta",
conflicts_with = "ref-seq"
Expand All @@ -96,7 +96,7 @@ enum Commands {
/// path to FASTA file with extra spliced sequence to add to the index
#[arg(
long,
help_heading="Expanded Reference Options",
help_heading = "Expanded Reference Options",
display_order = 7,
requires = "fasta",
conflicts_with = "ref_seq"
Expand All @@ -106,16 +106,15 @@ enum Commands {
/// path to FASTA file with extra unspliced sequence to add to the index
#[arg(
long,
help_heading="Expanded Reference Options",
help_heading = "Expanded Reference Options",
display_order = 8,
requires = "fasta",
conflicts_with = "ref_seq"
)]
unspliced: Option<PathBuf>,

/// use piscem instead of salmon for indexing and mapping
#[arg(long, help_heading="Piscem Index Options",
display_order = 1)]
#[arg(long, help_heading = "Piscem Index Options", display_order = 1)]
use_piscem: bool,

/// the value of m to be used to construct the piscem index (must be < k)
Expand All @@ -124,34 +123,39 @@ enum Commands {
long = "minimizer-length",
default_value_t = 19,
requires = "use_piscem",
help_heading="Piscem Index Options",
help_heading = "Piscem Index Options",
display_order = 2
)]
minimizer_length: u32,

/// path to output directory (will be created if it doesn't exist)
#[arg(short, long,
display_order = 1)]
#[arg(short, long, display_order = 1)]
output: PathBuf,

/// number of threads to use when running
#[arg(short, long, default_value_t = 16,
display_order = 2)]
#[arg(short, long, default_value_t = 16, display_order = 2)]
threads: u32,

/// the value of k to be used to construct the index
#[arg(short = 'k', long = "kmer-length", default_value_t = 31,
display_order = 3)]
#[arg(
short = 'k',
long = "kmer-length",
default_value_t = 31,
display_order = 3
)]
kmer_length: u32,

/// keep duplicated identical sequences when constructing the index
#[arg(long,
display_order = 4)]
#[arg(long, display_order = 4)]
keep_duplicates: bool,

/// if this flag is passed, build the sparse rather than dense index for mapping
#[arg(short = 'p', long = "sparse", conflicts_with = "use_piscem",
display_order = 5)]
#[arg(
short = 'p',
long = "sparse",
conflicts_with = "use_piscem",
display_order = 5
)]
sparse: bool,
},
/// add a new custom chemistry to geometry mapping
Expand Down Expand Up @@ -179,19 +183,18 @@ enum Commands {
.args(["index", "map_dir"])
))]
Quant {

/// chemistry
#[arg(short, long)]
chemistry: String,

/// output directory
#[arg(short, long)]
output: PathBuf,

/// number of threads to use when running
#[arg(short, long, default_value_t = 16)]
threads: u32,

/// path to index
#[arg(
short = 'i',
Expand Down Expand Up @@ -394,7 +397,8 @@ fn build_ref_and_index(af_home_path: PathBuf, index_args: Commands) -> anyhow::R
match ref_type {
ReferenceType::SplicedUnspliced => {
let v = rp.pyroe.clone().unwrap().version;
if let Err(e) = prog_utils::check_version_constraints("pyroe", ">=0.7.1, <1.0.0", &v)
if let Err(e) =
prog_utils::check_version_constraints("pyroe", ">=0.7.1, <1.0.0", &v)
{
bail!(e);
}
Expand Down Expand Up @@ -553,7 +557,7 @@ fn build_ref_and_index(af_home_path: PathBuf, index_args: Commands) -> anyhow::R
let output_index_dir = output.join("index");
let index_duration;
if use_piscem {
// ensure we have piscem
// ensure we have piscem
if rp.piscem.is_none() {
bail!("The construction of a piscem index was requested, but a valid piscem executable was not available. \n\
Please either set a path using the `set-paths` command, or ensure the `PISCEM` environment variable is set properly.");
Expand Down Expand Up @@ -618,7 +622,7 @@ fn build_ref_and_index(af_home_path: PathBuf, index_args: Commands) -> anyhow::R
)
.with_context(|| format!("could not write {}", index_json_file.display()))?;
} else {
// ensure we have piscem
// ensure we have piscem
if rp.salmon.is_none() {
bail!("The construction of a salmon index was requested, but a valid piscem executable was not available. \n\
Please either set a path using the `simpleaf set-paths` command, or ensure the `SALMON` environment variable is set properly.");
Expand Down Expand Up @@ -1376,23 +1380,19 @@ fn main() -> anyhow::Result<()> {
piscem,
alevin_fry,
pyroe,
} => {
set_paths(
af_home_path,
Commands::SetPaths {
salmon,
piscem,
alevin_fry,
pyroe,
},
)
}
} => set_paths(
af_home_path,
Commands::SetPaths {
salmon,
piscem,
alevin_fry,
pyroe,
},
),
Commands::AddChemistry { name, geometry } => {
add_chemistry(af_home_path, Commands::AddChemistry { name, geometry })
}
Commands::Inspect {} => {
inspect_simpleaf(af_home_path)
}
Commands::Inspect {} => inspect_simpleaf(af_home_path),
// if we are building the reference and indexing
Commands::Index {
ref_type,
Expand All @@ -1410,28 +1410,26 @@ fn main() -> anyhow::Result<()> {
minimizer_length,
sparse,
threads,
} => {
build_ref_and_index(
af_home_path,
Commands::Index {
ref_type,
fasta,
gtf,
rlen,
spliced,
unspliced,
dedup,
keep_duplicates,
ref_seq,
output,
use_piscem,
kmer_length,
minimizer_length,
sparse,
threads,
},
)
}
} => build_ref_and_index(
af_home_path,
Commands::Index {
ref_type,
fasta,
gtf,
rlen,
spliced,
unspliced,
dedup,
keep_duplicates,
ref_seq,
output,
use_piscem,
kmer_length,
minimizer_length,
sparse,
threads,
},
),

// if we are running mapping and quantification
Commands::Quant {
Expand All @@ -1453,31 +1451,29 @@ fn main() -> anyhow::Result<()> {
t2g_map,
chemistry,
output,
} => {
map_and_quant(
af_home_path,
Commands::Quant {
index,
use_piscem,
map_dir,
reads1,
reads2,
threads,
use_selective_alignment,
expected_ori,
knee,
unfiltered_pl,
explicit_pl,
forced_cells,
expect_cells,
min_reads,
resolution,
t2g_map,
chemistry,
output,
},
)
}
} => map_and_quant(
af_home_path,
Commands::Quant {
index,
use_piscem,
map_dir,
reads1,
reads2,
threads,
use_selective_alignment,
expected_ori,
knee,
unfiltered_pl,
explicit_pl,
forced_cells,
expect_cells,
min_reads,
resolution,
t2g_map,
chemistry,
output,
},
),
}
// success, yay!
}
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