@click.command()
@click.option('-s', '--sample', type=click.Path(exists=True), help='Sample FASTA file.')
@click.option('-r', '--ref', type=click.Path(exists=True), help='Reference genome FASTA file.')
@click.option('-a', '--amplicon', type=click.Path(exists=True), help='Amplicon FASTA file.')
@click.option('--ychr', type=click.Path(exists=True), help='Y chromosome FASTA file (overrides the reference ychr).')
@click.option('-n', '--name', required=True, help='Signature name.')
@click.option('-o', '--output-file', required=True, callback=validate_zip_file, help='Output file with .zip extension.')
@click.option('-b', '--batch-size', default=100000, type=int, show_default=True, help='Batch size for sample sketching.')
@click.option('-c', '--cores', default=4, type=int, show_default=True, help='Number of CPU cores to use.')
@click.option('-k', '--ksize', default=51, type=int, show_default=True, help='K-mer size.')
@click.option('-f', '--force', is_flag=True, help='Overwrite existing output file.')
@click.option('--scale', default=10000, type=int, show_default=True, help='sourmash scale factor.')
@click.option('--debug', is_flag=True, default=False, hidden=True, help='Enable debugging.')
@click.pass_context
def sketch(ctx, sample: Optional[str], ref: Optional[str], amplicon: Optional[str],
ychr: Optional[str], name: str, output_file: str, batch_size: int,
cores: int, ksize: int, scale: int, force: bool, debug: bool):
"""
Sketch genomic data to generate signatures for QC.
This command allows you to generate sketches from sample, reference, or amplicon FASTA files. Only one input type (`--sample`, `--ref`, or `--amplicon`) can be specified at a time.
## Usage
```bash
snipe sketch [OPTIONS]
```
## Options
- `-s`, `--sample PATH`
Sample FASTA file.
- `-r`, `--ref PATH`
Reference genome FASTA file.
- `-a`, `--amplicon PATH`
Amplicon FASTA file.
- `--ychr PATH`
Y chromosome FASTA file (overrides the reference ychr).
- `-n`, `--name TEXT` **[required]**
Signature name.
- `-o`, `--output-file PATH` **[required]**
Output file with `.zip` extension.
- `-b`, `--batch-size INTEGER` **[default: 100000]**
Batch size for sample sketching.
- `-c`, `--cores INTEGER` **[default: 4]**
Number of CPU cores to use.
- `-k`, `--ksize INTEGER` **[default: 51]**
K-mer size.
- `-f`, `--force`
Overwrite existing output file.
- `--scale INTEGER` **[default: 10000]**
Sourmash scale factor.
- `--debug`
Enable debugging.
## Examples
### Sketching a Reference Genome
Generate a sketch from a reference genome FASTA file.
```bash
snipe sketch -r reference.fasta -n genome_ref -o genome_output.zip --cores 8 --debug
```
### Sketching a Sample FASTA File
Generate a sketch from a sample FASTA file.
```bash
snipe sketch -s sample.fasta -n sample_name -o sample_output.zip
```
### Sketching an Amplicon FASTA File with Custom Batch Size
```bash
snipe sketch -a amplicon.fasta -n amplicon_name -o amplicon_output.zip -b 50000
```
### Overwriting an Existing Output File
```bash
snipe sketch -r reference.fasta -n genome_ref -o genome_output.zip --force
```
### Using a Custom Y Chromosome File
```bash
snipe sketch -r reference.fasta -n genome_ref -o genome_output.zip --ychr custom_y.fasta
```
"""
samples = [sample, ref, amplicon]
provided = [s for s in samples if s]
if len(provided) != 1:
click.echo('Error: Exactly one of --sample, --ref, or --amplicon must be provided.')
sys.exit(1)
# Handle existing output file
if os.path.exists(output_file):
if force:
try:
os.remove(output_file)
click.echo(f"Overwriting existing output file {output_file}.")
except Exception as e:
click.echo(f"Failed to remove existing file {output_file}: {e}")
sys.exit(1)
else:
click.echo(f"Output file {output_file} already exists. Please provide a new output file or use --force to overwrite.")
sys.exit(1)
# Determine the mode and set SigType accordingly
if sample:
mode = 'sample'
sig_type = SigType.SAMPLE
input_file = sample
elif ref:
mode = 'ref'
sig_type = SigType.GENOME
input_file = ref
elif amplicon:
mode = 'amplicon'
sig_type = SigType.AMPLICON
input_file = amplicon
else:
# This should not happen due to mutual exclusivity check
raise click.UsageError('You must specify one of --sample, --ref, or --amplicon.')
# Instantiate and execute SnipeSketch with logging based on debug flag
try:
sketcher = SnipeSketch(enable_logging=debug)
except Exception as e:
click.echo(f'Error instantiating SnipeSketch: {e}')
sys.exit(1)
# Sketching start time
start_time = time.time()
try:
if sig_type == SigType.SAMPLE:
# Modify sample name for clarity
snipe_modification_to_name = f"{name}-snipesample"
# Perform sample sketching
sample_signature = sketcher.sample_sketch(
filename=sample,
sample_name=snipe_modification_to_name,
num_processes=cores,
batch_size=batch_size,
ksize=ksize,
scale=scale,
)
# Export the signature to a ZIP file
SnipeSketch.export_sigs_to_zip(
[sample_signature],
output_file,
)
elif sig_type == SigType.GENOME:
# Print sketching parameters for user information
click.echo(f"Sketching genome with ksize={ksize}, scale={scale}, cores={cores}")
snipe_modification_to_name = f"{name}-snipegenome"
# Perform genome sketching
genome_sig, chr_to_sig = sketcher.parallel_genome_sketching(
fasta_file=ref,
cores=cores,
ksize=ksize,
scale=scale,
assigned_genome_name=snipe_modification_to_name,
)
# Rename genome signature for consistency
genome_sig.name = snipe_modification_to_name
# If Y chromosome is provided, perform amplicon sketching
if ychr:
if not sig_type == SigType.GENOME:
click.echo("Error: --ychr is only applicable with --ref.")
sys.exit(1)
snipe_ychr_name = "sex-y"
y_chr_sig = sketcher.amplicon_sketching(
fasta_file=ychr,
ksize=ksize,
scale=scale,
amplicon_name=snipe_ychr_name,
)
chr_to_sig[snipe_ychr_name] = y_chr_sig
# Log the detected chromosomes
autosomal = [name for name in chr_to_sig.keys() if "autosome" in name.lower()]
sex = [name for name in chr_to_sig.keys() if "sex" in name.lower()]
click.echo("Autodetected chromosomes:")
for i, chr_name in enumerate(chr_to_sig.keys(), 1):
print(f"{chr_name}", end="\t")
if i % 6 == 0:
click.echo()
if len(chr_to_sig) % 6 != 0:
click.echo() # For newline after the last line
click.echo(f"Autosomal chromosomes: {len(autosomal)}, Sex chromosomes: {len(sex)}")
# Export genome and chromosome signatures to a ZIP file
SnipeSketch.export_sigs_to_zip(
[genome_sig] + list(chr_to_sig.values()),
output_file,
)
elif sig_type == SigType.AMPLICON:
snipe_modification_to_name = f"{name}-snipeamplicon"
# Perform amplicon sketching
amplicon_signature = sketcher.amplicon_sketching(
fasta_file=amplicon,
ksize=ksize,
scale=scale,
amplicon_name=snipe_modification_to_name,
)
# Export the signature to a ZIP file
SnipeSketch.export_sigs_to_zip(
[amplicon_signature],
output_file,
)
except Exception as e:
click.echo(f"Error during sketching: {e}")
sys.exit(1)
# Sketching end time
end_time = time.time()
elapsed_time = end_time - start_time
click.echo(f"Sketching completed in {elapsed_time:.2f} seconds.")