Snipe CLI Documentation¶
apply_operations(signatures, operations, logger)
¶
Apply the list of operations to the signatures in the specified order.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
signatures
|
List[SnipeSig]
|
List of SnipeSig instances. |
required |
operations
|
List[tuple]
|
List of operations to apply. |
required |
logger
|
Logger
|
Logger for logging messages. |
required |
Source code in src/snipe/cli/cli_ops.py
common(ctx, sig_files, sigs_from_file, reset_abundance, trim_singletons, min_abund, max_abund, trim_below_median, output_file, name, debug, force)
¶
Extract hashes that are common to all input signatures.
This command identifies hashes that are present in every input signature and creates a new signature containing only these common hashes. The abundance values from the first signature are retained.
Example:
snipe ops common sample1.sig.zip sample2.sig.zip sample3.sig.zip -o common_hashes.sig.zip
This command will
- Load
sample1.sig.zip
,sample2.sig.zip
, andsample3.sig.zip
. - Apply any specified operations.
- Identify hashes common to all signatures.
- Retain abundance values from
sample1.sig.zip
for these common hashes. - Export the resulting common hashes signature to
common_hashes.sig.zip
.
Source code in src/snipe/cli/cli_ops.py
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|
common_options(func)
¶
Decorator to add common options to all ops subcommands.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
func
|
The Click command function to decorate. |
required |
Returns:
Type | Description |
---|---|
The decorated function with added options. |
Source code in src/snipe/cli/cli_ops.py
intersect(ctx, sig_files, sigs_from_file, reset_abundance, trim_singletons, min_abund, max_abund, trim_below_median, output_file, name, debug, force)
¶
Compute the intersection of multiple signatures, retaining only common hashes.
This command identifies hashes that are present in all input signatures and retains their abundance from the first signature.
Example:
snipe ops intersect sample1.sig.zip sample2.sig.zip -o intersection.sig.zip
This command will
- Load
sample1.sig.zip
andsample2.sig.zip
. - Apply any specified operations.
- Retain only hashes common to both signatures.
- Use the abundance values from
sample1.sig.zip
for the common hashes. - Export the resulting intersection to
intersection.sig.zip
.
Source code in src/snipe/cli/cli_ops.py
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|
load_signatures(sig_paths, logger, allow_duplicates=False)
¶
Load SnipeSig signatures from the provided file paths.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
sig_paths
|
List[str]
|
List of file paths to load signatures from. |
required |
logger
|
Logger
|
Logger for logging messages. |
required |
allow_duplicates
|
bool
|
Flag to allow loading duplicate signature files. |
False
|
Returns:
Type | Description |
---|---|
List[SnipeSig]
|
List[SnipeSig]: List of loaded SnipeSig instances. |
Raises:
Type | Description |
---|---|
SystemExit
|
If loading a signature fails. |
Source code in src/snipe/cli/cli_ops.py
ops()
¶
Perform operations on SnipeSig signatures.
Subcommands
sum
Merge multiple signatures by summing their abundances.intersect
Compute the intersection of multiple signatures.union
Compute the union of multiple signatures.subtract
Subtract one signature from another.common
Extract hashes common to all input signatures.
Use 'snipe ops
Source code in src/snipe/cli/cli_ops.py
parse_operation_order(ctx, **kwargs)
¶
Parse the order of operations based on the command line arguments.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
ctx
|
Click context. |
required | |
kwargs
|
Command options. |
{}
|
Returns:
Type | Description |
---|---|
List[tuple]: A list of tuples containing operation names and their corresponding values. |
Source code in src/snipe/cli/cli_ops.py
subtract(ctx, sig_files, sigs_from_file, reset_abundance, trim_singletons, min_abund, max_abund, trim_below_median, output_file, name, debug, force)
¶
Subtract one signature from another.
This command removes the hashes present in the second signature from the first signature. The resulting signature will contain only the hashes that are unique to the first signature.
Example:
snipe ops subtract sample1.sig.zip sample2.sig.zip -o subtracted.sig.zip
This command will
- Load
sample1.sig.zip
andsample2.sig.zip
. - Apply any specified operations.
- Subtract the hashes of
sample2.sig.zip
fromsample1.sig.zip
. - Export the resulting signature to
subtracted.sig.zip
.
Source code in src/snipe/cli/cli_ops.py
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|
sum(ctx, sig_files, sigs_from_file, reset_abundance, trim_singletons, min_abund, max_abund, trim_below_median, output_file, name, debug, force)
¶
Merge multiple signatures by summing their abundances.
This command loads multiple signature files, applies specified operations (like resetting abundances), and then sums them to create a new signature where the abundance of each hash is the sum of its abundances across all input signatures.
Example:
snipe ops sum sample1.sig.zip sample2.sig.zip -o summed.sig.zip --reset-abundance
This command will
- Load
sample1.sig.zip
andsample2.sig.zip
. - Reset the abundance of each hash in both signatures to 1.
- Sum the signatures, resulting in
summed.sig.zip
where each hash has an abundance of 2.
Source code in src/snipe/cli/cli_ops.py
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|
union(ctx, sig_files, sigs_from_file, reset_abundance, trim_singletons, min_abund, max_abund, trim_below_median, output_file, name, debug, force)
¶
Merge multiple signatures by taking the union of their hashes.
This command combines multiple signatures, retaining all unique hashes from each. If a hash appears in multiple signatures, its abundance in the resulting signature is the sum of its abundances across all input signatures.
Example:
snipe ops union sample1.sig.zip sample2.sig.zip -o union.sig.zip
This command will
- Load
sample1.sig.zip
andsample2.sig.zip
. - Apply any specified operations.
- Combine the signatures, summing abundances for overlapping hashes.
- Export the resulting union signature to
union.sig.zip
.
Source code in src/snipe/cli/cli_ops.py
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|
validate_sig_output(ctx, param, value)
¶
Validate that the output file has a supported extension.
Supported extensions: .zip, .sig
Parameters:
Name | Type | Description | Default |
---|---|---|---|
ctx
|
Click context. |
required | |
param
|
Click parameter. |
required | |
value
|
str
|
The value passed to the parameter. |
required |
Returns:
Name | Type | Description |
---|---|---|
str |
str
|
The validated output file path. |
Raises:
Type | Description |
---|---|
BadParameter
|
If the file extension is not supported. |
Source code in src/snipe/cli/cli_ops.py
validate_sig_path(ctx, param, value)
¶
Validate that the provided signature file path exists.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
ctx
|
Click context. |
required | |
param
|
Click parameter. |
required | |
value
|
str
|
The value passed to the parameter. |
required |
Returns:
Name | Type | Description |
---|---|---|
str |
str
|
The validated signature file path. |
Raises:
Type | Description |
---|---|
BadParameter
|
If the file does not exist. |