`kb_python.utils`¶

Module Contents¶

Classes¶

TqdmLoggingHandler

Custom logging handler so that logging does not affect progress bars.

Functions¶

`update_filename`(filename, code)	Update the provided path with the specified code.
`make_directory`(path)	Quietly make the specified directory (and any subdirectories).
`remove_directory`(path)	Quietly make the specified directory (and any subdirectories).
`run_executable`(command, stdin=None, stdout=sp.PIPE, stderr=sp.PIPE, wait=True, stream=True, quiet=False, returncode=0, alias=True, record=True)	Execute a single shell command.
`get_kallisto_version`()	Get the provided Kallisto version.
`get_bustools_version`()	Get the provided Bustools version.
`parse_technologies`(lines)	Parse a list of strings into a list of supported technologies.
`get_supported_technologies`()	Runs ‘kallisto bus –list’ to fetch a list of supported technologies.
`whitelist_provided`(technology)	Determine whether or not the whitelist for a technology is provided.
`move_file`(source, destination)	Move a file from source to destination, overwriting the file if the
`copy_whitelist`(technology, out_dir)	Copies provided whitelist for specified technology.
`copy_map`(technology, out_dir)	Copies provided feature-to-cell barcode mapping for the speified technology.
`stream_file`(url, path)	Creates a FIFO file to use for piping remote files into processes.
`read_t2g`(t2g_path)	Given a transcript-to-gene mapping path, read it into a dictionary.
`import_tcc_matrix_as_anndata`(matrix_path, barcodes_path, ec_path, txnames_path, threads=8)	Import a TCC matrix as an Anndata object.
`import_matrix_as_anndata`(matrix_path, barcodes_path, genes_path, t2g_path=None, name='gene')	Import a matrix as an Anndata object.
`overlay_anndatas`(adata_spliced, adata_unspliced)	‘Overlays’ anndata objects by taking the intersection of the obs and var
`sum_anndatas`(adata_spliced, adata_unspliced)	Sum the counts in two anndata objects by taking the intersection of

Attributes¶

`TECHNOLOGY_PARSER`
`VERSION_PARSER`
`open_as_text`
`decompress_gzip`
`compress_gzip`
`concatenate_files`
`download_file`
`get_temporary_filename`

kb_python.utils.TECHNOLOGY_PARSER¶

kb_python.utils.VERSION_PARSER¶

kb_python.utils.open_as_text¶

kb_python.utils.decompress_gzip¶

kb_python.utils.compress_gzip¶

kb_python.utils.concatenate_files¶

kb_python.utils.download_file¶

kb_python.utils.get_temporary_filename¶

exception kb_python.utils.NotImplementedException¶

Bases: Exception

Common base class for all non-exit exceptions.

exception kb_python.utils.UnmetDependencyException¶

Bases: Exception

Common base class for all non-exit exceptions.

class kb_python.utils.TqdmLoggingHandler(level=logging.NOTSET)¶

Bases: logging.Handler

Custom logging handler so that logging does not affect progress bars.

emit(self, record)¶

Do whatever it takes to actually log the specified logging record.

This version is intended to be implemented by subclasses and so raises a NotImplementedError.

kb_python.utils.update_filename(filename, code)¶

Update the provided path with the specified code.

For instance, if the path is ‘output.bus’ and code is s (for sort), this function returns output.s.bus.

Parameters

filename (str) – filename (NOT path)
code (str) – code to append to filename

Returns

path updated with provided code

Return type

str

kb_python.utils.make_directory(path)¶

Quietly make the specified directory (and any subdirectories).

This function is a wrapper around os.makedirs. It is used so that the appropriate mkdir command can be printed for dry runs.

Parameters: path (str) – path to directory to make

kb_python.utils.remove_directory(path)¶

Quietly make the specified directory (and any subdirectories).

This function is a wrapper around shutil.rmtree. It is used so that the appropriate rm command can be printed for dry runs.

Parameters: path (str) – path to directory to remove

kb_python.utils.run_executable(command, stdin=None, stdout=sp.PIPE, stderr=sp.PIPE, wait=True, stream=True, quiet=False, returncode=0, alias=True, record=True)¶

Execute a single shell command.

Parameters

command (list) – a list representing a single shell command
stdin (stream, optional) – object to pass into the stdin argument for subprocess.Popen, defaults to None
stdout (stream, optional) – object to pass into the stdout argument for subprocess.Popen, defaults to subprocess.PIPE
stderr (stream, optional) – object to pass into the stderr argument for subprocess.Popen, defaults to subprocess.PIPE
wait (bool, optional) – whether to wait until the command has finished, defaults to True
stream (bool, optional) – whether to stream the output to the command line, defaults to True
quiet (bool, optional) – whether to not display anything to the command line and not check the return code, defaults to False
returncode (int, optional) – the return code expected if the command runs as intended, defaults to 0
alias (bool, optional) – whether to use the basename of the first element of command, defaults to True
record (bool, optional) – whether to record the call statistics, defaults to True

Returns

the spawned process

Return type

subprocess.Process

kb_python.utils.get_kallisto_version()¶

Get the provided Kallisto version.

This function parses the help text by executing the included Kallisto binary.

Returns: tuple of major, minor, patch versions
Return type: tuple

kb_python.utils.get_bustools_version()¶

Get the provided Bustools version.

This function parses the help text by executing the included Bustools binary.

Returns: tuple of major, minor, patch versions
Return type: tuple

kb_python.utils.parse_technologies(lines)¶

Parse a list of strings into a list of supported technologies.

This function parses the technologies printed by running kallisto bus –list.

Parameters: lines (list) – the output of kallisto bus –list split into lines
Returns: list of technologies
Return type: list

kb_python.utils.get_supported_technologies()¶

Runs ‘kallisto bus –list’ to fetch a list of supported technologies.

Returns: list of technologies
Return type: list

kb_python.utils.whitelist_provided(technology)¶

Determine whether or not the whitelist for a technology is provided.

Parameters: technology (str) – the name of the technology
Returns: whether the whitelist is provided
Return type: bool

kb_python.utils.move_file(source, destination)¶

Move a file from source to destination, overwriting the file if the destination exists.

Parameters

source (str) – path to source file
destination (str) – path to destination

Returns

path to moved file

Return type

str

kb_python.utils.copy_whitelist(technology, out_dir)¶

Copies provided whitelist for specified technology.

Parameters

technology (str) – the name of the technology
out_dir (str) – directory to put the whitelist

Returns

path to whitelist

Return type

str

kb_python.utils.copy_map(technology, out_dir)¶

Copies provided feature-to-cell barcode mapping for the speified technology.

Parameters

technology (str) – the name of the technology
out_dir (str) – directory to put the map

Returns

path to map

Return type

str

kb_python.utils.stream_file(url, path)¶

Creates a FIFO file to use for piping remote files into processes.

This function spawns a new thread to download the remote file into a FIFO file object. FIFO file objects are only supported on unix systems.

Parameters

url (str) – url to the file
path (str) – path to place FIFO file

Raises

UnsupportedOSException – if the OS is Windows

Returns

path to FIFO file

Return type

str

kb_python.utils.read_t2g(t2g_path)¶

Given a transcript-to-gene mapping path, read it into a dictionary. The first column is always assumed to tbe the transcript IDs.

Parameters: t2g_path (str) – path to t2g
Returns: dictionary containing transcript IDs as keys and all other columns as a tuple as values
Return type: dict

kb_python.utils.import_tcc_matrix_as_anndata(matrix_path, barcodes_path, ec_path, txnames_path, threads=8)¶

Import a TCC matrix as an Anndata object.

Parameters

matrix_path (str) – path to the matrix ec file
barcodes_path (str) – path to the barcodes txt file
genes_path (str) – path to the ec txt file
txnames_path (str) – path to transcripts.txt generated by kallisto bus

Returns

a new Anndata object

Return type

anndata.Anndata

kb_python.utils.import_matrix_as_anndata(matrix_path, barcodes_path, genes_path, t2g_path=None, name='gene')¶

Import a matrix as an Anndata object.

Parameters

matrix_path (str) – path to the matrix ec file
barcodes_path (str) – path to the barcodes txt file
genes_path (str) – path to the genes txt file
t2g_path (str, optional) – path to transcript-to-gene mapping. If this is provided, the third column of the mapping is appended to the anndata var, defaults to None
name (str, optional) – name of the columns, defaults to “gene”

Returns

a new Anndata object

Return type

anndata.Anndata

kb_python.utils.overlay_anndatas(adata_spliced, adata_unspliced)¶

‘Overlays’ anndata objects by taking the intersection of the obs and var of each anndata.

Parameters

adata_spliced (anndata.Anndata) – an Anndata object
adata_unspliced (anndata.Anndata) – an Anndata object

Returns

a new Anndata object

Return type

anndata.Anndata

kb_python.utils.sum_anndatas(adata_spliced, adata_unspliced)¶

Sum the counts in two anndata objects by taking the intersection of both matrices and adding the values together.

Parameters

adata_spliced (anndata.Anndata) – an Anndata object
adata_unspliced (anndata.Anndata) – an Anndata object

Returns

a new Anndata object

Return type

anndata.Anndata

kb_python.utils¶

Module Contents¶

Classes¶

Functions¶

Attributes¶

`kb_python.utils`¶