kb_python.count

Module Contents

Functions

kallisto_pseudo(batch_path, index_path, out_dir, threads=8) Runs kallisto pseudo.
kallisto_bus(fastqs, index_path, technology, out_dir, threads=8, n=False, k=False) Runs kallisto bus.
kallisto_bus_split(fastqs, index_paths, technology, out_dir, temp_dir=’tmp’, threads=8, memory=‘4G’) Runs kallisto bus with split indices.
bustools_mash(out_dirs, out_dir) Runs bustools mash. Additionally, combines the `run_info.json`s into
bustools_merge(bus_path, out_dir, ecmap_path, txnames_path) Runs bustools merge.
bustools_project(bus_path, out_path, map_path, ecmap_path, txnames_path) Runs bustools project.
bustools_sort(bus_path, out_path, temp_dir=’tmp’, threads=8, memory=‘4G’, flags=False) Runs bustools sort.
bustools_inspect(bus_path, out_path, whitelist_path, ecmap_path) Runs bustools inspect.
bustools_correct(bus_path, out_path, whitelist_path) Runs bustools correct.
bustools_count(bus_path, out_prefix, t2g_path, ecmap_path, txnames_path, tcc=False, mm=False) Runs bustools count.
bustools_capture(bus_path, out_path, capture_path, ecmap_path, txnames_path, capture_type=’transcripts’) Runs bustools capture.
bustools_whitelist(bus_path, out_path) Runs bustools whitelist.
write_smartseq_batch(pairs_1, pairs_2, out_path) Write a 3-column TSV specifying batch information for Smart-seq reads.
matrix_to_cellranger(matrix_path, barcodes_path, genes_path, t2g_path, out_dir) Convert bustools count matrix to cellranger-format matrix.
convert_matrix(counts_dir, matrix_path, barcodes_path, genes_path=None, ec_path=None, t2g_path=None, txnames_path=None, name=’gene’, loom=False, h5ad=False, tcc=False, threads=8) Convert a gene count or TCC matrix to loom or h5ad.
convert_matrices(counts_dir, matrix_paths, barcodes_paths, genes_paths=None, ec_paths=None, t2g_path=None, txnames_path=None, name=’gene’, loom=False, h5ad=False, nucleus=False, tcc=False, threads=8) Convert a gene count or TCC matrix to loom or h5ad.
filter_with_bustools(bus_path, ecmap_path, txnames_path, t2g_path, whitelist_path, filtered_bus_path, counts_prefix=None, tcc=False, mm=False, kite=False, temp_dir=’tmp’, threads=8, memory=‘4G’, count=True, loom=False, h5ad=False, cellranger=False) Generate filtered count matrices with bustools.
stream_fastqs(fastqs, temp_dir=’tmp’) Given a list of fastqs (that may be local or remote paths), stream any
copy_or_create_whitelist(technology, bus_path, out_dir) Copies a pre-packaged whitelist if it is provided. Otherwise, runs
count(index_paths, t2g_path, technology, out_dir, fastqs, whitelist_path=None, tcc=False, mm=False, filter=None, kite=False, FB=False, temp_dir=’tmp’, threads=8, memory=‘4G’, overwrite=False, loom=False, h5ad=False, cellranger=False, inspect=True, report=False) Generates count matrices for single-cell RNA seq.
count_smartseq(index_paths, t2g_path, technology, out_dir, fastqs, temp_dir=’tmp’, threads=8, memory=‘4G’, overwrite=False, loom=False, h5ad=False) Generates gene or isoform count matrices from Smart-seq reads.
count_velocity(index_paths, t2g_path, cdna_t2c_path, intron_t2c_path, technology, out_dir, fastqs, whitelist_path=None, tcc=False, mm=False, filter=None, temp_dir=’tmp’, threads=8, memory=‘4G’, overwrite=False, loom=False, h5ad=False, cellranger=False, report=False, inspect=True, nucleus=False) Generates RNA velocity matrices for single-cell RNA seq.
kb_python.count.logger
kb_python.count.INSPECT_PARSER
kb_python.count.kallisto_pseudo(batch_path, index_path, out_dir, threads=8)

Runs kallisto pseudo.

Parameters:
  • batch_path (str) – path to textfile containing batch definitions
  • index_path (str) – path to kallisto index
  • out_dir (str) – path to output directory
  • threads (int, optional) – number of threads to use, defaults to 8
Returns:

dictionary containing output files
Return type:

dict
kb_python.count.kallisto_bus(fastqs, index_path, technology, out_dir, threads=8, n=False, k=False)

Runs kallisto bus.

Parameters:
  • fastqs (list) – list of FASTQ file paths
  • index_path (str) – path to kallisto index
  • technology (str) – single-cell technology used
  • out_dir (str) – path to output directory
  • threads (int, optional) – number of threads to use, defaults to 8
  • n (bool, optional) – include number of read in flag column (used when splitting indices), defaults to False
  • k (bool, optional) – alignment is done per k-mer (used when splitting indices), defaults to False
Returns:

dictionary containing paths to generated files
Return type:

dict
kb_python.count.kallisto_bus_split(fastqs, index_paths, technology, out_dir, temp_dir='tmp', threads=8, memory='4G')

Runs kallisto bus with split indices.

Parameters:
  • fastqs (list) – list of FASTQ file paths or URLs
  • index_paths (list) – paths to kallisto indices
  • technology (str) – single-cell technology used
  • out_dir (str) – path to output directory
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • threads (int, optional) – number of threads to use, defaults to 8
  • memory (str, optional) – amount of memory to use, defaults to 4G
Returns:

dictionary containing paths to generated files
Return type:

dict
kb_python.count.bustools_mash(out_dirs, out_dir)

Runs bustools mash. Additionally, combines the `run_info.json`s into one.

Parameters:
  • out_dirs (list) – list of kallisto bus output directories. Note that BUS files should be sorted by flag
  • out_dir (str) – path to output directory
Returns:

dictionary containing paths to generated files
Return type:

dict
kb_python.count.bustools_merge(bus_path, out_dir, ecmap_path, txnames_path)

Runs bustools merge.

Parameters:
  • bus_path (str) – path to BUS file to merge
  • out_dir (str) – path to output directory, where the merged BUS file and ecmap will be written
  • ecmap_path (str) – path to ecmap file, as generated by kallisto bus
  • txnames_path (str) – path to transcript names file, as generated by kallisto bus
Returns:

dictionary containing path to generated BUS file and merged ecmap
Return type:

dict
kb_python.count.bustools_project(bus_path, out_path, map_path, ecmap_path, txnames_path)

Runs bustools project.

Parameters:
  • bus_path (str) – path to BUS file to sort
  • out_dir (str) – path to output directory
  • map_path (str) – path to file containing source-to-destination mapping
  • ecmap_path (str) – path to ecmap file, as generated by kallisto bus
  • txnames_path (str) – path to transcript names file, as generated by kallisto bus
Returns:

dictionary containing path to generated BUS file
Return type:

dict
kb_python.count.bustools_sort(bus_path, out_path, temp_dir='tmp', threads=8, memory='4G', flags=False)

Runs bustools sort.

Parameters:
  • bus_path (str) – path to BUS file to sort
  • out_dir (str) – path to output BUS path
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • threads (int, optional) – number of threads to use, defaults to 8
  • memory (str, optional) – amount of memory to use, defaults to 4G
  • flags (bool, optional) – whether to supply the –flags argument to sort, defaults to False
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.count.bustools_inspect(bus_path, out_path, whitelist_path, ecmap_path)

Runs bustools inspect.

Parameters:
  • bus_path (str) – path to BUS file to sort
  • out_path (str) – path to output inspect JSON file
  • whitelist_path (str) – path to whitelist
  • ecmap_path (str) – path to ecmap file, as generated by kallisto bus
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.count.bustools_correct(bus_path, out_path, whitelist_path)

Runs bustools correct.

Parameters:
  • bus_path (str) – path to BUS file to correct
  • out_path (str) – path to output corrected BUS file
  • whitelist_path (str) – path to whitelist
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.count.bustools_count(bus_path, out_prefix, t2g_path, ecmap_path, txnames_path, tcc=False, mm=False)

Runs bustools count.

Parameters:
  • bus_path (str) – path to BUS file to correct
  • out_prefix (str) – prefix of the output files to generate
  • t2g_path (str) – path to output transcript-to-gene mapping
  • ecmap_path (str) – path to ecmap file, as generated by kallisto bus
  • txnames_path (str) – path to transcript names file, as generated by kallisto bus
  • tcc (bool, optional) – whether to generate a TCC matrix instead of a gene count matrix, defaults to False
  • mm (bool, optional) – whether to include BUS records that pseudoalign to multiple genes, defaults to False
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.count.bustools_capture(bus_path, out_path, capture_path, ecmap_path, txnames_path, capture_type='transcripts')

Runs bustools capture.

Parameters:
  • bus_path (str) – path to BUS file to capture
  • out_path (str) – path to BUS file to generate
  • capture_path (str) – path transcripts-to-capture list
  • ecmap_path (str) – path to ecmap file, as generated by kallisto bus
  • txnames_path (str) – path to transcript names file, as generated by kallisto bus
  • capture_type (str) – the type of information in the capture list. can be one of transcripts, umis, barcode.
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.count.bustools_whitelist(bus_path, out_path)

Runs bustools whitelist.

Parameters:
  • bus_path (str) – path to BUS file generate the whitelist from
  • out_path (str) – path to output whitelist
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.count.write_smartseq_batch(pairs_1, pairs_2, out_path)

Write a 3-column TSV specifying batch information for Smart-seq reads. This file is required to use kallisto pseudo on multiple samples (= cells).

Parameters:
  • pairs_1 (list) – list of paths to FASTQs corresponding to pair 1
  • pairs_2 (list) – list of paths to FASTQS corresponding to pair 2
  • out_path (str) – path to batch file to output
Returns:

dictionary of written batch file
Return type:

dict
kb_python.count.matrix_to_cellranger(matrix_path, barcodes_path, genes_path, t2g_path, out_dir)

Convert bustools count matrix to cellranger-format matrix.

Parameters:
  • matrix_path (str) – path to matrix
  • barcodes_path (str) – list of paths to barcodes.txt
  • genes_path (str) – path to genes.txt
  • t2g_path (str) – path to transcript-to-gene mapping
  • out_dir (str) – path to output matrix
Returns:

dictionary of matrix files
Return type:

dict
kb_python.count.convert_matrix(counts_dir, matrix_path, barcodes_path, genes_path=None, ec_path=None, t2g_path=None, txnames_path=None, name='gene', loom=False, h5ad=False, tcc=False, threads=8)

Convert a gene count or TCC matrix to loom or h5ad.

Parameters:
  • counts_dir (str) – path to counts directory
  • matrix_path (str) – path to matrix
  • barcodes_path (str) – list of paths to barcodes.txt
  • genes_path (str, optional) – path to genes.txt, defaults to None
  • ec_path (str, optional) – path to ec.txt, defaults to None
  • 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
  • txnames_path (str, optional) – path to transcripts.txt, defaults to None
  • name (str, optional) – name of the columns, defaults to “gene”
  • loom (bool, optional) – whether to generate loom file, defaults to False
  • h5ad (bool, optional) – whether to generate h5ad file, defaults to False
  • tcc (bool, optional) – whether the matrix is a TCC matrix, defaults to False
  • threads (int, optional) – number of threads to use, defaults to 8
Returns:

dictionary of generated files
Return type:

dict
kb_python.count.convert_matrices(counts_dir, matrix_paths, barcodes_paths, genes_paths=None, ec_paths=None, t2g_path=None, txnames_path=None, name='gene', loom=False, h5ad=False, nucleus=False, tcc=False, threads=8)

Convert a gene count or TCC matrix to loom or h5ad.

Parameters:
  • counts_dir (str) – path to counts directory
  • matrix_paths (list) – list of paths to matrices
  • barcodes_paths (list) – list of paths to barcodes.txt
  • genes_paths (list, optional) – list of paths to genes.txt, defaults to None
  • ec_paths (list, optional) – list of path to ec.txt, defaults to None
  • 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
  • txnames_path (str, optional) – list of paths to transcripts.txt, defaults to None
  • name (str, optional) – name of the columns, defaults to “gene”
  • loom (bool, optional) – whether to generate loom file, defaults to False
  • h5ad (bool, optional) – whether to generate h5ad file, defaults to False
  • nucleus (bool, optional) – whether the matrices contain single nucleus counts, defaults to False
  • tcc (bool, optional) – whether the matrix is a TCC matrix, defaults to False
  • threads (int, optional) – number of threads to use, defaults to 8
Returns:

dictionary of generated files
Return type:

dict
kb_python.count.filter_with_bustools(bus_path, ecmap_path, txnames_path, t2g_path, whitelist_path, filtered_bus_path, counts_prefix=None, tcc=False, mm=False, kite=False, temp_dir='tmp', threads=8, memory='4G', count=True, loom=False, h5ad=False, cellranger=False)

Generate filtered count matrices with bustools.

Parameters:
  • bus_path (str) – path to sorted, corrected, sorted BUS file
  • ecmap_path (str) – path to matrix ec file
  • txnames_path (str) – path to list of transcripts
  • t2g_path (str) – path to transcript-to-gene mapping
  • whitelist_path (str) – path to filter whitelist to generate
  • filtered_bus_path (str) – path to filtered BUS file to generate
  • counts_prefix (str, optional) – prefix of count matrix, defaults to None
  • tcc (bool, optional) – whether to generate a TCC matrix instead of a gene count matrix, defaults to False
  • mm (bool, optional) – whether to include BUS records that pseudoalign to multiple genes, defaults to False
  • kite (bool, optional) – Whether this is a KITE workflow
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • threads (int, optional) – number of threads to use, defaults to 8
  • memory (str, optional) – amount of memory to use, defaults to 4G
  • loom (bool, optional) – whether to convert the final count matrix into a loom file, defaults to False
  • h5ad (bool, optional) – whether to convert the final count matrix into a h5ad file, defaults to False
  • cellranger (bool, optional) – whether to convert the final count matrix into a cellranger-compatible matrix, defaults to False
Returns:

dictionary of generated files
Return type:

dict
kb_python.count.stream_fastqs(fastqs, temp_dir='tmp')

Given a list of fastqs (that may be local or remote paths), stream any remote files. Internally, calls utils.

Parameters:
  • fastqs (list) – list of (remote or local) fastq paths
  • temp_dir (str) – temporary directory
Returns:

all remote paths substituted with a local path
Return type:

list
kb_python.count.copy_or_create_whitelist(technology, bus_path, out_dir)

Copies a pre-packaged whitelist if it is provided. Otherwise, runs bustools whitelist to generate a whitelist.

Parameters:
  • technology (str) – single-cell technology used
  • bus_path (str) – path to BUS file generate the whitelist from
  • out_dir (str) – path to output directory
Returns:

path to copied or generated whitelist
Return type:

str
kb_python.count.count(index_paths, t2g_path, technology, out_dir, fastqs, whitelist_path=None, tcc=False, mm=False, filter=None, kite=False, FB=False, temp_dir='tmp', threads=8, memory='4G', overwrite=False, loom=False, h5ad=False, cellranger=False, inspect=True, report=False)

Generates count matrices for single-cell RNA seq.

Parameters:
  • index_paths (list) – paths to kallisto indices
  • t2g_path (str) – path to transcript-to-gene mapping
  • technology (str) – single-cell technology used
  • out_dir (str) – path to output directory
  • fastqs (list) – list of FASTQ file paths
  • whitelist_path (str, optional) – path to whitelist, defaults to None
  • tcc (bool, optional) – whether to generate a TCC matrix instead of a gene count matrix, defaults to False
  • mm (bool, optional) – whether to include BUS records that pseudoalign to multiple genes, defaults to False
  • filter (str, optional) – filter to use to generate a filtered count matrix, defaults to None
  • kite (bool, optional) – Whether this is a KITE workflow
  • FB (bool, optional) – whether 10x Genomics Feature Barcoding technology was used, defaults to False
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • threads (int, optional) – number of threads to use, defaults to 8
  • memory (str, optional) – amount of memory to use, defaults to 4G
  • overwrite (bool, optional) – overwrite an existing index file, defaults to False
  • loom (bool, optional) – whether to convert the final count matrix into a loom file, defaults to False
  • h5ad (bool, optional) – whether to convert the final count matrix into a h5ad file, defaults to False
  • cellranger (bool, optional) – whether to convert the final count matrix into a cellranger-compatible matrix, defaults to False
  • inspect (bool, optional) – whether or not to inspect the output BUS file and generate the inspect.json
  • report (bool, optional) – generate an HTMl report, defaults to False
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.count.count_smartseq(index_paths, t2g_path, technology, out_dir, fastqs, temp_dir='tmp', threads=8, memory='4G', overwrite=False, loom=False, h5ad=False)

Generates gene or isoform count matrices from Smart-seq reads.

kb_python.count.count_velocity(index_paths, t2g_path, cdna_t2c_path, intron_t2c_path, technology, out_dir, fastqs, whitelist_path=None, tcc=False, mm=False, filter=None, temp_dir='tmp', threads=8, memory='4G', overwrite=False, loom=False, h5ad=False, cellranger=False, report=False, inspect=True, nucleus=False)

Generates RNA velocity matrices for single-cell RNA seq.

Parameters:
  • index_paths (list) – paths to kallisto indices
  • t2g_path (str) – path to transcript-to-gene mapping
  • cdna_t2c_path (str) – path to cDNA transcripts-to-capture file
  • intron_t2c_path (str) – path to intron transcripts-to-capture file
  • technology (str) – single-cell technology used
  • out_dir (str) – path to output directory
  • fastqs (list) – list of FASTQ file paths
  • whitelist_path (str, optional) – path to whitelist, defaults to None
  • tcc (bool, optional) – whether to generate a TCC matrix instead of a gene count matrix, defaults to False
  • mm (bool, optional) – whether to include BUS records that pseudoalign to multiple genes, defaults to False
  • filter (str, optional) – filter to use to generate a filtered count matrix, defaults to None
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • threads (int, optional) – number of threads to use, defaults to 8
  • memory (str, optional) – amount of memory to use, defaults to 4G
  • overwrite (bool, optional) – overwrite an existing index file, defaults to False
  • loom (bool, optional) – whether to convert the final count matrix into a loom file, defaults to False
  • h5ad (bool, optional) – whether to convert the final count matrix into a h5ad file, defaults to False
  • cellranger (bool, optional) – whether to convert the final count matrix into a cellranger-compatible matrix, defaults to False
  • report (bool, optional) – generate HTML reports, defaults to False
  • inspect (bool, optional) – whether or not to inspect the output BUS file and generate the inspect.json
  • nucleus (bool, optional) – whether this is a single-nucleus experiment. if True, the spliced and unspliced count matrices will be summed, defaults to False
Returns:

dictionary containing path to generated index
Return type:

dict