kb_python.count
¶
Module Contents¶
Functions¶
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Runs kallisto pseudo. |
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Runs kallisto bus. |
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Runs kallisto bus with split indices. |
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Runs bustools mash. Additionally, combines the `run_info.json`s into |
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Runs bustools merge. |
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Runs bustools project. |
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Runs bustools sort. |
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Runs bustools inspect. |
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Runs bustools correct. |
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Runs bustools count. |
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Runs bustools capture. |
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Runs bustools whitelist. |
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Write a 3-column TSV specifying batch information for Smart-seq reads. |
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Convert bustools count matrix to cellranger-format matrix. |
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Convert a gene count or TCC matrix to loom or h5ad. |
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Convert a gene count or TCC matrix to loom or h5ad. |
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Generate filtered count matrices with bustools. |
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Given a list of fastqs (that may be local or remote paths), stream any |
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Copies a pre-packaged whitelist if it is provided. Otherwise, runs |
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Convert a textfile containing transcript IDs to another textfile containing |
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Generates count matrices for single-cell RNA seq. |
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Generates gene or isoform count matrices from Smart-seq reads. |
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Generates RNA velocity matrices for single-cell RNA seq. |
Attributes¶
- 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(fastq_pairs, cell_ids, 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
fastq_pairs (list) – list of pairs of FASTQs
cell_ids (list) – list of cell IDs
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.convert_transcripts_to_genes(txnames_path, t2g_path, genes_path)¶
Convert a textfile containing transcript IDs to another textfile containing gene IDs, given a transcript-to-gene mapping.
- Parameters
txnames_path (str) – path to transcripts.txt
t2g_path (str) – path to transcript-to-genes mapping
genes_path (str) – path to output genes.txt
- Returns
path to written genes.txt
- 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, fastq_pairs, cell_ids=None, 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