kb_python.ref

Module Contents

Functions

sort_gtf(gtf_path, out_path) Sorts a GTF file based on its chromosome, start position, line number.
sort_fasta(fasta_path, out_path) Sorts a FASTA file based on its header.
check_chromosomes(fasta_chromosomes, gtf_chromosomes) Compares the two chromosome sets and outputs warnings if there are
create_t2g_from_fasta(fasta_path, t2g_path) Parse FASTA headers to get transcripts-to-gene mapping.
create_t2g_from_gtf(gtf_path, t2g_path, intron=False) Creates a transcript-to-gene mapping from a GTF file.
create_t2c(fasta_path, t2c_path) Creates a transcripts-to-capture list from a FASTA file.
kallisto_index(fasta_path, index_path, k=31) Runs kallisto index.
split_and_index(fasta_path, index_prefix, n=2, k=31, temp_dir=’tmp’) Split a FASTA file into n parts and index each one.
download_reference(reference, files, temp_dir=’tmp’, overwrite=False) Downloads a provided reference file from a static url.
decompress_file(path, temp_dir=’tmp’) Decompress the given path if it is a .gz file. Otherwise, return the
ref(fasta_paths, gtf_paths, cdna_path, index_path, t2g_path, n=1, k=None, temp_dir=’tmp’, overwrite=False) Generates files necessary to generate count matrices for single-cell RNA-seq.
ref_kite(feature_path, fasta_path, index_path, t2g_path, n=1, k=None, no_mismatches=False, temp_dir=’tmp’, overwrite=False) Generates files necessary for feature barcoding with the KITE workflow.
ref_lamanno(fasta_paths, gtf_paths, cdna_path, intron_path, index_path, t2g_path, cdna_t2c_path, intron_t2c_path, n=1, k=None, flank=None, temp_dir=’tmp’, overwrite=False) Generates files necessary to generate RNA velocity matrices for single-cell RNA-seq.
kb_python.ref.logger
kb_python.ref.sort_gtf(gtf_path, out_path)

Sorts a GTF file based on its chromosome, start position, line number.

Parameters:gtf_path (str) – path to GTF file
Returns:path to sorted GTF file, set of chromosomes in GTF file
Return type:tuple
kb_python.ref.sort_fasta(fasta_path, out_path)

Sorts a FASTA file based on its header.

Parameters:fasta_path (str) – path to FASTA file
Returns:path to sorted FASTA file, set of chromosomes in FASTA file
Return type:tuple
kb_python.ref.check_chromosomes(fasta_chromosomes, gtf_chromosomes)

Compares the two chromosome sets and outputs warnings if there are unique chromosomes in either set.

Parameters:
  • fasta_chromosomes (set) – set of chromosomes found in FASTA
  • gtf_chromosomes (set) – set of chromosomes found in GTF
Returns:

intersection of the two sets
Return type:

set
kb_python.ref.create_t2g_from_fasta(fasta_path, t2g_path)

Parse FASTA headers to get transcripts-to-gene mapping.

Parameters:
  • fasta_path (str) – path to FASTA file
  • t2g_path (str) – path to output transcript-to-gene mapping
Returns:

dictionary containing path to generated t2g mapping
Return type:

dict
kb_python.ref.create_t2g_from_gtf(gtf_path, t2g_path, intron=False)

Creates a transcript-to-gene mapping from a GTF file.

GTF entries that have transcript as its feature are parsed for the transcript_id, gene_id and gene_name.

Parameters:
  • gtf_path (str) – path to GTF file
  • t2g_path (str) – path to output transcript-to-gene mapping
  • intron (bool, optional) – whether or not to include intron transcript ids (with the -I prefix), defaults to False
Returns:

dictionary containing path to generated t2g mapping
Return type:

dict
kb_python.ref.create_t2c(fasta_path, t2c_path)

Creates a transcripts-to-capture list from a FASTA file.

Parameters:
  • fasta_path (str) – path to FASTA file
  • t2c_path (str) – path to output transcripts-to-capture list
Returns:

dictionary containing path to generated t2c list
Return type:

dict
kb_python.ref.kallisto_index(fasta_path, index_path, k=31)

Runs kallisto index.

Parameters:
  • fasta_path (str) – path to FASTA file
  • index_path (str) – path to output kallisto index
  • k (int, optional) – k-mer length, defaults to 31
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.ref.split_and_index(fasta_path, index_prefix, n=2, k=31, temp_dir='tmp')

Split a FASTA file into n parts and index each one.

Parameters:
  • fasta_path (str) – path to FASTA file
  • index_prefix (str) – prefix of output kallisto indices
  • n (int, optional) – split the index into n files, defaults to 2
  • k (int, optional) – k-mer length, defaults to 31
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
Returns:

dictionary containing path to generated index
Return type:

dict
kb_python.ref.download_reference(reference, files, temp_dir='tmp', overwrite=False)

Downloads a provided reference file from a static url.

The configuration for provided references is in config.py.

Parameters:
  • reference (Reference) – a Reference object, as defined in config.py
  • files (dict) – dictionary that has the command-line option as keys and the path as values. used to determine if all the required paths to download the given reference have been provided
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • overwrite (bool, optional) – overwrite an existing index file, defaults to False
Raises:

Exception – if the required options are not provided
Returns:

dictionary containing paths to generated file(s)
Return type:

dict
kb_python.ref.decompress_file(path, temp_dir='tmp')

Decompress the given path if it is a .gz file. Otherwise, return the original path.

Parameters:path (str) – path to the file
Returns:unaltered path if the file is not a .gz file, otherwise path to the uncompressed file
Return type:str
kb_python.ref.ref(fasta_paths, gtf_paths, cdna_path, index_path, t2g_path, n=1, k=None, temp_dir='tmp', overwrite=False)

Generates files necessary to generate count matrices for single-cell RNA-seq.

Parameters:
  • fasta_paths (list) – list of paths to genomic FASTA files
  • gtf_paths (list) – list of paths to GTF files
  • cdna_path (str) – path to generate the cDNA FASTA file
  • t2g_path (str) – path to output transcript-to-gene mapping
  • n (int) – split the index into n files
  • k (int, optional) – override default kmer length 31, defaults to None
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • overwrite (bool, optional) – overwrite an existing index file, defaults to False
Returns:

dictionary containing paths to generated file(s)
Return type:

dict
kb_python.ref.ref_kite(feature_path, fasta_path, index_path, t2g_path, n=1, k=None, no_mismatches=False, temp_dir='tmp', overwrite=False)

Generates files necessary for feature barcoding with the KITE workflow.

Parameters:
  • feature_path (str) – path to TSV containing barcodes and feature names
  • fasta_path (str) – path to generate fasta file containing all sequences that are 1 hamming distance from the provide barcodes (including the actual sequence)
  • t2g_path (str) – path to output transcript-to-gene mapping
  • n (int) – split the index into n files
  • k (int, optional) – override calculated optimal kmer length, defaults to None
  • no_mismatches (bool, optional) – whether to generate hamming distance 1 variants, defaults to False
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • overwrite (bool, optional) – overwrite an existing index file, defaults to False
Returns:

dictionary containing paths to generated file(s)
Return type:

dict
kb_python.ref.ref_lamanno(fasta_paths, gtf_paths, cdna_path, intron_path, index_path, t2g_path, cdna_t2c_path, intron_t2c_path, n=1, k=None, flank=None, temp_dir='tmp', overwrite=False)

Generates files necessary to generate RNA velocity matrices for single-cell RNA-seq.

Parameters:
  • fasta_paths (list) – list of paths to genomic FASTA files
  • gtf_paths (list) – list of paths to GTF files
  • cdna_path (str) – path to generate the cDNA FASTA file
  • intron_path (str) – path to generate the intron FASTA file
  • t2g_path (str) – path to output transcript-to-gene mapping
  • cdna_t2c_path (str) – path to generate the cDNA transcripts-to-capture file
  • intron_t2c_path (str) – path to generate the intron transcripts-to-capture file
  • n (int) – split the index into n files
  • k (int, optional) – override default kmer length (31), defaults to None
  • flank (int, optional) – number of bases to include from the flanking regions when generating the intron FASTA, defaults to None, which sets the flanking region to be k - 1 bases.
  • temp_dir (str, optional) – path to temporary directory, defaults to tmp
  • overwrite (bool, optional) – overwrite an existing index file, defaults to False
Returns:

dictionary containing paths to generated file(s)
Return type:

dict