omicverse.alignment.ref

omicverse.alignment.ref(index_path, t2g_path, fasta_paths=None, gtf_paths=None, cdna_path=None, workflow='standard', d=None, k=None, threads=8, overwrite=False, temp_dir='tmp', make_unique=False, include=None, exclude=None, dlist=None, dlist_overhang=1, aa=False, max_ec_size=None, nucleus=False, f2=None, c1=None, c2=None, flank=None, feature=None, no_mismatches=False, distinguish=False, **kwargs)[source]

Build kallisto index and transcript-to-gene mapping files via kb ref.

Parameters:

  • index_path (str) – Output path for generated kallisto index file.

  • t2g_path (str) – Output path for transcript-to-gene mapping table.

  • fasta_paths (str|list[str]|None, optional) – Input transcript/genome FASTA file(s) used to build the reference.

  • gtf_paths (str|list[str]|None, optional) – Input GTF annotation file(s) aligned with fasta_paths.

  • cdna_path (str|None, optional) – Optional cDNA FASTA output path required by some workflows.

  • workflow (str, optional) – kb workflow mode (for example standard, nucleus, lamanno, kite).

  • d (str|None, optional) – Prebuilt reference bundle shortcut (kb ref -d).

  • k (int|None, optional) – K-mer length for kallisto index construction.

  • threads (int, optional) – Number of threads for kb execution.

  • overwrite (bool, optional) – Whether to overwrite existing output files.

  • temp_dir (str, optional) – Temporary directory root for kb intermediate files.

  • make_unique (bool, optional) – Make feature IDs unique when duplicate names are detected.

  • include (list[dict[str,str]]|None, optional) – Attribute filters to include specific transcript/gene records.

  • exclude (list[dict[str,str]]|None, optional) – Attribute filters to exclude records.

  • dlist (str|None, optional) – Decoy list file for selective-alignment workflows.

  • dlist_overhang (int, optional) – Overhang length used when generating decoy targets.

  • aa (bool, optional) – Enable amino-acid mode where supported by kb workflow.

  • max_ec_size (int|None, optional) – Maximum equivalence-class size for index generation.

  • nucleus (bool, optional) – Shortcut to switch from standard to nucleus workflow.

  • f2 (str|None, optional) – Secondary FASTA output/input path for nucleus/velocity workflows.

  • c1 (str|None, optional) – Spliced transcript capture output path for velocity workflows.

  • c2 (str|None, optional) – Intronic transcript capture output path for velocity workflows.

  • flank (int|None, optional) – Flanking sequence length for selected workflows.

  • feature (str|None, optional) – Feature FASTA path used by kite workflow.

  • no_mismatches (bool, optional) – Disable mismatches for feature barcoding workflows.

  • distinguish (bool, optional) – Distinguish overlapping features when supported by kb.

  • **kwargs – Additional kb flags passed through (for example kallisto, bustools, opt_off).

Returns:

Metadata dictionary with workflow info and generated output paths.

Return type:

dict[str,str]