KAPTIVE.PY(1)

💖 KAPTIVE.PY 💖

okay bestie, so this is the manual page for kaptive.py, living in section 1 of the Unix manuals (User Commands, obvs), and it's literally here to hand you the tea on K and O types for Klebsiella genome assemblies. no cap. 🦋

✨ NAME ✨

kaptive.py — obtain information about K and O types for Klebsiella genome assemblies

🌸 SYNOPSIS 🌸

kaptive.py [-h] [--version] -a ASSEMBLY [ASSEMBLY ...] -k K_REFS [-g
ALLELIC_TYPING] [-o OUT] [-v] [-t THREADS] [--no_seq_out] [--no_table]
[--no_json] [--start_end_margin START_END_MARGIN] [--min_gene_cov
MIN_GENE_COV] [--min_gene_id MIN_GENE_ID] [--low_gene_id LOW_GENE_ID]
[--min_assembly_piece MIN_ASSEMBLY_PIECE] [--gap_fill_size
GAP_FILL_SIZE] [--locus_label LOCUS_LABEL]

like, that's the whole vibe in one block, periodt.

👑 OPTIONS 👑

optional arguments:

• -h, --help — show this help message and exit. your lil emergency exit when you're lost 💅
• --version — Show Kaptive's version number and exit
• -a ASSEMBLY [ASSEMBLY ...], --assembly ASSEMBLY [ASSEMBLY ...] — FASTA file(s) for assemblies (default: None). yes bestie, plural, you can hand it a whole lil squad of files 🎀
• -k K_REFS, --k_refs K_REFS — GenBank file with reference loci (default: None)
• -g ALLELIC_TYPING, --allelic_typing ALLELIC_TYPING — SRST2-formatted FASTA file of allelic typing genes to include in results (default: None)
• -o OUT, --out OUT — Output directory/prefix (default: ./kaptive_results)
• -v, --verbose — Display detailed information about each assembly in stdout (default: False). the way it tells you everything?? obsessed 🫶
• -t THREADS, --threads THREADS — The number of threads to use for the BLAST searches (default: 4)
• --no_seq_out — Suppress output files of sequences matching locus (default: False)
• --no_table — Suppress output of tab-delimited table (default: False)
• --no_json — Suppress output of JSON file (default: False)
• --start_end_margin START_END_MARGIN — Missing bases at the ends of locus allowed in a perfect match. (default: 10)
• --min_gene_cov MIN_GENE_COV — minimum required % coverage for genes (default: 90.0)
• --min_gene_id MIN_GENE_ID — minimum required % identity for genes (default: 80.0)
• --low_gene_id LOW_GENE_ID — genes with a % identity below this value will be flagged as low identity (default: 95.0). lowkey a lil warning label for your genes, iykyk 💀
• --min_assembly_piece MIN_ASSEMBLY_PIECE — minimum locus matching assembly piece to return (default: 100)
• --gap_fill_size GAP_FILL_SIZE — when separate parts of the assembly are found within this distance, they will be merged (default: 100). it's giving matchmaker energy fr fr 💖
• --locus_label LOCUS_LABEL — In the Genbank file, the source feature must have a note identifying the locus name, starting with this label followed by a colon (e.g. /note="K locus: K1") (default: automatically determined). so like if your note says /note="K locus: K1" you're golden ✨

🧚 AUTHOR 🧚

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

ok that's the whole thing, no notes, ate and left no crumbs 👑

and a lil sign-off bestie: this is all about kaptive.py version 0.6.0, dated September 2019, and it's the KAPTIVE.PY(1) manual page you just read. slay 💅🌈