Command reference
This page lists command options and their defaults. install-* commands write
to --db-path; download-* commands write to --output-dir.
Common options
| Option | Default | Description |
|---|---|---|
SPECIES, -s, --species | command-specific | Species or genome assembly. |
VERSION, -v, --ver | def where supported | Release or version. |
-d, --db-path DIR | ~/.sjcab_peak2anno_db | Database/cache directory. |
-o, --output-dir DIR | . for download commands | Download or generated-file directory. |
-name NAME | unset | Custom installed species name. |
-n, --workers N | 2 for selector commands | Parallel independent TSS/TES output writers. |
-j, --processes N | 4 | Independent GTF workers for install/download feature commands. |
-g, --gtf-path FILE | unset | Use an existing local GTF. |
-u, --url URL | resolved URL | Override the GTF URL. |
--ucsc-source {ens,refseq} | ens | UCSC gene-table source. |
--clean-cache [DAYS] | 90 when configured | Remove old cache files after generation. |
--sizes-clean [0|1] | 1 | Create .sizes.clean files. |
-dry-run | off | Resolve URLs without downloading where supported. |
-n/--workers is intentionally separate from -j/--processes: workers apply
to the independent left/right-style TSS/TES outputs produced by the selector
commands, while processes apply to independent GTF jobs.
install
sjcab-peak2anno-db install [COMPONENT ...]
Components are genebed, feature, blacklists, and cgi. With no component,
or with def or default, all configured default components are installed.
The default overwrite behavior is off; use --overwrite to regenerate files.
install-feature and download-feature
| Option | Default |
|---|---|
--promoter-bp, -p |
2kb |
--promoter-down |
same as --promoter-bp |
--distal-bp, -D |
50kb |
--distal-down |
same as --distal-bp |
--tes-bp, -e |
2kb |
--tes-up |
same as --tes-bp |
--prefix, -P |
promoter-size label |
--include-tss-base, -B |
off |
--no-overwrite, -n |
off; existing files may be regenerated |
--processes, -j |
4 |
dedup-genebed, filter-genebed, dedup-feature, and filter-feature
| Option | Default |
|---|---|
--method, -m |
longcol5 for dedup-genebed; required for filter-genebed |
--promoter-bp, -p |
2kb |
--promoter-down |
same as --promoter-bp |
--gene-key, -K |
symbol |
--workers, -n |
2 |
--exclusive |
off; inclusive matching is used |
--output-dir, -o |
. |
dedup-feature and filter-feature accept the same selector options as their
*-bed counterparts. They retain transcript IDs using the GeneBED selection
and regenerate FeatureBEDs from only those transcripts. dedup-feature falls
back to the longest transcript; filter-feature omits genes without selector
support.
Other commands
list def: lists the default bundled GeneBED resources. Uselist genebed,list feature,list blacklists,list cgi,list chromhmm, orlist segwayto select another group; output is aligned likecolumn -tand uses asourcecolumn.path: prints a resource path;--install/-Iinstalls missing resources.install-genebed/download-genebed: generate GeneBEDs from GTF input.install-blacklists,install-cgi,install-chromhmm, andinstall-segway: install the corresponding external resource sets.
Run sjcab-peak2anno-db COMMAND -h for command-specific help.