Options

usage: bedshape [-h] {alias,profile} ...

Sub-commands:

alias

Manage aliases for filenames.

bedshape alias [-h] {list,add,rm} ...

Sub-commands:

list

List all available aliases.

bedshape alias list [-h]

add

Add a new alias.

bedshape alias add [-h] --reference REFERENCE --modified MODIFIED
                   [--unmodified UNMODIFIED] [--denatured DENATURED]
                   name

Positional Arguments

name

Name of alias to add

Named Arguments

--reference, -r

Absolute path to reference for this alias.

--modified, -m

Absolute path to the modified alignment for this alias.

--unmodified, --untreated, -u

Absolute path to the unmodified alignment for this alias.

--denatured, -d

Absolute path to the denatured alignment for this alias.

rm

Remove aliases.

bedshape alias rm [-h] name

Positional Arguments

name

Name of alias to remove

profile

Calculate reactivity profiles.

bedshape profile [-h] [--alias ALIAS] [--reference REFERENCE]
                 [--modified MODIFIED] [--unmodified UNMODIFIED]
                 [--denatured DENATURED] [--region REGION] [--bed BED]
                 [--min-depth MIN_DEPTH] [--min-mapq MIN_MAPQ]
                 [--max-bg MAX_BG] [--skip-plot] [--skip-shape]
                 [--outdir OUTDIR] [--keep]

Named Arguments

--alias, -a

Alias to use. This, or a combination of –reference and –modified, is required.

--reference, -r

Reference to use. A combination of this and –modified, or –alias, is required.

--modified, -m

Modified alignment to use. A combination of this and –reference, or –alias, is required.

--unmodified, -u

Unmodified alignment to use.

--denatured, -d

Denatured alignment to use.

--region, -rg

Region to use. <rname>:<start>-<stop>. Commas are allowed in <start> and <stop>. This, or –bed is required.

--bed, -b

BED file containing regions to use. This, or –region is required.

--min-depth

Minimum depth to be passed to shapemapper2’s make_reactivity_profile.py and render_figures.py.

Default: 0

--min-mapq

Minimum mapping quality to be passed to shapemapper2’s shapemapper_mutation_parser in both of its –min_mapq and –min_qual arguments.

Default: 0

--max-bg

Maximum background mutation rate to be passed to shapemapper2’s make_reactivity_profile.py andrender_figures.py. Should be a float between 0 and 1.

Default: 1

--skip-plot

If specified, will not run render_figures.py (i.e. no reactivity plot will be produced.

Default: False

--skip-shape

If specified, will not run tab_to_shape.py (i.e. no shape file will be produced.

Default: False

--outdir, -o

Directory to place output files within.

Default: “./”

--keep, -k

If specified, will not delete temp directory when done.

Default: False