show

Query a DNA/RNA sequence against a Malva Index and visualize spatial distribution (if spatial coordinates have been provided during indexing)

usage: malva show [-h] [--index-in INDEX_IN] --query QUERY --image-out IMAGE_OUT [--multichannel] [--save-npy] [--scalebar] [--render-scale RENDER_SCALE] [--render-smoothing RENDER_SMOOTHING]

Named Arguments

--index-in

Valid directory where the malva index (and metadata) is located.

The directory must contain the file malva_index.h5. Otherwise, an exception will be thrown.

--query

FASTA file containing the query sequences.

--image-out

Directory where the image results will be saved into.

One image in TIFF format will be created per query sequence, under the directory specified in Filenames are generated from the FASTA header per sequence.

--multichannel

Will save a single image where channels are the individual query sequences (named)

Default: False

--save-npy

Additionally to TIFF images, the coordinates of spots and the amount of

signal is stored as a N_SPOTS-by-(X, Y, INTENSITY) pickled numpy array.

Default: False

--scalebar

A scalebar is automatically displayed.

The size is by default 25/100 of the image width.

Default: False

--render-scale

What is the scale, respect to the original index spatial dimensions per unit, used for rendering.

Default: 1

--render-smoothing

Sigma value for gaussian smoothing of pseudoimages (for rendering purposes)

Default: 1.5