dave-doty
commented
2 years ago Release notes
Plate maps
You can now print a plate map of all or some of the strands in the design that have Strand.idt.plate and Strand.idt.well specified.
For example, the following code:
import scadnano as sc
helices = [sc.Helix(max_offset=100)]
design = sc.Design(helices=helices, strands=[], grid=sc.square)
design.draw_strand(0, 0).move(10).with_name('strand 0').with_idt(plate='plate 1', well='A1')
design.draw_strand(0, 10).move(10).with_name('strand 1').with_idt(plate='plate 1', well='A2')
design.draw_strand(0, 20).move(10).with_name('strand 2').with_idt(plate='plate 1', well='B2')
design.draw_strand(0, 30).move(10).with_name('strand 3').with_idt(plate='plate 1', well='B3')
design.draw_strand(0, 40).move(10).with_name('strand 4').with_idt(plate='plate 1', well='D7')
# plate_maps = design.plate_maps_markdown(well_marker='X', strands=[design.strands[0], design.strands[3]])
plate_maps = design.plate_maps_markdown()
plate_map = plate_maps['plate 1']
print(plate_map)prints the following Markdown representation of the plate:
## plate 1
| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-----|----------|----------|----------|-----|-----|-----|----------|-----|-----|------|------|------|
| A | strand 0 | strand 1 | | | | | | | | | | |
| B | | strand 2 | strand 3 | | | | | | | | | |
| C | | | | | | | | | | | | |
| D | | | | | | | strand 4 | | | | | |
| E | | | | | | | | | | | | |
| F | | | | | | | | | | | | |
| G | | | | | | | | | | | | |
| H | | | | | | | | | | | | |One can specify only a subset of strands, and use a different entry than the strand's name:
plate_maps = design.plate_maps_markdown(well_marker='X', strands=[design.strands[0], design.strands[3]])which prints
## plate 1
| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|------|------|------|
| A | X | | | | | | | | | | | |
| B | | | X | | | | | | | | | |
| C | | | | | | | | | | | | |
| D | | | | | | | | | | | | |
| E | | | | | | | | | | | | |
| F | | | | | | | | | | | | |
| G | | | | | | | | | | | | |
| H | | | | | | | | | | | | |
If IDT fields are specified with plate and well positions, scadnano should be able to write a plate map showing strand names in the well positions.
TODO: draw a mockup figure of how this should look.