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fixed errors in plate map documentation
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@dave-doty
dave-doty committed May 25, 2022
1 parent 00451a8 commit 75e4740
Showing 1 changed file with 66 additions and 42 deletions.
108 changes: 66 additions & 42 deletions scadnano/scadnano.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4044,7 +4044,58 @@ def to_table(
from IPython.display import display, Markdown
display(Markdown(maps_strs))
It uses the Python tabulate package (https://pypi.org/project/tabulate/).
Markdown format is used by default, generating a string such as this:
.. code-block:: none
plate "5 monomer synthesis"
| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-----|------|--------|--------|------|----------|-----|-----|-----|-----|------|------|------|
| A | mon0 | mon0_F | | adp0 | | | | | | | | |
| B | mon1 | mon1_Q | mon1_F | adp1 | adp_sst1 | | | | | | | |
| C | mon2 | mon2_F | mon2_Q | adp2 | adp_sst2 | | | | | | | |
| D | mon3 | mon3_Q | mon3_F | adp3 | adp_sst3 | | | | | | | |
| E | mon4 | | mon4_Q | adp4 | adp_sst4 | | | | | | | |
| F | | | | adp5 | | | | | | | | |
| G | | | | | | | | | | | | |
| H | | | | | | | | | | | | |
or, with the :meth:`PlateMap.to_table` parameter `well_marker` set to ``'*'``
(in case you don't need to see the strand names and just want to see which wells are marked):
.. code-block:: none
| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|------|------|------|
| A | * | * | | * | | | | | | | | |
| B | * | * | * | * | * | | | | | | | |
| C | * | * | * | * | * | | | | | | | |
| D | * | * | * | * | * | | | | | | | |
| E | * | | * | * | * | | | | | | | |
| F | | | | * | | | | | | | | |
| G | | | | | | | | | | | | |
| H | | | | | | | | | | | | |
If `well_marker` is not specified, then each strand must have a name. `well_marker` can also
be a function of the well; for instance, if it is the identity function ``lambda x:x``, then each
well has its own address as the entry:
.. code-block:: none
| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|------|------|------|
| A | A1 | A2 | | A4 | | | | | | | | |
| B | B1 | B2 | B3 | B4 | B5 | | | | | | | |
| C | C1 | C2 | C3 | C4 | C5 | | | | | | | |
| D | D1 | D2 | D3 | D4 | D5 | | | | | | | |
| E | E1 | | E3 | E4 | E5 | | | | | | | |
| F | | | | F4 | | | | | | | | |
| G | | | | | | | | | | | | |
| H | | | | | | | | | | | | |
This method uses the Python tabulate package (https://pypi.org/project/tabulate/).
The parameters are identical to that of the `tabulate` function and are passed along to it,
except for `tabular_data` and `headers`, which are computed from this plate map.
In particular, the parameter `tablefmt` has default value `'pipe'`,
Expand Down Expand Up @@ -5190,9 +5241,13 @@ def plate_maps(self,
strands: Optional[Iterable[Strand]] = None,
) -> List[PlateMap]:
"""
Generates plate maps from this :any:`Design` in Markdown format, for example:
Returns a list of :any:`PlateMap`'s from this :any:`Design`. Each :any:`PlateMap` can be
exported to a string, in Markdown format by default, by calling :meth:`PlateMap.to_table`,
generating a string such as this:
.. code-block::
.. code-block:: none
plate "5 monomer synthesis"
| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-----|------|--------|--------|------|----------|-----|-----|-----|-----|------|------|------|
Expand All @@ -5205,44 +5260,13 @@ def plate_maps(self,
| G | | | | | | | | | | | | |
| H | | | | | | | | | | | | |
or, with `well_marker` set to ``'*'`` (in case you don't need to see the strand names and just
want to see which wells are marked):
.. code-block::
| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|------|------|------|
| A | * | * | | * | | | | | | | | |
| B | * | * | * | * | * | | | | | | | |
| C | * | * | * | * | * | | | | | | | |
| D | * | * | * | * | * | | | | | | | |
| E | * | | * | * | * | | | | | | | |
| F | | | | * | | | | | | | | |
| G | | | | | | | | | | | | |
| H | | | | | | | | | | | | |
If `well_marker` is not specified, then each strand must have a name. `well_marker` can also
be a function of the well; for instance, if it is the identity function ``lambda x:x``, then each
well has its own address as the entry:
.. code-block::
| | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|------|------|------|
| A | A1 | A2 | | A4 | | | | | | | | |
| B | B1 | B2 | B3 | B4 | B5 | | | | | | | |
| C | C1 | C2 | C3 | C4 | C5 | | | | | | | |
| D | D1 | D2 | D3 | D4 | D5 | | | | | | | |
| E | E1 | | E3 | E4 | E5 | | | | | | | |
| F | | | | F4 | | | | | | | | |
| G | | | | | | | | | | | | |
| H | | | | | | | | | | | | |
See the documentation for :meth:`PlateMap.to_table` for more information on configuring the
returned string format.
All :any:`Strand`'s in the design that have a field :data:`Strand.idt` with :data:`Strand.idt.plate`
specified are exported. The number of strings in the returned list is equal to the number of
different plate names specified across all :any:`Strand`'s in the design.
specified are included in some returned :any:`PlateMap`. The number of :any:`PlateMap`'s in the
returned list is equal to the number of different plate names specified across all
:any:`Strand`'s in the design.
If parameter `strands` is given, then a subset of strands is included. This is useful for
specifying a mix of strands for a particular experiment, which come from a plate but does not
Expand All @@ -5254,10 +5278,10 @@ def plate_maps(self,
:param plate_type:
Type of plate: 96 or 384 well.
:param strands:
If specified, only the :any:`Strand`'s in `strands` are put in the plate map.
If specified, only the :any:`Strand`'s in `strands` are put in the :any:`PlateMap`.
:return:
dict mapping plate names to markdown strings specifying plate maps for :any:`Strand`'s
in this design with IDT plates specified
list of :any:`PlateMap`'s for :any:`Strand`'s in this design with IDT plates specified;
length of list is equal to number of unique plate names among all :any:`Strand`'s in this design
"""
if strands is None:
strands = self.strands
Expand Down

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