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Merge pull request #25 from BojarLab/dev
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add dev optional install for quarto
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@Bribak
Bribak authored May 20, 2023
2 parents 291a334 + 70d9c3d commit 14a52ad
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2 changes: 2 additions & 0 deletions _proc/setup
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Expand Up @@ -29,6 +29,8 @@ setuptools.setup(
"python-louvain"],
extras_require={'all':["torch_geometric", "pycairo", "CairoSVG",
"drawSvg~=2.0"],
'dev':["torch_geometric", "pycairo", "CairoSVG",
"drawSvg~=2.0"],
'ml':["torch_geometric"],
'draw':["pycairo", "CairoSVG", "drawSvg~=2.0"]},
)
114 changes: 42 additions & 72 deletions glycowork.egg-info/PKG-INFO
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Expand Up @@ -42,11 +42,6 @@ Description: glycowork
cite [Thomes et al.,
2021](https://academic.oup.com/glycob/advance-article/doi/10.1093/glycob/cwab067/6311240).

The inspiration for `glycowork` can be found in [Bojar et al.,
2020](https://doi.org/10.1016/j.chom.2020.10.004) and [Burkholz et al.,
2021](https://pubmed.ncbi.nlm.nih.gov/34133929/). There, you can also
find examples of possible use cases for the functions in `glycowork`.

The full documentation for `glycowork` can be found here:
https://bojarlab.github.io/glycowork/

Expand All @@ -62,6 +57,12 @@ Description: glycowork
`pip install git+https://github.com/BojarLab/glycowork.git` <br>
`import glycowork`

Note that we have optional extra installs for specialized use (even
further instructions can be found in the `Examples` tab), such as: <br>
*deep learning* <br> `pip install glycowork[ml]` <br> *drawing glycan
images with GlycoDraw* <br> `pip install glycowork[draw]` <br>
*everything* <br> `pip install glycowork[all]` <br>

## Data & Models

`Glycowork` currently contains the following main datasets that are
Expand Down Expand Up @@ -104,8 +105,8 @@ Description: glycowork
models, including train-test-split, getting glycan representations,
etc.
- **`motif`**
- contains functions for processing glycan sequences, identifying
motifs and features, and analyzing them
- contains functions for processing & drawing glycan sequences,
identifying motifs and features, and analyzing them
- **`network`**
- contains functions for constructing and analyzing glycan networks
(e.g., biosynthetic networks)
Expand All @@ -126,6 +127,14 @@ Description: glycowork
properties
- constructing and analyzing biosynthetic networks

``` python
#drawing publication-quality glycan figures
from glycowork.motif.draw import GlycoDraw
GlycoDraw("Neu5Ac(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-2)Man(a1-3)[Neu5Gc(a2-6)Gal(b1-4)GlcNAc(b1-2)Man(a1-6)][GlcNAc(b1-4)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc")
```

![](index_files/figure-commonmark/cell-3-output-1.svg)

``` python
#get motifs, graph features, and sequence features of a set of glycan sequences to train models or analyze glycan properties
glycans = ['Man(a1-3)[Man(a1-6)][Xyl(b1-2)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-3)]GlcNAc',
Expand Down Expand Up @@ -263,6 +272,7 @@ Description: glycowork
<th>LPS_core</th>
<th>Nglycan_complex</th>
<th>Nglycan_complex2</th>
<th>Oglycan_core1</th>
<th>Oglycan_core2</th>
<th>Oglycan_core3</th>
<th>Oglycan_core4</th>
Expand Down Expand Up @@ -338,40 +348,29 @@ Description: glycowork
<th>entropyStation</th>
<th>N</th>
<th>dens</th>
<th>Fuc</th>
<th>GalNAc</th>
<th>GlcN</th>
<th>GlcN1P</th>
<th>Man</th>
<th>Fuc</th>
<th>GlcN4P</th>
<th>GlcNAc</th>
<th>GlcNAcA</th>
<th>Kdo</th>
<th>Man</th>
<th>Xyl</th>
<th>a1-2</th>
<th>a1-3</th>
<th>a1-4</th>
<th>a1-6</th>
<th>a2-4</th>
<th>a2-5</th>
<th>a2-6</th>
<th>b1-2</th>
<th>b1-4</th>
<th>b1-6</th>
<th>b1-7</th>
<th>Fuc(a1-3)GlcNAc</th>
<th>GalNAc</th>
<th>GlcNAc</th>
<th>GlcN1P</th>
<th>Kdo(a2-6)GlcN4P</th>
<th>GlcN4P(b1-6)GlcN1P</th>
<th>GlcNAcA(a1-4)Kdo</th>
<th>Xyl(b1-2)Man</th>
<th>GlcNAc(b1-4)GlcNAc</th>
<th>GalNAc(a1-4)GlcNAcA</th>
<th>GlcN(b1-7)Kdo</th>
<th>Fuc(a1-3)GlcNAc</th>
<th>Kdo(a2-5)Kdo</th>
<th>Man(b1-4)GlcNAc</th>
<th>Kdo(a2-4)Kdo</th>
<th>Man(a1-6)Man</th>
<th>GlcN(b1-7)Kdo</th>
<th>GlcNAcA(a1-4)Kdo</th>
<th>GlcN4P(b1-6)GlcN1P</th>
<th>Kdo(a2-6)GlcN4P</th>
<th>Xyl(b1-2)Man</th>
<th>GlcNAc(b1-4)GlcNAc</th>
<th>Man(a1-3)Man</th>
<th>Kdo(a2-5)Kdo</th>
<th>Man(a1-2)Man</th>
</tr>
</thead>
Expand Down Expand Up @@ -531,6 +530,7 @@ Description: glycowork
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>8.0</td>
<td>1.0</td>
<td>4.0</td>
Expand Down Expand Up @@ -577,41 +577,30 @@ Description: glycowork
<td>-2.075921</td>
<td>13.0</td>
<td>12.0</td>
<td>1</td>
<td>0</td>
<td>2</td>
<td>3</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>3</td>
<td>1</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>1</td>
<td>0</td>
<td>0</td>
</tr>
<tr>
<th>Man(a1-2)Man(a1-2)Man(a1-3)[Man(a1-3)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc</th>
Expand Down Expand Up @@ -768,6 +757,7 @@ Description: glycowork
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>10.0</td>
<td>1.0</td>
<td>3.0</td>
Expand Down Expand Up @@ -814,20 +804,10 @@ Description: glycowork
<td>-2.658737</td>
<td>15.0</td>
<td>14.0</td>
<td>0</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>6</td>
<td>0</td>
<td>2</td>
<td>2</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>0</td>
Expand All @@ -837,17 +817,16 @@ Description: glycowork
<td>0</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>1</td>
<td>0</td>
<td>1</td>
</tr>
<tr>
Expand Down Expand Up @@ -1005,6 +984,7 @@ Description: glycowork
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>10.0</td>
<td>2.0</td>
<td>4.0</td>
Expand Down Expand Up @@ -1051,40 +1031,29 @@ Description: glycowork
<td>-2.688625</td>
<td>15.0</td>
<td>14.0</td>
<td>0</td>
<td>1</td>
<td>4</td>
<td>1</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>1</td>
<td>3</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>1</td>
<td>1</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>1</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>0</td>
</tr>
</tbody>
Expand Down Expand Up @@ -1144,5 +1113,6 @@ Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: all
Provides-Extra: dev
Provides-Extra: ml
Provides-Extra: draw
6 changes: 6 additions & 0 deletions glycowork.egg-info/requires.txt
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Expand Up @@ -20,6 +20,12 @@ pycairo
CairoSVG
drawSvg~=2.0

[dev]
torch_geometric
pycairo
CairoSVG
drawSvg~=2.0

[draw]
pycairo
CairoSVG
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2 changes: 2 additions & 0 deletions setup.py
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Expand Up @@ -29,6 +29,8 @@
"python-louvain"],
extras_require={'all':["torch_geometric", "pycairo", "CairoSVG",
"drawSvg~=2.0"],
'dev':["torch_geometric", "pycairo", "CairoSVG",
"drawSvg~=2.0"],
'ml':["torch_geometric"],
'draw':["pycairo", "CairoSVG", "drawSvg~=2.0"]},
)

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