https://github.com/tlambert03/fpbasepy
Python wrapper for FPBase.org GraphQL API.
https://github.com/tlambert03/fpbasepy
api-graphql fluorescent fpbase proteins
Last synced: 6 months ago
JSON representation
Python wrapper for FPBase.org GraphQL API.
- Host: GitHub
- URL: https://github.com/tlambert03/fpbasepy
- Owner: tlambert03
- License: bsd-3-clause
- Created: 2024-11-18T14:08:29.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2024-11-20T19:28:57.000Z (6 months ago)
- Last Synced: 2024-12-01T07:03:46.791Z (6 months ago)
- Topics: api-graphql, fluorescent, fpbase, proteins
- Language: Python
- Homepage:
- Size: 50.8 KB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Python FPbase API
[](https://github.com/tlambert03/fpbasepy/raw/main/LICENSE)
[](https://pypi.org/project/fpbase)
[](https://python.org)
[](https://github.com/tlambert03/fpbasepy/actions/workflows/ci.yml)
[](https://codecov.io/gh/tlambert03/fpbasepy)
Python wrapper for FPBase.org GraphQL API.
See for an interactive playground and full documentation on the graphql schema
(click the little book icon on the top left corner).
## Installation
```sh
pip install fpbase
```
## API
See all response model types in `fpbase.models`.
### Functions that return a single object
* `fpbase.get_fluorophore` (can return either protein or dye)
* `fpbase.get_protein` (will only return proteins)
* `fpbase.get_microscope`
* `fpbase.get_filter`
* `fpbase.get_light_source`
* `fpbase.get_camera`
### Functions that return a list of available object keys
* `fpbase.list_fluorophores` (includes both proteins and dyes)
* `fpbase.list_proteins`
* `fpbase.list_dyes`
* `fpbase.list_microscopes`
* `fpbase.list_filters`
* `fpbase.list_light_sources`
* `fpbase.list_cameras`
### Other
* `fpbase.graphql_query` : Send generic GraphQL query to FPbase (see for full documentation on the graphql schema and an interactive playground)
## Example Usage
```python
import fpbase
fpbase.get_fluorophore("mCherry")
# NOTE: you can also use `get_protein()` if you want to ensure that the
# fluorophore is a protein and the response is an `fpbase.models.Protein`
```
output
```python
Protein(
name='mCherry',
id='ZERB6',
default_state=State(
id=336,
name='mCherry',
exMax=587.0,
emMax=610.0,
emhex='#f70000',
exhex='#ff4600',
ext_coeff=72000.0,
qy=0.22,
spectra=[
Spectrum(id=79, subtype='EX', owner_filter=None, owner_camera=None, owner_light=None),
Spectrum(id=80, subtype='EM', owner_filter=None, owner_camera=None, owner_light=None),
Spectrum(id=158, subtype='A_2P', owner_filter=None, owner_camera=None, owner_light=None)
],
lifetime=1.4
),
seq='MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK',
pdb=['2H5Q'],
genbank='AAV52164',
uniprot='X5DSL3',
agg=,
switch_type=,
primary_reference=Reference(doi='10.1038/nbt1037', url='https://doi.org/10.1038/nbt1037'),
references=[
Reference(doi='10.1038/nbt1037', url='https://doi.org/10.1038/nbt1037'),
Reference(doi='10.1021/bi060773l', url='https://doi.org/10.1021/bi060773l'),
Reference(doi='10.1038/nmeth1062', url='https://doi.org/10.1038/nmeth1062'),
Reference(doi='10.1038/nmeth.1596', url='https://doi.org/10.1038/nmeth.1596'),
Reference(doi='10.1038/nmeth.1955', url='https://doi.org/10.1038/nmeth.1955'),
Reference(doi='10.1091/mbc.e16-01-0063', url='https://doi.org/10.1091/mbc.e16-01-0063'),
Reference(doi='10.1038/s41598-017-12212-x', url='https://doi.org/10.1038/s41598-017-12212-x'),
Reference(doi='10.1038/s41598-018-28858-0', url='https://doi.org/10.1038/s41598-018-28858-0'),
Reference(doi='10.1002/pld3.112', url='https://doi.org/10.1002/pld3.112'),
Reference(doi='10.1371/journal.pone.0219886', url='https://doi.org/10.1371/journal.pone.0219886'),
Reference(doi='10.1073/pnas.2017379117', url='https://doi.org/10.1073/pnas.2017379117'),
Reference(doi='10.1038/s41467-023-40647-6', url='https://doi.org/10.1038/s41467-023-40647-6')
]
)
```
```python
fpbase.get_fluorophore("DAPI")
```
output
```python
Fluorophore(
name='DAPI',
id='15',
default_state=State(
id=15,
name='DAPI',
exMax=359.0,
emMax=461.0,
emhex='',
exhex='',
ext_coeff=None,
qy=None,
spectra=[
Spectrum(id=7754, subtype='AB', owner_filter=None, owner_camera=None, owner_light=None),
Spectrum(id=222, subtype='EX', owner_filter=None, owner_camera=None, owner_light=None),
Spectrum(id=223, subtype='EM', owner_filter=None, owner_camera=None, owner_light=None)
],
lifetime=None
)
)
```
```python
# fetch info for
fpbase.get_microscope("i6WL2W")
```
output
```python
Microscope(
id='i6WL2WdgcDMgJYtPrpZcaJ',
name='Example Widefield (Sedat)',
opticalConfigs=[
OpticalConfig(
name='Widefield Blue',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=52,
name='Chroma ET395/25x',
spectrum=Spectrum(id=375, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=10,
name='Chroma T425lpxr',
spectrum=Spectrum(id=333, subtype='LP', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=47,
name='Chroma ET460/50m',
spectrum=Spectrum(id=370, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
),
OpticalConfig(
name='Widefield Dual FRET',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=63,
name='Lumencor 470/24x',
spectrum=Spectrum(id=399, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=62,
name='Chroma 59022bs',
spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=689,
name='Semrock FF02-641/75',
spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
),
OpticalConfig(
name='Widefield Dual Green',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=63,
name='Lumencor 470/24x',
spectrum=Spectrum(id=399, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=62,
name='Chroma 59022bs',
spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=569,
name='Semrock FF03-525/50',
spectrum=Spectrum(id=905, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
),
OpticalConfig(
name='Widefield Dual Red',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=67,
name='Lumencor 575/25x',
spectrum=Spectrum(id=403, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=62,
name='Chroma 59022bs',
spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=689,
name='Semrock FF02-641/75',
spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
),
OpticalConfig(
name='Widefield Far-Red',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=445,
name='Chroma ET640/30x',
spectrum=Spectrum(id=781, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=6,
name='Chroma T660lpxr',
spectrum=Spectrum(id=329, subtype='LP', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=719,
name='Semrock FF01-698/70',
spectrum=Spectrum(id=1055, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
),
OpticalConfig(
name='Widefield Triple Cyan',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=79,
name='Lumencor 440/20x',
spectrum=Spectrum(id=415, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=60,
name='Chroma 69008bs',
spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=46,
name='Chroma ET470/24m',
spectrum=Spectrum(id=369, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
),
OpticalConfig(
name='Widefield Triple FRET',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=79,
name='Lumencor 440/20x',
spectrum=Spectrum(id=415, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=60,
name='Chroma 69008bs',
spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=36,
name='Chroma ET535/30m',
spectrum=Spectrum(id=359, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
),
OpticalConfig(
name='Widefield Triple Red',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=67,
name='Lumencor 575/25x',
spectrum=Spectrum(id=403, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=60,
name='Chroma 69008bs',
spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=689,
name='Semrock FF02-641/75',
spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
),
OpticalConfig(
name='Widefield Triple Yellow',
filters=[
FilterPlacement(
path='EX',
filter=Filter(
id=41,
name='Chroma ET500/20x',
spectrum=Spectrum(id=364, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='BS',
filter=Filter(
id=60,
name='Chroma 69008bs',
spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
),
FilterPlacement(
path='EM',
filter=Filter(
id=36,
name='Chroma ET535/30m',
spectrum=Spectrum(id=359, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer='',
bandcenter=None,
bandwidth=None,
edge=None
),
reflects=False
)
],
camera=Camera(
id=4,
name='Andor Zyla 4.2 PLUS',
spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
light=LightSource(
id=9,
name='SOLA 395',
spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),
manufacturer=''
),
laser=None
)
]
)
```