Spaces:
Runtime error
Runtime error
Create new file
Browse files
test.py
ADDED
@@ -0,0 +1,49 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
######## GRADIO INPUT ########
|
2 |
+
|
3 |
+
import gradio as gr
|
4 |
+
from ConstructBuilder.builder import build
|
5 |
+
from Bio import SeqIO
|
6 |
+
import pandas as pd
|
7 |
+
import uuid
|
8 |
+
import os
|
9 |
+
|
10 |
+
def LabFusion(name, file , uni_seq , orientation:str="NC", gfp:bool=False, sol_tag:list=[]):
|
11 |
+
dick = {}
|
12 |
+
if file:
|
13 |
+
sequences = SeqIO.to_dict(SeqIO.parse(file.name, "fasta"))
|
14 |
+
|
15 |
+
for key in sequences:
|
16 |
+
seq = sequences[key]
|
17 |
+
dick[key] = build(str(seq.seq), sol_tag, gfp, orientation)
|
18 |
+
else:
|
19 |
+
dick[name] = build(uni_seq, sol_tag, gfp, orientation)
|
20 |
+
table = pd.DataFrame.from_dict(dick)
|
21 |
+
|
22 |
+
table.to_csv(f"/home/ubuntu/1TB_disk/constructos/gradio_projects/constructs_{name}.csv")
|
23 |
+
return table, f"/home/ubuntu/1TB_disk/constructos/gradio_projects/constructs_{name}.csv"
|
24 |
+
|
25 |
+
|
26 |
+
int_align = gr.Interface(fn=LabFusion,
|
27 |
+
inputs=[
|
28 |
+
gr.Textbox(label="Project name"),
|
29 |
+
gr.File(label="Insert a Fasta file"),
|
30 |
+
gr.Textbox(label="Insert a unique amino acid sequence"),
|
31 |
+
gr.Dropdown(choices=["N","C", "N+C"], label="Protein Orientarion"),
|
32 |
+
gr.Checkbox(value=False, label="do you want GFP in your constructs?"),
|
33 |
+
gr.CheckboxGroup(choices=['MBP', 'SUMO', 'Fh8', 'GST',
|
34 |
+
'NusA', 'Thioredoxin', 'FLAG',
|
35 |
+
'S-tag', 'CBP', 'STREPII', 'BAP', 'NT11',
|
36 |
+
'Tab2', 'Z-basic', 'ProteinA', 'IMPACT',
|
37 |
+
'mysB', 'PolyR', 'c-myc', 'S', 'SBP-tag',
|
38 |
+
'Strep-tag', 'Twin-Strep-tag', 'HAT',
|
39 |
+
'BCCP', 'HaloTag','all'], label="Solubility Tags")],
|
40 |
+
outputs=[gr.DataFrame(label = " Constructs ") ,
|
41 |
+
gr.File(label="CSV output file")],
|
42 |
+
title="ConstructMaker",
|
43 |
+
live=True
|
44 |
+
)
|
45 |
+
|
46 |
+
inter = gr.TabbedInterface([int_align],
|
47 |
+
["LabFusion"])
|
48 |
+
|
49 |
+
inter.launch(share=True)
|