lbugnon commited on
Commit
c3b15fe
·
1 Parent(s): 7f7e729

fix outputs

Browse files
Files changed (1) hide show
  1. app.py +8 -5
app.py CHANGED
@@ -7,10 +7,13 @@ def fold(id, sequence):
7
  ct_file = f"output/{id}.ct"
8
  structure_draw = f"output/{id}.png"
9
 
10
- sp.run(f"sincFold pred {sequence} --name {id} -o output --draw", shell=True)
11
  dotbracket = ct2dot(ct_file)
 
 
 
12
 
13
- return dotbracket, ct_file, structure_draw
14
 
15
 
16
  def run():
@@ -21,15 +24,15 @@ def run():
21
  lines=1,
22
  value="16s_C.elegans_domain2"),
23
  gr.Textbox(label="RNA Sequence",
24
- info="RNA Sequence",
25
  lines=3,
26
  value="GAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCCAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGCCAAUAGAAAUCGGCGUAAAGAGUGUUUUAGAUCAAUCCCCCAAUAAAGCUAAAAUUCACCUG")],
27
  outputs=[
 
28
  gr.Textbox(label="Dotbracket structure",
29
- info="Sequence ID",
30
  lines=3),
 
31
  gr.File(label="CT file"),
32
- gr.Image(label="Structure")])
33
 
34
  demo.launch(server_name="0.0.0.0", server_port=7860)
35
 
 
7
  ct_file = f"output/{id}.ct"
8
  structure_draw = f"output/{id}.png"
9
 
10
+ sp.run(f"sincFold pred {sequence} --name {id} -o output --draw --draw-resolution 10", shell=True)
11
  dotbracket = ct2dot(ct_file)
12
+ fasta_file = f"output/{id}.fasta"
13
+ with open(fasta_file, "w") as f:
14
+ f.write(f">{id}\n{sequence}\n{dotbracket}")
15
 
16
+ return structure_draw, dotbracket, fasta_file, ct_file
17
 
18
 
19
  def run():
 
24
  lines=1,
25
  value="16s_C.elegans_domain2"),
26
  gr.Textbox(label="RNA Sequence",
 
27
  lines=3,
28
  value="GAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCCAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGCCAAUAGAAAUCGGCGUAAAGAGUGUUUUAGAUCAAUCCCCCAAUAAAGCUAAAAUUCACCUG")],
29
  outputs=[
30
+ gr.Image(label="Structure"),
31
  gr.Textbox(label="Dotbracket structure",
 
32
  lines=3),
33
+ gr.File(label="Fasta file"),
34
  gr.File(label="CT file"),
35
+ ])
36
 
37
  demo.launch(server_name="0.0.0.0", server_port=7860)
38