fix

.gitattributes

@@ -36,3 +36,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.jar filter=lfs diff=lfs merge=lfs -text
 mafft-linux64/** filter=lfs diff=lfs merge=lfs -text
 seqkit filter=lfs diff=lfs merge=lfs -text
+tipars/Benchmark_datasets/** filter=lfs diff=lfs merge=lfs -text
+tipars/ref-tree/** filter=lfs diff=lfs merge=lfs -text

app.py

@@ -4,60 +4,70 @@ import os
 import pandas as pd
 import subprocess
 
+
 def get_sequence_example(example):
-    if example.startswith('H5-20'):
-        return open('tipars/ref-tree/Influenza-A-H5/H5-20-tests.fas').read()
-    elif example.startswith('H5-67'):
-        return open('tipars/ref-tree/Influenza-A-H5/H5-67-tests.fasta').read()
-    elif example.startswith('SARS-CoV-2'):
-        return open('tipars/ref-tree/sars-cov-2/sars2.fasta').read()
-
-def mirror(a,b,c,d):
-    return a,b,c,d
-
-def insertion(task,
-            tipars_file1,tipars_file2,tipars_file3,tipars_file4,
-            input_textbox1,
-            input_textbox2):
+    if example.startswith("H5-20"):
+        return open("tipars/ref-tree/Influenza-A-H5/H5-20-tests.fas").read()
+    elif example.startswith("H5-67"):
+        return open("tipars/ref-tree/Influenza-A-H5/H5-67-tests.fasta").read()
+    elif example.startswith("SARS-CoV-2"):
+        return open("tipars/ref-tree/sars-cov-2/sars2.fasta").read()
+
+
+def mirror(a, b, c, d):
+    return a, b, c, d
+
+
+def insertion(
+    task,
+    tipars_file1,
+    tipars_file2,
+    tipars_file3,
+    tipars_file4,
+    input_textbox1,
+    input_textbox2,
+):
     # remove tipars.tree if exists
-    if os.path.exists('tipars/tipars.tree'):
-        os.remove('tipars/tipars.tree')
-    if task == 'tipars':
-        print(tipars_file1.name,tipars_file2.name,tipars_file3.name,tipars_file4.name)
+    if os.path.exists("tipars/tipars.tree"):
+        os.remove("tipars/tipars.tree")
+    if task == "tipars":
+        print(
+            tipars_file1.name, tipars_file2.name, tipars_file3.name, tipars_file4.name
+        )
         query = tipars_file1.name
         tree = tipars_file2.name
         msa = tipars_file3.name
         anc = tipars_file4.name
-    if task == 'h5':
-        
-        with open('tipars/test.fasta', 'w') as f:
+    if task == "h5":
+
+        with open("tipars/test.fasta", "w") as f:
             f.write(input_textbox2)
-        query = 'tipars/test.fasta'
-        
-        tree = 'tipars/ref-tree/Influenza-A-H5/tree.nwk'
-        msa = 'tipars/ref-tree/Influenza-A-H5/taxa.fast'
-        anc = 'tipars/ref-tree/Influenza-A-H5/anc.fas'
-    elif task == 'sars':
-        
-        with open('tipars/test.fasta', 'w') as f:
+        query = "tipars/test.fasta"
+
+        tree = "tipars/ref-tree/Influenza-A-H5/tree.nwk"
+        msa = "tipars/ref-tree/Influenza-A-H5/taxa.fasta"
+        anc = "tipars/ref-tree/Influenza-A-H5/anc.fas"
+    elif task == "sars":
+
+        with open("tipars/test.fasta", "w") as f:
             f.write(input_textbox1)
-        query = 'tipars/test.fasta'  
-        tree = 'tipars/ref-tree/sars-cov-2/sars-cov-2_ready.tree'
-        msa = 'tipars/ref-tree/sars-cov-2/sars-cov-2_taxa.fasta'
-        anc = 'tipars/ref-tree/sars-cov-2/sars-cov-2_anc.fas'
+        query = "tipars/test.fasta"
+        tree = "tipars/ref-tree/sars-cov-2/sars-cov-2_ready.tree"
+        msa = "tipars/ref-tree/sars-cov-2/sars-cov-2_taxa.fasta"
+        anc = "tipars/ref-tree/sars-cov-2/sars-cov-2_anc.fas"
     # open query fasta file
     # and add '(Query)' after '>'
     # print(query, tree, msa, anc)
-    with open(query, 'r') as f:
+    with open(query, "r") as f:
         lines = f.readlines()
-        with open('tipars/query.fasta', 'w') as f:
+        with open("tipars/query.fasta", "w") as f:
             for line in lines:
-                if line.startswith('>'):
-                    f.write(line.strip() + '_query\n')
+                if line.startswith(">"):
+                    f.write(line.strip() + "_query\n")
                 else:
                     f.write(line)
-    output = 'tipars/tipars.tree'
-    query = 'tipars/query.fasta'
+    output = "tipars/tipars.tree"
+    query = "tipars/query.fasta"
     command = ["mafft-linux64/mafft.bat", "--add", query, "--keeplength", msa]
     with open("mafft_output.fas", "w") as output_file:
         subprocess.run(command, stdout=output_file, text=True)
@@ -67,12 +77,25 @@ def insertion(task,
     command = ["./seqkit", "grep", "-f", "query-name.txt", "mafft_output.fas"]
     with open(query, "w") as output_file:
         subprocess.run(command, stdout=output_file, text=True)
-    subprocess.run(['tipars/tipars', '-t', tree, '-s', msa, '-a', anc,'-q', 'tipars/query.fasta','-o', output])
+    subprocess.run(
+        [
+            "tipars/tipars",
+            "-t",
+            tree,
+            "-s",
+            msa,
+            "-a",
+            anc,
+            "-q",
+            "tipars/query.fasta",
+            "-o",
+            output,
+        ]
+    )
     fig = plot_fig(output)
     return fig
 
 
-
 css = """
 h1 {
     text-align: center;
@@ -82,20 +105,31 @@ h1 {
 """
 
 with gr.Blocks(css=css) as demo:
-    gr.Image("tipars/tipars.svg",width=50,height=50, min_width=0,container=False,show_download_button=False)
-    
+    gr.Image(
+        "tipars/tipars.svg",
+        width=50,
+        height=50,
+        min_width=0,
+        container=False,
+        show_download_button=False,
+    )
+
     task_selected = gr.State("sars")
-    
-    gr.Markdown("""# TIPars
-                TIPars is JAVA program to do fast and accurate insertion or placement of new samples onto a reference phylogenetic tree based on parsimony criterion and utilized the pre-computed ancestral sequences.""")
+
+    gr.Markdown(
+        """# TIPars
+                TIPars is JAVA program to do fast and accurate insertion or placement of new samples onto a reference phylogenetic tree based on parsimony criterion and utilized the pre-computed ancestral sequences."""
+    )
     with gr.Row():
-        
+
         with gr.Column():
-            gr.Markdown("""## Input
+            gr.Markdown(
+                """## Input
                         Input your query sequences.
-            """)
+            """
+            )
             with gr.Tab("SARS-Cov-2 Full Genome Tree") as sars_tab:
-                
+
                 gr.Markdown(
                     """
                 ### Query Sequences
@@ -104,16 +138,17 @@ with gr.Blocks(css=css) as demo:
                 )
                 input_textbox1 = gr.Textbox(label="Query Sequences")
                 gr.Examples(
-                examples=[
-                    ["SARS-CoV-2"],
-                ],
-                inputs=input_textbox1,
-                fn=get_sequence_example,
-                cache_examples=True,
-                outputs=input_textbox1,)
-                
+                    examples=[
+                        ["SARS-CoV-2"],
+                    ],
+                    inputs=input_textbox1,
+                    fn=get_sequence_example,
+                    cache_examples=True,
+                    outputs=input_textbox1,
+                )
+
             with gr.Tab("Influenza-A-H5 HA Tree") as h5_tab:
-                
+
                 gr.Markdown(
                     """
                 ### Query Sequences
@@ -122,82 +157,114 @@ with gr.Blocks(css=css) as demo:
                 )
                 input_textbox2 = gr.Textbox(label="Sequence")
                 gr.Examples(
-                examples=[
-                    ["H5-20"],
-                    ["H5-67"]
-                ],
-                inputs=input_textbox2,
-                fn=get_sequence_example,
-                cache_examples=True,
-                outputs=input_textbox2,
-            )
-                
-                
-            
+                    examples=[["H5-20"], ["H5-67"]],
+                    inputs=input_textbox2,
+                    fn=get_sequence_example,
+                    cache_examples=True,
+                    outputs=input_textbox2,
+                )
+
             with gr.Tab("TIPars") as tipars_tab:
-                
-                
+
                 gr.Markdown(
                     """
                 ### Query Sequences
                 Sequences to be insert to Reference Tree (.fasta)
                 """
                 )
-                tipars_file1 = gr.File(label="Query Sequences",file_types=["fasta", "fas", "fna", "ffn", "faa", "frn", "fa"])
+                tipars_file1 = gr.File(
+                    label="Query Sequences",
+                    file_types=["fasta", "fas", "fna", "ffn", "faa", "frn", "fa"],
+                )
                 gr.Markdown(
                     """
                 ### Rooted Reference Tree
                 The tree which new sample shall be inserted to (.nwk)
                 """
                 )
-                tipars_file2 = gr.File(label="Rooted Reference Tree",file_types=["nwk", "new", "tree"])
+                tipars_file2 = gr.File(
+                    label="Rooted Reference Tree", file_types=["nwk", "new", "tree"]
+                )
                 gr.Markdown(
                     """
                 ### Tree MSA (Multiple Sequence Alignment)
                 The multiple sequence alignment of taxa that built the Reference Tree (.fasta)
                 """
                 )
-                tipars_file3 = gr.File(label="Tree MSA (Multiple Sequence Alignment)",file_types=["fasta", "fas", "fna", "ffn", "faa", "frn", "fa"])
+                tipars_file3 = gr.File(
+                    label="Tree MSA (Multiple Sequence Alignment)",
+                    file_types=["fasta", "fas", "fna", "ffn", "faa", "frn", "fa"],
+                )
                 gr.Markdown(
                     """
                 ### Ancestral Sequence Alignment
                 Ancestral sequence (aligned) obtained from PastML or TreeTime (.fasta)
                 """
                 )
-                tipars_file4 = gr.File(label="Ancestral Sequence Alignment",file_types=["fasta", "fas", "fna", "ffn", "faa", "frn", "fa"])
+                tipars_file4 = gr.File(
+                    label="Ancestral Sequence Alignment",
+                    file_types=["fasta", "fas", "fna", "ffn", "faa", "frn", "fa"],
+                )
                 gr.Examples(
                     examples=[
-                        [(os.path.join(os.path.dirname(__file__),"tipars/Benchmark_datasets/H5/H5_query.fas")), 
-                         (os.path.join(os.path.dirname(__file__),"tipars/Benchmark_datasets/H5/H5_tree.nwk")), 
-                         (os.path.join(os.path.dirname(__file__),"tipars/Benchmark_datasets/H5/H5_taxa.fas")), 
-                         (os.path.join(os.path.dirname(__file__),"tipars/Benchmark_datasets/H5/H5_anc.fas"))]
-                        
+                        [
+                            (
+                                os.path.join(
+                                    os.path.dirname(__file__),
+                                    "tipars/Benchmark_datasets/NDV/NDV_query.fas",
+                                )
+                            ),
+                            (
+                                os.path.join(
+                                    os.path.dirname(__file__),
+                                    "tipars/Benchmark_datasets/NDV/NDV_tree.nwk",
+                                )
+                            ),
+                            (
+                                os.path.join(
+                                    os.path.dirname(__file__),
+                                    "tipars/Benchmark_datasets/NDV/NDV_taxa.fas",
+                                )
+                            ),
+                            (
+                                os.path.join(
+                                    os.path.dirname(__file__),
+                                    "tipars/Benchmark_datasets/NDV/NDV_anc.fas",
+                                )
+                            ),
+                        ]
                     ],
-                    inputs=[tipars_file1,tipars_file2,tipars_file3,tipars_file4],
+                    inputs=[tipars_file1, tipars_file2, tipars_file3, tipars_file4],
                     fn=mirror,
                     # cache_examples=True,
-                    outputs=[tipars_file1,tipars_file2,tipars_file3,tipars_file4],
+                    outputs=[tipars_file1, tipars_file2, tipars_file3, tipars_file4],
                 )
 
-            
-                    
-            
             btn = gr.Button("Run")
         with gr.Column():
-            gr.Markdown("""## Output
+            gr.Markdown(
+                """## Output
                         TIPars insertion result:
-            """)
-                
+            """
+            )
+
             charts = gr.Plot(label="Tree")
     h5_tab.select(lambda: "h5", inputs=None, outputs=task_selected)
     sars_tab.select(lambda: "sars", inputs=None, outputs=task_selected)
     tipars_tab.select(lambda: "tipars", inputs=None, outputs=task_selected)
-   
 
-    
-    btn.click(fn=insertion, inputs=[task_selected,
-                                    tipars_file1,tipars_file2,tipars_file3,tipars_file4,
-                                    input_textbox1,
-                                    input_textbox2], outputs=[charts])
+    btn.click(
+        fn=insertion,
+        inputs=[
+            task_selected,
+            tipars_file1,
+            tipars_file2,
+            tipars_file3,
+            tipars_file4,
+            input_textbox1,
+            input_textbox2,
+        ],
+        outputs=[charts],
+    )
 if __name__ == "__main__":
-    demo.launch()
+    demo.launch(server_name="0.0.0.0", server_port=7860)

tipars/Benchmark_datasets/16S/16S_anc.fas

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tipars/Benchmark_datasets/16S/16S_taxa.fas

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