first commit

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.238.0/containers/jupyter-datascience-notebooks
+{
+	"name": "BLAST-SummarAIzer",
+	"image": "astrabert/blast-summaraizer:latest",
+	// Forward Jupyter port locally, mark required
+	"forwardPorts": [7860],
+	"portsAttributes": {
+		"7860": {
+			"label": "Gradio"
+		}
+	},
+
+	// Configure tool-specific properties.
+	"customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"ms-python.python"
+			]
+		}
+	}
+}

.gitignore

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+16S_*
+tax*

Dockerfile

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+# Use an official Python runtime as a parent image
+FROM astrabert/blast-summaraizer
+
+RUN cp -r /usr/local/ncbi-blast-2.15.0+/bin/* /usr/local/bin/
+
+EXPOSE 7860
+
+ENTRYPOINT [ "python3", "app.py" ]

README.md

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+# BLAST-SummAIrizer
+
+An easy-to-use, intuitive chat interface to ease and speed BLAST results interpretation, starting from 16S rRNA local blasting within the Docker container or from a Description Table (CSV) downloaded from online BLAST results.

app.py

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+import gradio as gr
+from gradio_client import Client
+import subprocess as sp
+import time
+import requests
+
+def upload_to_fileio(file_path):
+    with open(file_path, 'rb') as f:
+        response = requests.post('https://file.io', files={'file': f})
+    if response.status_code == 200:
+        return response.json().get('link')
+    else:
+        return "#"
+
+api_client = Client("eswardivi/Phi-3-mini-128k-instruct")
+
+def blast_search(inputfile, matchesnumber, qcovcutoff, evaluecutoff):
+    sp.run("echo 'QUERY_SEQ\tTAXON\tQUERY_COVERAGE\tPERC_ID\tLENGTH\tMISMATCHES\tGAPS\tE_VALUE\tBITSCORE' > results.txt", shell=True)
+    sp.run(f"blastn -query {inputfile} -db 16S_ribosomal_RNA -outfmt '6 qseqid sscinames qcov pident length mismatch gapopen evalue bitscore' -max_target_seqs {matchesnumber} -evalue {evaluecutoff} -qcov_hsp_perc {qcovcutoff} >> results.txt", shell=True)
+    f = open("results.txt")
+    content = f.read()
+    f.close()
+    link = upload_to_fileio("results.txt")
+    return content, link
+
+def reply(user_prompt, history, inputfile, matchesnumber, qcovcutoff, evaluecutoff):
+    context, filelink = blast_search(inputfile, matchesnumber, qcovcutoff, evaluecutoff)
+    instructions = "You are a helpful assistant whose job is to summarize in a straight-to-the-point but effective way the result of a BLAST search conducted on a 16S rRNA bacterial sequences database from NCBI."
+    full_prompt = f"{instructions} Based on thr content of this TSV file resulting from a BLAST search: \"\"\"{context}\"\"\", summarize the mentioned output complying with these user-provided instructions: {user_prompt}"
+    response = api_client.predict(
+        full_prompt,	# str  in 'Message' Textbox component
+        0.2,	# float (numeric value between 0 and 1) in 'Temperature' Slider component
+        True,	# bool  in 'Sampling' Checkbox component
+        512,	# float (numeric value between 128 and 4096) in 'Max new tokens' Slider component
+        api_name="/chat"
+    )
+    response = response + f"\n\nDownload you BLAST results [at this link]({filelink})"
+    this_hist = ''
+    for char in response:
+        this_hist += char
+        time.sleep(0.0001)
+        yield this_hist
+
+def summarize_description_table(description_table_file):
+    f = open(description_table_file)
+    lines = f.readlines()
+    if len(lines) > 10:
+        incipit = "**⚠️: The number of hits was higher than 10. Only the first 10 hits were taken into account.**\n\n"
+        lines = lines[:11]
+    else:
+        incipit = ""
+    content = "".join(lines)
+    return incipit, content
+
+def ai_summarize(user_prompt, history, inputfile):
+    incipit, context = summarize_description_table(inputfile)
+    instructions = "You are a helpful assistant whose job is to summarize in a straight-to-the-point but effective way the result of a BLAST search conducted online on NCBI databases."
+    full_prompt = f"{instructions} Based on thr content of this CSV file resulting from a BLAST search: \"\"\"{context}\"\"\", summarize the mentioned output complying with these user-provided instructions: {user_prompt}"
+    response = api_client.predict(
+        full_prompt,	# str  in 'Message' Textbox component
+        0.2,	# float (numeric value between 0 and 1) in 'Temperature' Slider component
+        True,	# bool  in 'Sampling' Checkbox component
+        512,	# float (numeric value between 128 and 4096) in 'Max new tokens' Slider component
+        api_name="/chat"
+    )
+    response = incipit+response
+    this_hist = ''
+    for char in response:
+        this_hist += char
+        time.sleep(0.0001)
+        yield this_hist
+
+
+user_file = gr.File(label="Upload FASTA File")
+
+user_file1 = gr.File(label="Upload Description Table (CSV) Downloadable From Online BLAST Results")
+
+user_max_matches = gr.Slider(5, 50, value=20, label="Max Hits per Sequence", info="Select maximum number of BLAST hits per sequence (higher number of hits will result in a longer latency)")
+
+user_qcov = gr.Slider(0, 100, value=0, label="Minimum Query Coverage", info="Minimum query coverage for a hit to be considered")
+
+user_evalue = gr.Textbox(label="E-value threshold",info="All the hits below the threshold will be considered",value="1e-10")
+
+additional_accordion = gr.Accordion(label="Parameters to be set before you start chatting", open=True)
+
+demo0 = gr.ChatInterface(fn=reply, additional_inputs=[user_file, user_max_matches, user_qcov, user_evalue], additional_inputs_accordion=additional_accordion, title="""<h2 align='center'>Bacteria 16S rRNA</h2>
+    <h3 align='center'>BLAST 16S rRNA bacterial sequences and get a nice summary of the results with the power of AI!</h3>
+    <h4 align='center'>Support this space with a ⭐ on <a href='https://github.com/AstraBert/BLAST-SummarAIzer'>GitHub</a></h4>""")
+
+demo1 = gr.ChatInterface(fn=ai_summarize, additional_inputs=[user_file1], additional_inputs_accordion=additional_accordion, title="""<h2 align='center'>Online BLAST results</h2>
+    <h3 align='center'>Upload a Description Table from Online BLAST results and get a nice summary with the power of AI!</h3>
+    <h4 align='center'>Support this space with a ⭐ on <a href='https://github.com/AstraBert/BLAST-SummarAIzer'>GitHub</a></h4>""")
+
+demo = gr.TabbedInterface([demo0, demo1], ["16S rRNA", "Online BLAST results"], title="BLAST SummarAIzer")
+
+if __name__=="__main__":
+    demo.launch(server_name="0.0.0.0", share=False)

requirements.txt

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+gradio
+gradio_client
+requests

results.txt

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+QUERY_SEQ	TAXON	QUERY_COVERAGE	PERC_ID	LENGTH	MISMATCHES	GAPS	E_VALUE	BITSCORE
+NR_024570.1	Escherichia coli	100.000	1450	0	0	0.0	2667
+NR_024570.1	Escherichia fergusonii ATCC 35469	99.242	1452	9	2	0.0	2625
+NR_024570.1	Shigella flexneri	99.237	1442	9	2	0.0	2606
+NR_024570.1	Escherichia coli	99.233	1434	9	2	0.0	2597
+NR_024570.1	Shigella sonnei	99.098	1441	11	2	0.0	2593
+NR_024570.1	Escherichia fergusonii	98.954	1434	13	2	0.0	2580
+NR_024570.1	Escherichia fergusonii ATCC 35469	99.089	1427	11	2	0.0	2569
+NR_024570.1	Shigella boydii	98.815	1434	15	2	0.0	2558
+NR_024570.1	Pseudescherichia vulneris	98.135	1448	20	7	0.0	2545
+NR_024570.1	Escherichia marmotae	98.209	1452	24	2	0.0	2542
+NR_024570.1	Escherichia albertii	98.605	1434	18	2	0.0	2542
+NR_024570.1	Shigella dysenteriae	98.405	1442	20	3	0.0	2538
+NR_024570.1	Phytobacter palmae	97.521	1452	34	2	0.0	2486
+NR_024570.1	Citrobacter koseri	97.561	1435	31	4	0.0	2468
+NR_024570.1	Citrobacter koseri	97.561	1435	31	4	0.0	2464
+NR_024570.1	Citrobacter koseri	97.556	1432	29	6	0.0	2455
+NR_024570.1	Raoultella planticola ATCC 33531	97.552	1430	31	4	0.0	2453
+NR_024570.1	Citrobacter youngae	97.115	1456	33	8	0.0	2453
+NR_024570.1	Salmonella bongori	97.043	1454	37	6	0.0	2447
+NR_024570.1	Phytobacter massiliensis JC163	97.041	1453	39	4	0.0	2447