initial commit

.gitattributes

@@ -33,3 +33,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+
+*.png

LICENSE.txt

@@ -0,0 +1,19 @@
+Copyright (c) 2021 scpeiyao
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

README.md

@@ -10,4 +10,116 @@ pinned: false
 license: mit
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+ARGNet
+======
+A deep nueral network for robust identification and annotation of antibiotic resistance genes.
+
+The input can be long amino acid sequences(full length/contigs), long nucleotide sequences, 
+short amino acid reads (30-50aa), short nucleotide reads (100-150nt) in fasta format.
+If your input is short reads you should assign 'argnet-s' model, or if your input is full-length/contigs
+you should assign 'argnet-l' to make the predict. </br>
+
+![alt text](https://github.com/patience111/ARGNet/blob/main/pics/ARGNet_workflow.png)</br>
+
+
+Installation
+------------
+clone the program to your local machine:</br>
+git clone https://github.com/patience111/ARGNet
+
+
+**1. Setting up environment**
+
+
+**1.1 Installation with conda**
+
+
+1.1.1 For **CPU** inference, you could install the program with conda YAML file in the installation directory with the following commands:
+
+```
+cd ./installation 
+conda env create -f ARGNet-CPU.yml -n ARGNet-cpu
+conda activate ARGNet-cpu
+```
+
+(This was tested on Ubuntu 16.04, 20.04; Windows 10, macOS(14.1.1))</br>
+  ![alt text](https://github.com/patience111/ARGNet/blob/main/pics/argnet_conda_cpu_trial.png)</br>
+   
+   
+1.1.2 For **GPU** inference, you could install the program with conda YAML file in the installation directory with the following commands:</br>
+```
+cd ./installation
+conda env create -f ARGNet-GPU.yml -n ARGNet-gpu
+conda activate ARGNet-gpu
+```
+(This was tested on Ubuntu 16.04, cuda 10.1, Driver Version: 430.64)</br>
+    ![alt text](https://github.com/patience111/ARGNet/blob/main/pics/argnet_conda_gpu_trial.png)</br>
+
+**1.2 Or, if you prefer installing dependencies manually**, you might find this information useful:</br>
+      The program was tested with the following package version, you can install exactly the same version or other compatible versions.</br>
+
+```
+Biopython:  1.79
+tensorflow:  2.2.0 
+cuda: 10.2 (for GPU using)
+cudnn: 7.6.5.32 (for GPU using)
+numpy: 1.18.5
+scikit-learn: 0.24.1
+tqdm: 4.56.0
+```
+
+**2. Getting trained models**<br>
+```   
+cd ./model
+bash get-models.sh
+```
+Quickstart Guide
+----------------
+***for long sequences***
+
+```
+python argnet.py --input input_path_data  --type aa/nt --model argnet-l  --outname output_file_name
+```
+***for short reads***
+
+```
+python argnet.py --input input_path_data --type aa/nt --model argnet-s --outname output_file_name
+```
+    
+**general options:**</br>
+     --input/-i&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;the test file as input </br>
+     --type/-t &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;molecular type of your test data (aa for amino acid, nt for nucleotide)</br>
+     --model/-m&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;the model you assign to make the prediction (argnet-l for long sequences, argnet-s for short reads) </br>
+     --outname/-on&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;the output file name </br>
+
+**optional arguments:**</br>
+  -h, --help            show this help message and exit</br></br>
+  ![alt text](https://github.com/patience111/ARGNet/blob/main/pics/ARGNet_help.jpeg)</br>
+  -i INPUT, --input INPUT </br>
+                        the test data as input </br></br>
+  -t {aa,nt}, --type {aa,nt} </br>
+                        molecular type of your input file </br></br>
+  -m {argnet-s,argnet-l}, --model {argnet-s,argnet-l} </br>
+                        the model to make the prediction </br></br>
+  -on OUTNAME, --outname OUTNAME </br>
+                        the name of results output </br></br>
+  
+ 
+Example
+----------
+if we predict the long amino acid contigs by using ARGNet-L model, we could use command line (if you are in ARGNet dirctory):</br></br>
+```
+python3 ./scripts/argnet.py -i ./tests/aa/long/arg100p.fasta -t aa -m argnet-l -on argnet_lsaa_test.txt
+```
+**output** will be like and saved in the **results** folder: </br>
+![alt text](https://github.com/patience111/ARGNet/blob/main/pics/lsaa_prediction.png)</br>
+the first column **test_id** is the sequence label of the test sequnece.</br>
+the second column **ARG_prediction** is the "ARG" or "non-ARG" prediction of the input sequence.</br>
+the third column **resistance_category** is the classifition of the 36 antibiotics categories of the input sequence resisting to.</br>
+the last column **probability** is the classifition probability of the antibiotic predition of the input sequence by the model.
+
+Contribute
+----------
+
+If you'd like to contribute to ARGNet, check out https://github.com/patience111/argnet</br>
+Hope you enjoy ARGNet journey, any problem please contact [email protected]

app.py

@@ -0,0 +1,112 @@
+"""
+gradio
+
+"""
+
+import gradio as gr
+from helper import *
+import scripts.script as script
+
+def process_data(input_type, input_text, input_file):
+    print(input_type)
+    if input_type == "Text":
+        if input_text:
+            print(input_text)
+            sequence = []
+            for line in input_text.splitlines():
+                if line.startswith(">"):
+                    sequence.append("")
+                else:
+                    sequence[-1] += line.strip().upper()
+            result = classify_sequence_type_length(sequence)
+            script.run_argnet(input_text, "output.txt", result[0], result[1])
+            df, pie_chart = script.view_stat("output.txt")
+        else:
+            result = "No input provided."
+    else:
+        if input_file:
+            sequence = []
+            with open(input_file.name, "r") as f:
+                for line in f:
+                    if line.startswith(">"):
+                        print(line.strip())
+                        sequence.append("")
+                    else:
+                        print(line.strip().upper())
+                        sequence[-1] += line.strip().upper()
+            result = classify_sequence_type_length(sequence)
+            script.run_argnet(input_text, "output.txt", result[0], result[1])
+            df, pie_chart = script.view_stat("output.txt")
+        else:
+            result = "No input provided."
+
+    return df, pie_chart
+
+
+# Create the interface with tabs
+with gr.Blocks() as whole_block:
+    tab_selected = gr.State("Text")
+
+    gr.HTML(
+        """
+    <center>
+    <h1>ARGnet</h1>
+    <p>A deep neural network for robust identification and annotation of Antibiotic Resistance genes</p>
+    </center>
+    """
+    )
+
+    with gr.Row():
+        with gr.Column():
+            gr.Markdown(
+                """
+            ## Input
+            """
+            )
+            with gr.Tab("Text") as text_tab:
+                gr.Markdown(
+                    """
+                ### Enter the sequence
+                """
+                )
+                input_textbox = gr.Textbox(label="Sequence")
+                input_textbox_2 = gr.Textbox(label="Sequence",visible=False)
+                gr.Examples(
+                    examples=[
+                        ["Amino Acid Long Sequence (>51aa)"],
+                        ["Amino Acid Short Sequence (30-50aa)"],
+                        ["Nucleotide Long Sequence (>150nt)"],
+                        ["Nucleotide Short Sequence (100-150nt)"],
+                    ],
+                    inputs=input_textbox,
+                    fn=get_sequence_example,
+                    cache_examples=True,
+                    outputs=input_textbox,
+                )
+            with gr.Tab("File") as file_tab:
+                gr.Markdown(
+                    """
+                ### Upload a FASTA file
+                """
+                )
+                input_file = gr.File(label="Sequence File")
+            submit_button = gr.Button("Submit")
+        with gr.Column():
+            gr.Markdown(
+                """
+            ## Output
+            """
+            )
+            table = gr.Dataframe(headers=["Test ID", "ARG Prediction", "Resistance Category", "Probability"])
+            pie_chart = gr.Plot(container=True)
+
+    text_tab.select(lambda: "Text", inputs=None, outputs=tab_selected)
+    file_tab.select(lambda: "File", inputs=None, outputs=tab_selected)
+
+    submit_button.click(
+        fn=process_data,
+        inputs=[tab_selected, input_textbox, input_file],
+        outputs=[table, pie_chart],
+    )
+
+whole_block.launch()

code_of_conduct.md

@@ -0,0 +1,130 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.
+

conf.py

@@ -0,0 +1,179 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'ARGNet'
+copyright = '2018, scpeiyao'
+author = 'scpeiyao'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = ''
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.coverage',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'argnetdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'argnet.tex', 'ARGNet Documentation',
+     'scpeiyao', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'argnet', 'ARGNet Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'argnet', 'ARGNet Documentation',
+     author, 'ARGNet', 'a deep neural network for antibitotic resistance genes identification',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,179 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'ARGNet'
+copyright = '2018, scpeiyao'
+author = 'scpeiyao'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = ''
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.coverage',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'argnetdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'argnet.tex', 'ARGNet Documentation',
+     'scpeiyao', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'argnet', 'ARGNet Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'argnet', 'ARGNet Documentation',
+     author, 'ARGNet', 'a deep neural network for antibitotic resistance genes identification',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------

docs/index.rst

@@ -0,0 +1,20 @@
+.. ARGNet documentation master file, created by
+   sphinx-quickstart on Mon Nov 12 14:17:27 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ARGNet's documentation!
+=======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

gradio_cached_examples/10/log.csv

@@ -0,0 +1,19 @@
+Sequence,flag,username,timestamp
+">CCP45025.1|FEATURES|hmdarg|isoniazid|kasA
+GARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMST
+RNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMV
+APAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYA
+PKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAV
+NNSFGFGGHN
+>gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB
+GSFGSGKTQTAFELHRRLNPSYVYDPEKMGFALRSMVPQEIAKDDFQSYPLWRAFNYSLL",,,2024-01-12 15:49:12.671073
+">gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB_0
+RGIIIVPMTIVYPEYFNEIIGRLRQEGRIV
+>AGQ48857.1|FEATURES|hmdarg|pleuromutilin|eatAv_0
+GNFSIYEEQKKLRDEFEMAQNEKLKKEVSR",,,2024-01-12 15:49:12.672885
+">AJ635405|FEATURES|resfinder|beta-lactam|blaLEN9
+GGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGTGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGT",,,2024-01-12 15:49:12.674371
+">S60108|FEATURES|resfinder|aminoglycoside|kgmB_0
+CCGCACCCGGCTCCCGGACCCGGCGATCCCGAGGACCCGAGGCTGGCGGAGGTCGTCGACGCGGTCCGGTCCAGCAGGCGCTACCAGAGCGTCGCGCCCG
+>APOK01000044|FEATURES|resfinder|beta-lactam|blaOXA-290_0
+ACATATGATGGGCAAACATTTCAAGAATATGGCAATGCGTTGAGTCGATCGAATACGGCTTATATTCCAGCCTCAACCTTCAAGATGTTAAATGCTCTGA",,,2024-01-12 15:49:12.675474

gradio_cached_examples/12/log.csv

@@ -0,0 +1,19 @@
+Sequence,flag,username,timestamp
+">CCP45025.1|FEATURES|hmdarg|isoniazid|kasA
+GARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMST
+RNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMV
+APAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYA
+PKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAV
+NNSFGFGGHN
+>gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB
+GSFGSGKTQTAFELHRRLNPSYVYDPEKMGFALRSMVPQEIAKDDFQSYPLWRAFNYSLL",,,2024-01-12 15:48:26.963370
+">gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB_0
+RGIIIVPMTIVYPEYFNEIIGRLRQEGRIV
+>AGQ48857.1|FEATURES|hmdarg|pleuromutilin|eatAv_0
+GNFSIYEEQKKLRDEFEMAQNEKLKKEVSR",,,2024-01-12 15:48:26.965339
+">AJ635405|FEATURES|resfinder|beta-lactam|blaLEN9
+GGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGTGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGT",,,2024-01-12 15:48:26.966367
+">S60108|FEATURES|resfinder|aminoglycoside|kgmB_0
+CCGCACCCGGCTCCCGGACCCGGCGATCCCGAGGACCCGAGGCTGGCGGAGGTCGTCGACGCGGTCCGGTCCAGCAGGCGCTACCAGAGCGTCGCGCCCG
+>APOK01000044|FEATURES|resfinder|beta-lactam|blaOXA-290_0
+ACATATGATGGGCAAACATTTCAAGAATATGGCAATGCGTTGAGTCGATCGAATACGGCTTATATTCCAGCCTCAACCTTCAAGATGTTAAATGCTCTGA",,,2024-01-12 15:48:26.967351

helper.py

@@ -0,0 +1,62 @@
+"""
+Helper function
+
+"""
+
+def get_sequence_example(example):
+    print(example)
+    if example.startswith("Amino Acid Long Sequence"):
+        return """\
+>CCP45025.1|FEATURES|hmdarg|isoniazid|kasA
+GARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMST
+RNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMV
+APAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYA
+PKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAV
+NNSFGFGGHN
+>gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB
+GSFGSGKTQTAFELHRRLNPSYVYDPEKMGFALRSMVPQEIAKDDFQSYPLWRAFNYSLL"""
+    elif example.startswith("Amino Acid Short Sequence"):
+        return """\
+>gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB_0
+RGIIIVPMTIVYPEYFNEIIGRLRQEGRIV
+>AGQ48857.1|FEATURES|hmdarg|pleuromutilin|eatAv_0
+GNFSIYEEQKKLRDEFEMAQNEKLKKEVSR"""
+    elif example.startswith("Nucleotide Long Sequence"):
+        return """\
+>AJ635405|FEATURES|resfinder|beta-lactam|blaLEN9
+GGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGTGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGT"""
+    elif example.startswith("Nucleotide Short Sequence"):
+        return """\
+>S60108|FEATURES|resfinder|aminoglycoside|kgmB_0
+CCGCACCCGGCTCCCGGACCCGGCGATCCCGAGGACCCGAGGCTGGCGGAGGTCGTCGACGCGGTCCGGTCCAGCAGGCGCTACCAGAGCGTCGCGCCCG
+>APOK01000044|FEATURES|resfinder|beta-lactam|blaOXA-290_0
+ACATATGATGGGCAAACATTTCAAGAATATGGCAATGCGTTGAGTCGATCGAATACGGCTTATATTCCAGCCTCAACCTTCAAGATGTTAAATGCTCTGA"""
+
+def classify_sequence(sequence):
+    nucleotide_chars = set("ATGC-")
+    if all(char in nucleotide_chars for char in sequence):
+        return "nt" # "Nucleotide"
+    else:
+        return "aa" # "Amino Acid
+
+def count_length_sequences(sequence):
+    count_length_sequences = []
+    for i in sequence:
+        count_length_sequences.append(len(i))
+    max_sequence_length = max(count_length_sequences)
+    return max_sequence_length
+
+def classify_sequence_type_length(sequence):
+    sequence_type = classify_sequence(sequence[0])
+    sequence_length = count_length_sequences(sequence)
+    if sequence_type == "nt": # nucleotide
+        if sequence_length > 150:
+            sequence_length_type = "l" # "long"
+        else:
+            sequence_length_type = "s" # "short"
+    else:  # amino acid
+        if sequence_length > 50 :
+            sequence_length_type = "l"
+        else:
+            sequence_length_type = "s"
+    return (sequence_type, sequence_length_type)

index.rst

@@ -0,0 +1,20 @@
+.. ARGNet documentation master file, created by
+   sphinx-quickstart on Mon Nov 12 14:17:27 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ARGNet's documentation!
+=======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

input.txt

@@ -0,0 +1,8 @@
+>CCP45025.1|FEATURES|hmdarg|isoniazid|kasA
+GARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMST
+RNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMV
+APAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYA
+PKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAV
+NNSFGFGGHN
+>gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB
+GSFGSGKTQTAFELHRRLNPSYVYDPEKMGFALRSMVPQEIAKDDFQSYPLWRAFNYSLL

installation/ARGNet-CPU.yml

@@ -0,0 +1,13 @@
+name: argnet
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - r
+dependencies:
+- python=3.11
+- tensorflow=2.12
+- scikit-learn
+- tqdm=4.56.0
+- biopython=1.79
+- numpy=1.23.5

installation/ARGNet-GPU.yml

@@ -0,0 +1,13 @@
+name: argnet
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - r
+dependencies:
+- python=3.9
+- tensorflow-gpu
+- scikit-learn
+- tqdm=4.56.0
+- biopython=1.79
+- numpy=1.23.5

make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

model/AELS_tall.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c89ceab91b8f96137035e954eecee7b59dee62fbb38889d6b1b08bf34968de3e
+size 192323176

model/AESS_tall.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:86a84ac7448f991d1efe8039d9600df014ac40cb0d2cd0ea1c5dfa1b090ea138
+size 158989048

model/classifier-ls_tall.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:958a79325990851989616dfdb73cd76b02b1ed3edbb8211939a3a4b2e7d5828a
+size 128849192

model/classifier-ss_tall.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:26060cf63dc6d9bb2ce37996674682cd00bcd82e1805e0dd92fc80db035cc741
+size 178555104

model/get-models.sh

@@ -0,0 +1,4 @@
+wget https://github.com/patience111/ARGNet/releases/download/v1.0.1/AELS_tall.h5
+wget https://github.com/patience111/ARGNet/releases/download/v1.0.1/AESS_tall.h5
+wget https://github.com/patience111/ARGNet/releases/download/v1.0.1/classifier-ls_tall.h5
+wget https://github.com/patience111/ARGNet/releases/download/v1.0.1/classifier-ss_tall.h5

requirements.txt

@@ -0,0 +1,7 @@
+scikit-learn
+tqdm
+biopython==1.79
+numpy==1.23.5
+tensorflow
+kito
+plotly

results/argnet-lsaa-intis_predict_simple.txt

@@ -0,0 +1 @@
+test_id	ARG_prediction	resistance_category	probability

sampleFile_laa.fasta

@@ -0,0 +1,9 @@
+>CCP45025.1|FEATURES|hmdarg|isoniazid|kasA
+GARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMST
+RNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMV
+APAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYA
+PKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAV
+NNSFGFGGHN
+>gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB
+GSFGSGKTQTAFELHRRLNPSYVYDPEKMGFALRSMVPQEIAKDDFQSYPLWRAFNYSLL
+ASLTDTYRGIIIVPMTIVYPEYFNEIIGRLRQEGRIVHHFTLMASKETLLKRLRTRAE

sampleFile_lnt.fasta

@@ -0,0 +1,2 @@
+>AJ635405|FEATURES|resfinder|beta-lactam|blaLEN9
+GGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGTGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGT

sampleFile_saa.fasta

@@ -0,0 +1,4 @@
+>gi:505065763:ref:WP_015252865.1:|FEATURES|deeparg|tunicamycin|tmrB_0
+RGIIIVPMTIVYPEYFNEIIGRLRQEGRIV
+>AGQ48857.1|FEATURES|hmdarg|pleuromutilin|eatAv_0
+GNFSIYEEQKKLRDEFEMAQNEKLKKEVSR

sampleFile_snt.fasta

@@ -0,0 +1,4 @@
+>S60108|FEATURES|resfinder|aminoglycoside|kgmB_0
+CCGCACCCGGCTCCCGGACCCGGCGATCCCGAGGACCCGAGGCTGGCGGAGGTCGTCGACGCGGTCCGGTCCAGCAGGCGCTACCAGAGCGTCGCGCCCG
+>APOK01000044|FEATURES|resfinder|beta-lactam|blaOXA-290_0
+ACATATGATGGGCAAACATTTCAAGAATATGGCAATGCGTTGAGTCGATCGAATACGGCTTATATTCCAGCCTCAACCTTCAAGATGTTAAATGCTCTGA