From b868db9adbe04d7be65411b8dbd97fe8aabb21d8 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 17:16:36 +0000
Subject: [PATCH 01/10] python project based gitignore

---
 .gitignore | 166 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 166 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 00000000..988900ea
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,166 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+tmp
+Genomes/GCF_000005845.2
+Genomes/GCF_000006765.1
\ No newline at end of file

From f07548760be51c73e358fabedf55c9a59291701d Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 17:24:29 +0000
Subject: [PATCH 02/10] requirements to run TargetRNA3

---
 requirements.txt | 106 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100644 requirements.txt

diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..efa925b3
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,106 @@
+anyio==4.4.0
+argon2-cffi==23.1.0
+argon2-cffi-bindings==21.2.0
+arrow==1.3.0
+asttokens==2.4.1
+async-lru==2.0.4
+attrs==23.2.0
+Babel==2.15.0
+beautifulsoup4==4.12.3
+bleach==6.1.0
+certifi==2024.6.2
+cffi==1.16.0
+charset-normalizer==3.3.2
+comm==0.2.2
+debugpy==1.8.1
+decorator==5.1.1
+defusedxml==0.7.1
+executing==2.0.1
+fastjsonschema==2.20.0
+fqdn==1.5.1
+gitdb==4.0.11
+GitPython==3.1.41
+h11==0.14.0
+httpcore==1.0.5
+httpx==0.27.0
+idna==3.7
+ipykernel==6.29.4
+ipython==8.25.0
+ipywidgets==8.1.3
+isoduration==20.11.0
+jedi==0.19.1
+Jinja2==3.1.4
+json5==0.9.25
+jsonpointer==3.0.0
+jsonschema==4.22.0
+jsonschema-specifications==2023.12.1
+jupyter==1.0.0
+jupyter-console==6.6.3
+jupyter-events==0.10.0
+jupyter-lsp==2.2.5
+jupyter_client==8.6.2
+jupyter_core==5.7.2
+jupyter_server==2.14.1
+jupyter_server_terminals==0.5.3
+jupyterlab==4.2.2
+jupyterlab_pygments==0.3.0
+jupyterlab_server==2.27.2
+jupyterlab_widgets==3.0.11
+MarkupSafe==2.1.5
+matplotlib-inline==0.1.7
+mistune==3.0.2
+nbclient==0.10.0
+nbconvert==7.16.4
+nbformat==5.10.4
+nest-asyncio==1.6.0
+notebook==7.2.1
+notebook_shim==0.2.4
+numpy==2.0.0
+overrides==7.7.0
+packaging==24.1
+pandas==2.2.2
+pandocfilters==1.5.1
+parso==0.8.4
+pexpect==4.9.0
+platformdirs==4.2.2
+prometheus_client==0.20.0
+prompt_toolkit==3.0.47
+psutil==6.0.0
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pycparser==2.22
+Pygments==2.18.0
+python-dateutil==2.9.0.post0
+python-json-logger==2.0.7
+pytz==2024.1
+PyYAML==6.0.1
+pyzmq==26.0.3
+qtconsole==5.5.2
+QtPy==2.4.1
+referencing==0.35.1
+requests==2.32.3
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rpds-py==0.18.1
+scipy==1.13.1
+Send2Trash==1.8.3
+setuptools==69.0.3
+six==1.16.0
+smmap==5.0.1
+sniffio==1.3.1
+soupsieve==2.5
+stack-data==0.6.3
+terminado==0.18.1
+tinycss2==1.3.0
+tornado==6.4.1
+traitlets==5.14.3
+types-python-dateutil==2.9.0.20240316
+tzdata==2024.1
+uri-template==1.3.0
+urllib3==2.2.2
+wcwidth==0.2.13
+webcolors==24.6.0
+webencodings==0.5.1
+websocket-client==1.8.0
+wheel==0.43.0
+widgetsnbextension==4.0.11

From b3fff59a9f2acd6861b14d9aaf50107e15659205 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 17:25:25 +0000
Subject: [PATCH 03/10] all dpendencies should be globally installed from now
 on

---
 AddGenome.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/AddGenome.py b/AddGenome.py
index a8a88633..9ae83dc8 100644
--- a/AddGenome.py
+++ b/AddGenome.py
@@ -210,7 +210,7 @@ def determine_closest_relatives(GENOME_DIR):
         seq_16S = get_16S_sequence(GENOME_DIR)
         with open(TEMP_FILENAME1, 'w') as out_file:
                 out_file.write('>16S' + '\n' + seq_16S + '\n')
-        p = subprocess.run(['./blastn', '-db', DB_16S, '-query', TEMP_FILENAME1, '-evalue', '0.01', '-max_target_seqs', str(BLAST_RESULTS+1), '-num_threads', str(NUM_THREADS), '-outfmt', '6 qseqid sseqid evalue bitscore', '-out', TEMP_FILENAME2], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['blastn', '-db', DB_16S, '-query', TEMP_FILENAME1, '-evalue', '0.01', '-max_target_seqs', str(BLAST_RESULTS+1), '-num_threads', str(NUM_THREADS), '-outfmt', '6 qseqid sseqid evalue bitscore', '-out', TEMP_FILENAME2], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
         # Read in BLAST results
         replicates = {}
@@ -310,14 +310,14 @@ def create_blast_filter_for_relatives(GENOME_DIR, target_ID_to_genome):
                         for t in targets: out_file.write(t + '\n')
 
         # Format Blast filter file
-        p = subprocess.run(['./blastdb_aliastool', '-seqid_file_in', FILTER_FILE], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['blastdb_aliastool', '-seqid_file_in', FILTER_FILE], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
 
 # Helper function for computing target homologs
 # PERFORM BLAST WITHOUT USING MULTIPLE PROCESSORS
 def blast_targets_against_database_SINGLE_PROCESS(protein_file):
         BLAST_OUTPUT_FILE = str(time.time()) + '.blast'
-        p = subprocess.run(['./blastp', '-db', DB_FAA, '-query', protein_file, '-outfmt', '6 qseqid sseqid evalue bitscore', '-out', BLAST_OUTPUT_FILE, '-evalue', '0.01', '-max_target_seqs', '100', '-num_threads', str(NUM_THREADS), '-seqidlist', FILTER_FILE + '.bsl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['blastp', '-db', DB_FAA, '-query', protein_file, '-outfmt', '6 qseqid sseqid evalue bitscore', '-out', BLAST_OUTPUT_FILE, '-evalue', '0.01', '-max_target_seqs', '100', '-num_threads', str(NUM_THREADS), '-seqidlist', FILTER_FILE + '.bsl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         if (os.path.exists(protein_file)): os.remove(protein_file)
         if (os.path.exists(FILTER_FILE)): os.remove(FILTER_FILE)
         if (os.path.exists(FILTER_FILE + '.bsl')): os.remove(FILTER_FILE + '.bsl')
@@ -331,7 +331,7 @@ def run_blast(target_subset):
                 for target in target_subset:
                         GENOME_DIR, accession, protein_seq = target
                         out_file.write('>' + accession + '\n' + protein_seq + '\n')
-        p = subprocess.run(['./blastp', '-db', DB_FAA, '-query', accession_file, '-outfmt', '6 qseqid sseqid evalue bitscore', '-out', GENOME_DIR + accession + '.blast.xyz', '-evalue', '0.01', '-max_target_seqs', '100', '-num_threads', str(NUM_THREADS), '-seqidlist', FILTER_FILE + '.bsl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['blastp', '-db', DB_FAA, '-query', accession_file, '-outfmt', '6 qseqid sseqid evalue bitscore', '-out', GENOME_DIR + accession + '.blast.xyz', '-evalue', '0.01', '-max_target_seqs', '100', '-num_threads', str(NUM_THREADS), '-seqidlist', FILTER_FILE + '.bsl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         if (os.path.exists(accession_file)): os.remove(accession_file)
 
 
@@ -482,7 +482,7 @@ def run_RNAplfold(target):
         accession, mRNA_name, mRNA_sequence, count = target
         with open(GENOME_DIR + RNAPLFOLD_DIR + accession + '____' + mRNA_name + '.fa', 'w') as out_file:
                 out_file.write('>' + accession + '____' + mRNA_name + '\n' + mRNA_sequence + '\n')
-        p = subprocess.run(['./RNAplfold', '-u', '40', '-O', '--plex_output', '--auto-id', '--id-prefix', 'TR' + count], input=mRNA_sequence.encode(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['RNAplfold', '-u', '40', '-O', '--plex_output', '--auto-id', '--id-prefix', 'TR' + count], input=mRNA_sequence.encode(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         if (p.returncode != 0) or (len(p.stderr.decode()) > 0):
                 error('Problem executing RNAplfold:\t' + str(p.stderr.decode()) + '\n')
         renameAndRemoveOutputFiles('TR' + count + '_0001', accession + '____' + mRNA_name)
@@ -501,7 +501,7 @@ def RNAplfold_MULTI_PROCESS(targets):
 # Helper function for computing target accessibility
 # CREATE BINARY VERSIONS OF ACCESSIBILITY FILES USING RNAplex
 def create_binary_files():
-        p = subprocess.run(['./RNAplex', '-a', GENOME_DIR + RNAPLFOLD_DIR, '-k'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['RNAplex', '-a', GENOME_DIR + RNAPLFOLD_DIR, '-k'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         filelist = os.listdir(GENOME_DIR + RNAPLFOLD_DIR)
         for f in filelist:
                 if (f.endswith('_openen')): os.remove(GENOME_DIR + RNAPLFOLD_DIR + f)

From 7499e8488f067671eae69fa517cbed05dab6ad29 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 17:25:56 +0000
Subject: [PATCH 04/10] Devcontainer configuration for vscode

---
 .devcontainer/Dockerfile        | 14 ++++++++++++++
 .devcontainer/devcontainer.json | 26 ++++++++++++++++++++++++++
 2 files changed, 40 insertions(+)
 create mode 100644 .devcontainer/Dockerfile
 create mode 100644 .devcontainer/devcontainer.json

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
new file mode 100644
index 00000000..63b0d9b1
--- /dev/null
+++ b/.devcontainer/Dockerfile
@@ -0,0 +1,14 @@
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bullseye
+
+# RUN apt update -y && apt install --no-install-recommends 
+
+# Install ViennaRNA package dependency to running AddGenome.py
+
+WORKDIR /tmp
+
+RUN wget https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ViennaRNA-2.6.4.tar.gz
+RUN tar -zxvf ViennaRNA-2.6.4.tar.gz
+RUN cd ViennaRNA-2.6.4
+RUN ./configure
+RUN make
+RUN sudo make install
\ No newline at end of file
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 00000000..3a4a067e
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,26 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python 3",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	// "image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+	"build": { "dockerfile": "Dockerfile" },
+	"features": {
+		"ghcr.io/akhildevelops/devcontainer-features/pip:0": {}
+	}
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "pip3 install --user -r requirements.txt",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

From 5848e7bc895dfb52ac123620e483bcd596bcf687 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 17:42:19 +0000
Subject: [PATCH 05/10] No more local program installation

---
 TargetRNA3.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/TargetRNA3.py b/TargetRNA3.py
index 1d68c725..121de456 100644
--- a/TargetRNA3.py
+++ b/TargetRNA3.py
@@ -251,10 +251,10 @@ def get_sRNA_homologs(SRNA_FILENAME, genome):
         RESTRICT_FILENAME = FILENAME + '.restrict'
         with open(RESTRICT_FILENAME, 'w') as out_file:
                 for accession in genome: out_file.write(accession + '\n')
-        p = subprocess.run(['./blastdb_aliastool', '-seqid_file_in', RESTRICT_FILENAME], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['blastdb_aliastool', '-seqid_file_in', RESTRICT_FILENAME], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
         # BLAST sRNA sequence
-        p = subprocess.run(['./blastn', '-db', DB, '-query', SRNA_FILENAME, '-outfmt', '6 qseqid sseqid evalue bitscore qstart qend', '-out', SRNA_HOMOLOGS_FILENAME, '-evalue', '0.01', '-max_target_seqs', '100', '-num_threads', str(NUM_THREADS), '-negative_seqidlist', RESTRICT_FILENAME + '.bsl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['blastn', '-db', DB, '-query', SRNA_FILENAME, '-outfmt', '6 qseqid sseqid evalue bitscore qstart qend', '-out', SRNA_HOMOLOGS_FILENAME, '-evalue', '0.01', '-max_target_seqs', '100', '-num_threads', str(NUM_THREADS), '-negative_seqidlist', RESTRICT_FILENAME + '.bsl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
         # Determine homologs of sRNA
         sRNA_homologs = {}
@@ -302,7 +302,7 @@ def determine_sRNA_accessibility(GENOME_DIR, sRNA_name, sRNA_sequence):
         p = subprocess.run(['nice', './RNAplfold', '-u', '40', '-O', '--plex_output', '-W', str(WINDOW_SIZE), '--auto-id', '--id-prefix', TIME_STR], input=sRNA_sequence.encode(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         if (p.returncode != 0) or (len(p.stderr.decode()) > 0):
                 sys.stderr.write('ERROR executing RNAplfold:\t' + str(p.stderr.decode()) + '\n')
-        p = subprocess.run(['./RNAplex', '-a', '.', '-k'], input=sRNA_sequence.encode(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['RNAplex', '-a', '.', '-k'], input=sRNA_sequence.encode(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
         # Clean up
         shutil.move(TIME_STR + '_0001_openen_bin', GENOME_DIR + RNAPLFOLD_DIR + sRNA_name + '_openen_bin')

From 19b68669f092159709aec30feab1c2ce05e869f9 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 17:43:00 +0000
Subject: [PATCH 06/10] ignoring subfolders

---
 .gitignore | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 988900ea..b7890680 100644
--- a/.gitignore
+++ b/.gitignore
@@ -162,5 +162,5 @@ cython_debug/
 #.idea/
 
 tmp
-Genomes/GCF_000005845.2
-Genomes/GCF_000006765.1
\ No newline at end of file
+Genomes/GCF_000005845.2/**
+Genomes/GCF_000006765.1/**
\ No newline at end of file

From f1b45eef4509f3ab8229e859b8491624615638b2 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 20:34:55 +0000
Subject: [PATCH 07/10] sklearn installed with correct version

---
 requirements.txt | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index efa925b3..8f18fa20 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,6 +11,7 @@ bleach==6.1.0
 certifi==2024.6.2
 cffi==1.16.0
 charset-normalizer==3.3.2
+cloudpickle==2.2.1
 comm==0.2.2
 debugpy==1.8.1
 decorator==5.1.1
@@ -30,6 +31,7 @@ ipywidgets==8.1.3
 isoduration==20.11.0
 jedi==0.19.1
 Jinja2==3.1.4
+joblib==1.4.2
 json5==0.9.25
 jsonpointer==3.0.0
 jsonschema==4.22.0
@@ -55,7 +57,7 @@ nbformat==5.10.4
 nest-asyncio==1.6.0
 notebook==7.2.1
 notebook_shim==0.2.4
-numpy==2.0.0
+numpy==1.26.4
 overrides==7.7.0
 packaging==24.1
 pandas==2.2.2
@@ -82,6 +84,7 @@ requests==2.32.3
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
 rpds-py==0.18.1
+scikit-learn==1.3.2
 scipy==1.13.1
 Send2Trash==1.8.3
 setuptools==69.0.3
@@ -91,6 +94,7 @@ sniffio==1.3.1
 soupsieve==2.5
 stack-data==0.6.3
 terminado==0.18.1
+threadpoolctl==3.5.0
 tinycss2==1.3.0
 tornado==6.4.1
 traitlets==5.14.3

From 703e984db5075eb62c96fab6c46c129792ebaa24 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 20:35:17 +0000
Subject: [PATCH 08/10] ignoring files

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index b7890680..3eae463a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -163,4 +163,5 @@ cython_debug/
 
 tmp
 Genomes/GCF_000005845.2/**
-Genomes/GCF_000006765.1/**
\ No newline at end of file
+Genomes/GCF_000006765.1/**
+DataFiles
\ No newline at end of file

From c338410e4d44e1510144f78afee5924b750f3e38 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 20:35:55 +0000
Subject: [PATCH 09/10] global program call

---
 TargetRNA3.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/TargetRNA3.py b/TargetRNA3.py
index 121de456..1161dee6 100644
--- a/TargetRNA3.py
+++ b/TargetRNA3.py
@@ -299,7 +299,7 @@ def get_homologs(GENOME_DIR, SRNA_FILENAME, genome, genes):
 def determine_sRNA_accessibility(GENOME_DIR, sRNA_name, sRNA_sequence):
         TIME_STR = str(time.time())
         WINDOW_SIZE = min(70, len(sRNA_sequence))
-        p = subprocess.run(['nice', './RNAplfold', '-u', '40', '-O', '--plex_output', '-W', str(WINDOW_SIZE), '--auto-id', '--id-prefix', TIME_STR], input=sRNA_sequence.encode(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['nice', 'RNAplfold', '-u', '40', '-O', '--plex_output', '-W', str(WINDOW_SIZE), '--auto-id', '--id-prefix', TIME_STR], input=sRNA_sequence.encode(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         if (p.returncode != 0) or (len(p.stderr.decode()) > 0):
                 sys.stderr.write('ERROR executing RNAplfold:\t' + str(p.stderr.decode()) + '\n')
         p = subprocess.run(['RNAplex', '-a', '.', '-k'], input=sRNA_sequence.encode(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
@@ -313,7 +313,7 @@ def determine_sRNA_accessibility(GENOME_DIR, sRNA_name, sRNA_sequence):
 
 # HELPER FUNCTION FOR COMPUTING INTERACTION ENERGIES. COMPUTES ENERGIES USING RNAPLEX.
 def run_RNAplex(GENOME_DIR, SRNA_FILENAME, f):
-        p = subprocess.run(['nice', './RNAplex', '-f', '0', '-q', SRNA_FILENAME, '-t', GENOME_DIR + RNAPLFOLD_DIR + f, '-a', GENOME_DIR + RNAPLFOLD_DIR, '-b'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        p = subprocess.run(['nice', 'RNAplex', '-f', '0', '-q', SRNA_FILENAME, '-t', GENOME_DIR + RNAPLFOLD_DIR + f, '-a', GENOME_DIR + RNAPLFOLD_DIR, '-b'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         structure_info = p.stdout.decode().strip().split('\n')[2]
         return (f, structure_info)
 

From 92a8dcd8c29bd7ec76ec525649bcef7d8865d110 Mon Sep 17 00:00:00 2001
From: Thiago M Souza <46378621+mtsz-thiago@users.noreply.github.com>
Date: Mon, 24 Jun 2024 21:18:31 +0000
Subject: [PATCH 10/10] devcontainer for project

---
 .devcontainer/Dockerfile         | 16 +++++++---------
 .devcontainer/devcontainer.json  | 31 ++++++++++++++++++-------------
 .devcontainer/docker-compose.yml | 26 ++++++++++++++++++++++++++
 .github/dependabot.yml           | 12 ++++++++++++
 requirements.txt                 |  1 -
 5 files changed, 63 insertions(+), 23 deletions(-)
 create mode 100644 .devcontainer/docker-compose.yml
 create mode 100644 .github/dependabot.yml

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 63b0d9b1..71aaff57 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,14 +1,12 @@
-FROM mcr.microsoft.com/devcontainers/python:1-3.12-bullseye
-
-# RUN apt update -y && apt install --no-install-recommends 
-
-# Install ViennaRNA package dependency to running AddGenome.py
+# Note: You can use any Debian/Ubuntu based image you want. 
+FROM mcr.microsoft.com/devcontainers/base:bullseye
 
 WORKDIR /tmp
 
 RUN wget https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ViennaRNA-2.6.4.tar.gz
 RUN tar -zxvf ViennaRNA-2.6.4.tar.gz
-RUN cd ViennaRNA-2.6.4
-RUN ./configure
-RUN make
-RUN sudo make install
\ No newline at end of file
+RUN cd ViennaRNA-2.6.4 && ./configure && make && sudo make install
+
+# [Optional] Uncomment this section to install additional OS packages.
+RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+    && apt-get -y install --no-install-recommends ncbi-blast+
\ No newline at end of file
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 3a4a067e..07dcd270 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,25 +1,30 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
-// README at: https://github.com/devcontainers/templates/tree/main/src/python
+// README at: https://github.com/devcontainers/templates/tree/main/src/docker-outside-of-docker-compose
 {
-	"name": "Python 3",
-	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-	// "image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
-	"build": { "dockerfile": "Dockerfile" },
+	"name": "Docker from Docker Compose",
+	"dockerComposeFile": "docker-compose.yml",
+	"service": "app",
+	"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
+
+	// Use this environment variable if you need to bind mount your local source code into a new container.
+	"remoteEnv": {
+		"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+	},
+
 	"features": {
+		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {
+			"version": "latest",
+			"enableNonRootDocker": "true",
+			"moby": "true"
+		},
+		"ghcr.io/devcontainers/features/python:1": {},
 		"ghcr.io/akhildevelops/devcontainer-features/pip:0": {}
 	}
-
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	// "features": {},
-
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	// "postCreateCommand": "pip3 install --user -r requirements.txt",
-
-	// Configure tool-specific properties.
-	// "customizations": {},
+	// "postCreateCommand": "docker --version",
 
 	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
 	// "remoteUser": "root"
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
new file mode 100644
index 00000000..73ad0bde
--- /dev/null
+++ b/.devcontainer/docker-compose.yml
@@ -0,0 +1,26 @@
+version: '3'
+
+services:
+  app:
+    build: 
+      context: .
+      dockerfile: Dockerfile
+
+    volumes:
+      # Forwards the local Docker socket to the container.
+      - /var/run/docker.sock:/var/run/docker-host.sock 
+      # Update this to wherever you want VS Code to mount the folder of your project
+      - ../..:/workspaces:cached
+
+    # Overrides default command so things don't shut down after the process ends.
+    entrypoint: /usr/local/share/docker-init.sh
+    command: sleep infinity 
+
+    # Uncomment the next four lines if you will use a ptrace-based debuggers like C++, Go, and Rust.
+    # cap_add:
+    #  - SYS_PTRACE
+    # security_opt:
+    #   - seccomp:unconfined
+
+    # Use "forwardPorts" in **devcontainer.json** to forward an app port locally. 
+    # (Adding the "ports" property to this file will not forward from a Codespace.)
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..f33a02cd
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for more information:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# https://containers.dev/guide/dependabot
+
+version: 2
+updates:
+ - package-ecosystem: "devcontainers"
+   directory: "/"
+   schedule:
+     interval: weekly
diff --git a/requirements.txt b/requirements.txt
index 8f18fa20..573776e7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -26,7 +26,6 @@ httpcore==1.0.5
 httpx==0.27.0
 idna==3.7
 ipykernel==6.29.4
-ipython==8.25.0
 ipywidgets==8.1.3
 isoduration==20.11.0
 jedi==0.19.1