diff --git a/docs/examples/alignment.ipynb b/docs/examples/alignment.ipynb
new file mode 100644
index 00000000..c8f10c3f
--- /dev/null
+++ b/docs/examples/alignment.ipynb
@@ -0,0 +1,160 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Align sequences"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "8b73afa8e8b444578f622d239c439673",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Output()"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n"
+ ],
+ "text/plain": []
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "import json\n",
+ "from pyeed.core import ProteinRecord\n",
+ "\n",
+ "\n",
+ "# load accession ids from json file\n",
+ "with open(\"ids.json\", \"r\") as f:\n",
+ " ids = json.load(f)\n",
+ "\n",
+ "sequences = ProteinRecord.get_ids(ids)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Multi Sequence Alignment\n",
+ "\n",
+ "A multi sequence alignment can be calculated by creating a `MSA` object and passing a list of `ProteinRecord`. The alignment can be executed by calling the `clustalo` method. In order for the `clustalo` method to work, the PyEED Docker Service must be running. The `clustalo` method will return an `AlignmentResult` containing all input `sequences` and `aligned_sequences`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "99f840a5cc0a4441a7d936127815ab36",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Output()"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n"
+ ],
+ "text/plain": []
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "✅ Alignment completed\n"
+ ]
+ }
+ ],
+ "source": [
+ "from pyeed.align import MSA\n",
+ "\n",
+ "alignment = MSA(sequences=sequences).clustalo()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Create a HMM profile\n",
+ "\n",
+ "To create a hidden markov model profile, you can use the `HMM` class. This method receives a `MSA` object to create the model. To check if a sequence belongs to the profile, you can use the `search` method. This method takes a `ProteinRecord` object and returns a `HMMResult` object containing the `sequence` and the `score` of the sequence in the profile."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from pyeed.align import HMM\n",
+ "\n",
+ "model = HMM(name=\"random profile\", alignment=alignment)\n",
+ "hits = model.search(sequence=sequences[0])"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "pye",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.11.5"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/docs/examples/basics.ipynb b/docs/examples/basics.ipynb
new file mode 100644
index 00000000..64e925fb
--- /dev/null
+++ b/docs/examples/basics.ipynb
@@ -0,0 +1,153 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Get rich sequence information\n",
+ "\n",
+ "## Acquire sequence information based on accession id(s)\n",
+ "\n",
+ "**Single accession ID**\n",
+ "\n",
+ "Single sequences can be retrieved using the `get_id` function. The function takes an accession id as input and returns the sequence as a `ProteinRecord` object. \n",
+ "The `ProteinRecord` object contains the sequence as a string and additional information such as information on the `Organism`, `Region` or `Site` annotations of the sequence.\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from pyeed.core import ProteinRecord\n",
+ "\n",
+ "matHM = ProteinRecord.get_id(\"MBP1912539.1\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "**Multiple accession IDs**\n",
+ "\n",
+ "To load multiple sequences at once, the `get_ids` function can be used. The function takes a list of accession IDs as input and returns a list of `ProteinRecord` objects."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import json\n",
+ "\n",
+ "# Load the saved ids from json\n",
+ "with open(\"ids.json\", \"r\") as f:\n",
+ " ids = json.load(f)\n",
+ "\n",
+ "# Get the protein info for each id\n",
+ "proteins = ProteinRecord.get_ids(ids)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Serach for similar sequences with BLAST\n",
+ "\n",
+ "The `ncbi_blast` method can be used to perform a BLAST search on the NCBI server. The method can be applied to a `ProteinRecord` object and returns a list of `ProteinRecord` objects that represent the hits of the BLAST search.\n",
+ "By specifying the `n_hits`, `e_value`, `db`, `matrix`, and `identity`, the search can be customized to number of hits, E-value, query database, substitution matrix, and identity to accept the hit, respectively.\n",
+ "\n",
+ "\n",
+ "
NCBI BLAST service might be slow
\n",
+ "
Due to the way NCBI handles requests to its BLAST API the service is quite slow. During peak working hours a single search might take more than 15 min.
\n",
+ "
/home/niklas/anaconda3/envs/pyeed/lib/python3.11/site-packages/numpy/core/getlimits.py:549: UserWarning: The value \n",
+ "of the smallest subnormal for <class 'numpy.float64'> type is zero.\n",
+ " setattr(self, word, getattr(machar, word).flat[0])\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "/home/niklas/anaconda3/envs/pyeed/lib/python3.11/site-packages/numpy/core/getlimits.py:549: UserWarning: The value \n",
+ "of the smallest subnormal for type is zero.\n",
+ " setattr(self, word, getattr(machar, word).flat[0])\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n"
+ ],
+ "text/plain": []
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# load ids\n",
+ "with open('ids.json', 'r') as f:\n",
+ " ids = json.load(f)\n",
+ "\n",
+ "# load sequences\n",
+ "sequences = ProteinRecord.get_ids(ids[:100])\n",
+ "\n",
+ "\n",
+ "base_url = 'http://cytoscape-desktop:1234/v1'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "c56bc3a6f2c443e194021f4b9d49d52b",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Output()"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n"
+ ],
+ "text/plain": []
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "graph = SequenceNetwork(sequences, base_url=base_url)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "In cyrest_get: Cannot find local or remote Cytoscape. Start Cytoscape and then proceed.\n"
+ ]
+ },
+ {
+ "ename": "RequestException",
+ "evalue": "Cannot find local or remote Cytoscape. Start Cytoscape and then proceed.",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mRequestException\u001b[0m Traceback (most recent call last)",
+ "Cell \u001b[0;32mIn[4], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m threshhold \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0.75\u001b[39m\n\u001b[0;32m----> 3\u001b[0m \u001b[43mgraph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_cytoscape_graph\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcollection\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mSequenceNetwork\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtitle\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mTest\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mthreshold\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mthreshhold\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 4\u001b[0m graph\u001b[38;5;241m.\u001b[39mset_nodes_size(column_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdegree_with_threshold_\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(threshhold), min_size\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m20\u001b[39m, max_size\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m100\u001b[39m)\n\u001b[1;32m 5\u001b[0m graph\u001b[38;5;241m.\u001b[39mcolor_nodes(column_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mphylum\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
+ "File \u001b[0;32m~/Desktop/Job_Niklas/pyeed/pyeed/network/network.py:187\u001b[0m, in \u001b[0;36mSequenceNetwork.create_cytoscape_graph\u001b[0;34m(self, collection, title, threshold)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcreate_cytoscape_graph\u001b[39m(\n\u001b[1;32m 184\u001b[0m \u001b[38;5;28mself\u001b[39m, collection: \u001b[38;5;28mstr\u001b[39m, title: \u001b[38;5;28mstr\u001b[39m, threshold: \u001b[38;5;28mfloat\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0.8\u001b[39m\n\u001b[1;32m 185\u001b[0m ):\n\u001b[1;32m 186\u001b[0m \u001b[38;5;66;03m# assert that the cytoscape API is running and cytoscape is running in the background\u001b[39;00m\n\u001b[0;32m--> 187\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[43mp4c\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcytoscape_ping\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 188\u001b[0m \u001b[43m \u001b[49m\u001b[43mbase_url\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_base_url\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCytoscape is not running in the background\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 190\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m p4c\u001b[38;5;241m.\u001b[39mcytoscape_version_info(\n\u001b[1;32m 191\u001b[0m base_url\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_base_url\n\u001b[1;32m 192\u001b[0m ), \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCytoscape API is not running\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 193\u001b[0m \u001b[38;5;66;03m# create a degree column for the nodes based on the current choosen threshold\u001b[39;00m\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/py4cytoscape_logger.py:133\u001b[0m, in \u001b[0;36mcy_log..wrapper_log\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m log_return(func, value)\n\u001b[1;32m 132\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[0;32m--> 133\u001b[0m \u001b[43mlog_exception\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43me\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 134\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 135\u001b[0m log_finally()\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/py4cytoscape_logger.py:130\u001b[0m, in \u001b[0;36mcy_log..wrapper_log\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 128\u001b[0m log_incoming(func, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 129\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 130\u001b[0m value \u001b[38;5;241m=\u001b[39m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# Call function being logged\u001b[39;00m\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m log_return(func, value)\n\u001b[1;32m 132\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/cytoscape_system.py:58\u001b[0m, in \u001b[0;36mcytoscape_ping\u001b[0;34m(base_url)\u001b[0m\n\u001b[1;32m 37\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Ping Cytoscape\u001b[39;00m\n\u001b[1;32m 38\u001b[0m \n\u001b[1;32m 39\u001b[0m \u001b[38;5;124;03mTests the connection to Cytoscape via CyREST and verifies that supported versions of Cytoscape and CyREST API are loaded.\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 55\u001b[0m \u001b[38;5;124;03m You are connected to Cytoscape!\u001b[39;00m\n\u001b[1;32m 56\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 57\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpy4cytoscape_utils\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m verify_supported_versions\n\u001b[0;32m---> 58\u001b[0m \u001b[43mverify_supported_versions\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m3.6\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbase_url\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbase_url\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 59\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m narrate(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mYou are connected to Cytoscape!\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/py4cytoscape_utils.py:819\u001b[0m, in \u001b[0;36mverify_supported_versions\u001b[0;34m(cyrest, cytoscape, base_url, caller)\u001b[0m\n\u001b[1;32m 794\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mverify_supported_versions\u001b[39m(cyrest\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m, cytoscape\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m3.6\u001b[39m, base_url\u001b[38;5;241m=\u001b[39mDEFAULT_BASE_URL, caller\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[1;32m 795\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Throws exception if min supported versions of api and cytoscape are not running.\u001b[39;00m\n\u001b[1;32m 796\u001b[0m \n\u001b[1;32m 797\u001b[0m \u001b[38;5;124;03m Extracts numerics from api and major cytoscape versions before making comparison.\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 817\u001b[0m \u001b[38;5;124;03m >>> verify_supported_versions(1, '3.10.1')\u001b[39;00m\n\u001b[1;32m 818\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 819\u001b[0m nogo \u001b[38;5;241m=\u001b[39m \u001b[43mcheck_supported_versions\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcyrest\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcyrest\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcytoscape\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcytoscape\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbase_url\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbase_url\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 821\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m nogo:\n\u001b[1;32m 822\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m caller \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m: caller \u001b[38;5;241m=\u001b[39m sys\u001b[38;5;241m.\u001b[39m_getframe(\u001b[38;5;241m1\u001b[39m)\u001b[38;5;241m.\u001b[39mf_code\u001b[38;5;241m.\u001b[39mco_name\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/py4cytoscape_utils.py:763\u001b[0m, in \u001b[0;36mcheck_supported_versions\u001b[0;34m(cyrest, cytoscape, base_url, caller, test_cytoscape)\u001b[0m\n\u001b[1;32m 739\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Checks to see if min supported versions of api and cytoscape are running.\u001b[39;00m\n\u001b[1;32m 740\u001b[0m \n\u001b[1;32m 741\u001b[0m \u001b[38;5;124;03mExtracts numerics from api, major and patch cytoscape versions before making comparison, per semantic versioning @ https://semver.org/\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 759\u001b[0m \u001b[38;5;124;03m >>> check_supported_versions(1, '3.10.0')\u001b[39;00m\n\u001b[1;32m 760\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 761\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(cytoscape, \u001b[38;5;28mfloat\u001b[39m): cytoscape \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mstr\u001b[39m(cytoscape)\n\u001b[0;32m--> 763\u001b[0m v \u001b[38;5;241m=\u001b[39m \u001b[43mcytoscape_system\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcytoscape_version_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbase_url\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbase_url\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 764\u001b[0m v_api_str \u001b[38;5;241m=\u001b[39m v[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mapiVersion\u001b[39m\u001b[38;5;124m'\u001b[39m]\n\u001b[1;32m 765\u001b[0m v_cy_str \u001b[38;5;241m=\u001b[39m v[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcytoscapeVersion\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;28;01mif\u001b[39;00m test_cytoscape \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;28;01melse\u001b[39;00m test_cytoscape\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/py4cytoscape_logger.py:133\u001b[0m, in \u001b[0;36mcy_log..wrapper_log\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m log_return(func, value)\n\u001b[1;32m 132\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[0;32m--> 133\u001b[0m \u001b[43mlog_exception\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43me\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 134\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 135\u001b[0m log_finally()\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/py4cytoscape_logger.py:130\u001b[0m, in \u001b[0;36mcy_log..wrapper_log\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 128\u001b[0m log_incoming(func, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 129\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 130\u001b[0m value \u001b[38;5;241m=\u001b[39m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# Call function being logged\u001b[39;00m\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m log_return(func, value)\n\u001b[1;32m 132\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/cytoscape_system.py:81\u001b[0m, in \u001b[0;36mcytoscape_version_info\u001b[0;34m(base_url)\u001b[0m\n\u001b[1;32m 61\u001b[0m \u001b[38;5;129m@cy_log\u001b[39m\n\u001b[1;32m 62\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcytoscape_version_info\u001b[39m(base_url\u001b[38;5;241m=\u001b[39mDEFAULT_BASE_URL):\n\u001b[1;32m 63\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Return the versions of the current Cytoscape and CyREST API.\u001b[39;00m\n\u001b[1;32m 64\u001b[0m \n\u001b[1;32m 65\u001b[0m \u001b[38;5;124;03m Args:\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 79\u001b[0m \u001b[38;5;124;03m {'apiVersion': 'v1', 'cytoscapeVersion': '3.8.1', 'automationAPIVersion': '0.0.0', 'py4cytoscapeVersion': '0.0.2'}\u001b[39;00m\n\u001b[1;32m 80\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m---> 81\u001b[0m versions \u001b[38;5;241m=\u001b[39m \u001b[43mcommands\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcyrest_get\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mversion\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbase_url\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbase_url\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(versions) \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 83\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CyError(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCyREST connection problem. py4cytoscape cannot continue!\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/py4cytoscape_logger.py:133\u001b[0m, in \u001b[0;36mcy_log..wrapper_log\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m log_return(func, value)\n\u001b[1;32m 132\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[0;32m--> 133\u001b[0m \u001b[43mlog_exception\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfunc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43me\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 134\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 135\u001b[0m log_finally()\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/py4cytoscape_logger.py:130\u001b[0m, in \u001b[0;36mcy_log..wrapper_log\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 128\u001b[0m log_incoming(func, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 129\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 130\u001b[0m value \u001b[38;5;241m=\u001b[39m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# Call function being logged\u001b[39;00m\n\u001b[1;32m 131\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m log_return(func, value)\n\u001b[1;32m 132\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/commands.py:159\u001b[0m, in \u001b[0;36mcyrest_get\u001b[0;34m(operation, parameters, base_url, require_json, raw_get)\u001b[0m\n\u001b[1;32m 157\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m r\u001b[38;5;241m.\u001b[39mtext\n\u001b[1;32m 158\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[0;32m--> 159\u001b[0m \u001b[43m_handle_error\u001b[49m\u001b[43m(\u001b[49m\u001b[43me\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/commands.py:149\u001b[0m, in \u001b[0;36mcyrest_get\u001b[0;34m(operation, parameters, base_url, require_json, raw_get)\u001b[0m\n\u001b[1;32m 147\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 148\u001b[0m url \u001b[38;5;241m=\u001b[39m build_url(base_url, operation)\n\u001b[0;32m--> 149\u001b[0m r \u001b[38;5;241m=\u001b[39m \u001b[43m_do_request\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mGET\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparams\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparameters\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbase_url\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbase_url\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mraw_request\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mraw_get\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 150\u001b[0m r\u001b[38;5;241m.\u001b[39mraise_for_status()\n\u001b[1;32m 151\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/commands.py:695\u001b[0m, in \u001b[0;36m_do_request\u001b[0;34m(method, url, base_url, raw_request, **kwargs)\u001b[0m\n\u001b[1;32m 693\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_do_request\u001b[39m(method, url, base_url\u001b[38;5;241m=\u001b[39mDEFAULT_BASE_URL, raw_request\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 694\u001b[0m \u001b[38;5;66;03m# Determine whether actual call is local or remote\u001b[39;00m\n\u001b[0;32m--> 695\u001b[0m requester, default_sandbox \u001b[38;5;241m=\u001b[39m \u001b[43m_get_requester\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbase_url\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 697\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m raw_request:\n\u001b[1;32m 698\u001b[0m do_initialize_sandbox(requester, base_url\u001b[38;5;241m=\u001b[39mbase_url) \u001b[38;5;66;03m# make sure there's a sandbox before executing a command\u001b[39;00m\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/commands.py:779\u001b[0m, in \u001b[0;36m_get_requester\u001b[0;34m(base_url)\u001b[0m\n\u001b[1;32m 777\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_get_requester\u001b[39m(base_url):\n\u001b[1;32m 778\u001b[0m \u001b[38;5;66;03m# Figure out whether CyREST available only via Jupyter-Bridge and what the default sandbox should be\u001b[39;00m\n\u001b[0;32m--> 779\u001b[0m environment \u001b[38;5;241m=\u001b[39m \u001b[43m_find_execution_environment\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbase_url\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 780\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m environment \u001b[38;5;241m==\u001b[39m ExecutionEnvironment\u001b[38;5;241m.\u001b[39mREMOTE_JUPYTER_BRIDGE:\n\u001b[1;32m 781\u001b[0m default_sandbox \u001b[38;5;241m=\u001b[39m set_default_sandbox(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msandbox_initializer(sandboxName\u001b[38;5;241m=\u001b[39mPREDEFINED_SANDBOX_NAME))\n",
+ "File \u001b[0;32m~/anaconda3/envs/pyeed/lib/python3.11/site-packages/py4cytoscape/commands.py:803\u001b[0m, in \u001b[0;36m_find_execution_environment\u001b[0;34m(base_url)\u001b[0m\n\u001b[1;32m 801\u001b[0m environment \u001b[38;5;241m=\u001b[39m check_execution_environment(base_url)\n\u001b[1;32m 802\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m environment \u001b[38;5;241m==\u001b[39m ExecutionEnvironment\u001b[38;5;241m.\u001b[39mUNKNOWN:\n\u001b[0;32m--> 803\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m requests\u001b[38;5;241m.\u001b[39mexceptions\u001b[38;5;241m.\u001b[39mRequestException(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCannot find local or remote Cytoscape. Start Cytoscape and then proceed.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 804\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m environment\n",
+ "\u001b[0;31mRequestException\u001b[0m: Cannot find local or remote Cytoscape. Start Cytoscape and then proceed."
+ ]
+ }
+ ],
+ "source": [
+ "threshhold = 0.75\n",
+ "\n",
+ "graph.create_cytoscape_graph(collection='SequenceNetwork', title='Test', threshold=threshhold)\n",
+ "graph.set_nodes_size(column_name=\"degree_with_threshold_{}\".format(threshhold), min_size=20, max_size=100)\n",
+ "graph.color_nodes(column_name='phylum')\n",
+ "graph.set_layout(layout_name = \"force-directed\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "p4c.notebook_export_show_image(filename=\"test\", type=\"png\", resolution=600, zoom=100.0, overwrite_file=True, base_url=base_url)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "pyeed",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.11.8"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/mkdocs.yml b/mkdocs.yml
index 8b3ef8c6..d750e55b 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -6,19 +6,22 @@ site_author: Max Häußler
nav:
- 🏠 Home: index.md
- - ⚡️ Quick Start:
+ - ⚡️ Examples:
+ - Basics: examples/basics.ipynb
+ - Alignments: examples/alignment.ipynb
+ - 🧰 Tools:
- quick_start/index.md
- The Sequence objects: quick_start/basics.md
- Finding Sequences: quick_start/blast.md
- Aligning Sequences: quick_start/alignments.md
- Clustering Sequences: quick_start/clustering.md
- Creating Sequence Networks: quick_start/networks.md
- - 🔎 Examples:
- - Basics: usecases/usecase1.md
- ⬇️ Installation:
- PyEED Docker Service: installation/docker.md
- via PIP: installation/via_pip.md
- #- deprecated: installation/jupyterlab.md
+
+plugins:
+ - mkdocs-jupyter
theme:
name: material
diff --git a/pyeed/core/abstractannotation.py b/pyeed/core/abstractannotation.py
index 06f98c82..1f6e3ad4 100644
--- a/pyeed/core/abstractannotation.py
+++ b/pyeed/core/abstractannotation.py
@@ -51,7 +51,7 @@ class AbstractAnnotation(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/alignmentresult.py b/pyeed/core/alignmentresult.py
index e1533a44..dc6cb9ba 100644
--- a/pyeed/core/alignmentresult.py
+++ b/pyeed/core/alignmentresult.py
@@ -51,7 +51,7 @@ class AlignmentResult(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/blastdata.py b/pyeed/core/blastdata.py
index 05669432..1a2a79f0 100644
--- a/pyeed/core/blastdata.py
+++ b/pyeed/core/blastdata.py
@@ -90,7 +90,7 @@ class BlastData(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/clustalomegaresult.py b/pyeed/core/clustalomegaresult.py
index 77f89a50..967d62ce 100644
--- a/pyeed/core/clustalomegaresult.py
+++ b/pyeed/core/clustalomegaresult.py
@@ -32,7 +32,7 @@ class ClustalOmegaResult(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/cluster.py b/pyeed/core/cluster.py
index 10fd36e1..80200d68 100644
--- a/pyeed/core/cluster.py
+++ b/pyeed/core/cluster.py
@@ -49,7 +49,7 @@ class Cluster(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/dnarecord.py b/pyeed/core/dnarecord.py
index 8b14fc29..0b688fb9 100644
--- a/pyeed/core/dnarecord.py
+++ b/pyeed/core/dnarecord.py
@@ -62,7 +62,7 @@ class DNARecord(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/organism.py b/pyeed/core/organism.py
index a6e4770b..5fb380a3 100644
--- a/pyeed/core/organism.py
+++ b/pyeed/core/organism.py
@@ -108,7 +108,7 @@ class Organism(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/pairwisealignmentresult.py b/pyeed/core/pairwisealignmentresult.py
index 035ee352..a4a8ebcd 100644
--- a/pyeed/core/pairwisealignmentresult.py
+++ b/pyeed/core/pairwisealignmentresult.py
@@ -60,7 +60,7 @@ class PairwiseAlignmentResult(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/proteinrecord.py b/pyeed/core/proteinrecord.py
index 9c59037a..630f9475 100644
--- a/pyeed/core/proteinrecord.py
+++ b/pyeed/core/proteinrecord.py
@@ -101,7 +101,7 @@ class ProteinRecord(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/region.py b/pyeed/core/region.py
index bbbb6e2f..20f91c2d 100644
--- a/pyeed/core/region.py
+++ b/pyeed/core/region.py
@@ -38,7 +38,7 @@ class Region(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/sequence.py b/pyeed/core/sequence.py
index afdfffef..3bd5f3cf 100644
--- a/pyeed/core/sequence.py
+++ b/pyeed/core/sequence.py
@@ -38,7 +38,7 @@ class Sequence(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/sequencerecord.py b/pyeed/core/sequencerecord.py
index e54cf57c..6ea84b92 100644
--- a/pyeed/core/sequencerecord.py
+++ b/pyeed/core/sequencerecord.py
@@ -62,7 +62,7 @@ class SequenceRecord(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/site.py b/pyeed/core/site.py
index 5e02ae0d..139b4699 100644
--- a/pyeed/core/site.py
+++ b/pyeed/core/site.py
@@ -35,7 +35,7 @@ class Site(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/core/standardnumbering.py b/pyeed/core/standardnumbering.py
index b3b09bed..5527bb37 100644
--- a/pyeed/core/standardnumbering.py
+++ b/pyeed/core/standardnumbering.py
@@ -47,7 +47,7 @@ class StandardNumbering(
_repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
_commit: Optional[str] = PrivateAttr(
- default="09207e10bb1bfb6e6916b6ef62932c6b08209190"
+ default="34eec88e986aa525aa9515b66d1b4d0aa46e71d3"
)
_raw_xml_data: Dict = PrivateAttr(default_factory=dict)
diff --git a/pyeed/tools/clustalo.py b/pyeed/tools/clustalo.py
index 0f890149..3eaa151c 100644
--- a/pyeed/tools/clustalo.py
+++ b/pyeed/tools/clustalo.py
@@ -4,6 +4,7 @@
import httpx
from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
+from pydantic import PrivateAttr
from pyeed.tools.abstract_tool import AbstractTool, ServiceURL
@@ -13,7 +14,7 @@ class ClustalOmega(AbstractTool):
Class for ClustalOmega aligner running as a REST service.
"""
- _service_url = ServiceURL.CLUSTALO.value
+ _service_url = PrivateAttr(ServiceURL.CLUSTALO.value)
def create_file(self, multifasta: List[str]) -> Dict[str, str]:
"""
@@ -41,8 +42,20 @@ def extract_output_data(self, response) -> MultipleSeqAlignment:
return alignment
def run_service(self, data) -> httpx.Response:
+ """Executes the ClustalOmega service."""
file = self.create_file(data)
- return httpx.post(self._service_url, files=file, timeout=600)
+ try:
+ return httpx.post(self._service_url, files=file, timeout=600)
+
+ except httpx.ConnectError as connect_error:
+ if connect_error.__context__.args[0].errno == 8:
+ self._service_url = self._service_url.replace("clustalo", "localhost")
+ try:
+ return httpx.post(self._service_url, files=file, timeout=600)
+ except httpx.ConnectError as connect_error:
+ raise httpx.ConnectError("PyEED Docker Service is not running.")
+
+ raise httpx.ConnectError("PyEED Docker Service is not running.")
def align(self, sequences: List[str]):
"""
diff --git a/pyproject.toml b/pyproject.toml
index 8f89f556..ae6d32a9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "pyeed"
-version = "0.3.0"
+version = "0.3.1"
description = "Enzyme engineering toolkit"
authors = ["haeussma <83341109+haeussma@users.noreply.github.com>"]
license = "MIT"
@@ -8,7 +8,7 @@ readme = "README.md"
packages = [{ include = "pyeed" }]
[tool.poetry.dependencies]
-python = ">=3.10,<3.12"
+python = ">=3.10,<3.13"
biopython = "^1.81"
sdrdm-database = { extras = [
"postgres",