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Merge branch 'main' of https://github.com/ModelSEED/ModelSEEDpy into main
# Conflicts: # modelseedpy/__init__.py # modelseedpy/core/__init__.py
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‎.gitignore

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# Jupyter Notebook
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.ipynb_checkpoints
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.idea
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# IPython
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profile_default/

‎examples/GCF_000005845.2_ASM584v2_protein.faa

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‎examples/Genomes.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"import modelseedpy\n",
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"from modelseedpy.core.msgenome import MSGenome\n",
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"from modelseedpy.core.rast_client import RastClient"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
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"rast = RastClient()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [],
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"source": [
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"genome = MSGenome.from_fasta('GCF_000005845.2_ASM584v2_protein.faa', split=' ')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Number of features: 4284\n"
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]
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}
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],
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"source": [
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"print('Number of features:', len(genome.features))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"[{'execution_time': 1622756127.36331,\n",
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" 'tool_name': 'kmer_search',\n",
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" 'hostname': 'pear',\n",
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" 'parameters': ['-a',\n",
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" '-g',\n",
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" 200,\n",
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" '-m',\n",
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" 5,\n",
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" '-d',\n",
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" '/opt/patric-common/data/kmer_metadata_v2',\n",
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" '-u',\n",
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" 'http://pear.mcs.anl.gov:6100/query'],\n",
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" 'id': '9CCA6D20-C4B3-11EB-A893-36A8BEF382BD'},\n",
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" {'parameters': ['annotate_hypothetical_only=1',\n",
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" 'dataset_name=Release70',\n",
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" 'kmer_size=8'],\n",
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" 'hostname': 'pear',\n",
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" 'tool_name': 'KmerAnnotationByFigfam',\n",
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" 'id': '9CE3769E-C4B3-11EB-A893-36A8BEF382BD',\n",
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" 'execution_time': 1622756127.52738},\n",
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" {'execute_time': 1622756127.88296,\n",
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" 'hostname': 'pear',\n",
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" 'parameters': [],\n",
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" 'tool_name': 'annotate_proteins_similarity',\n",
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" 'id': '9D19B7EA-C4B3-11EB-9714-71B3BDF382BD'}]"
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]
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},
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"execution_count": 14,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"rast.annotate_genome(genome)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"### Equivalent call from the client it self"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 15,
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"metadata": {},
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"outputs": [],
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"source": [
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"#genome, res = rast.annotate_genome_from_fasta('GCF_000005845.2_ASM584v2_protein.faa', split=' ')\n",
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"#res"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": 22,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": 34,
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"metadata": {},
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"outputs": [],
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"source": [
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"feature = genome.features.get_by_id('YP_588478.1')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 36,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"{'RAST': 'DUF1435 domain-containing protein YjjZ [Escherichia coli str. K-12 substr. MG1655]'}"
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]
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},
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"execution_count": 36,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"feature.ontology_terms"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"feature.add_ontology_term('')"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

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