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‎SCIE2100_Practical5/__pycache__/godata.cpython-38.pyc‎

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‎SCIE2100_Practical5/try_prac5.ipynb‎

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‎SCIE2100_Practical6/sstruct.py‎

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‎SCIE2100_Practical_Assessment_2/.ipynb_checkpoints/try_ass2-checkpoint.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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"from sequence import *\n",
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"from phylo import *"
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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": 3,
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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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"array([[0. , 1.50692857],\n",
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" [1.50692857, 0. ]])"
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]
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},
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"execution_count": 3,
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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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"eh_aln = readClustalFile('eh.aln', Protein_Alphabet)\n",
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"d = eh_aln.calcDistances('gamma', 3.25)\n",
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"d"
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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": 11,
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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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"A0A1A8AU08:0.00261\n",
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"G3PS36:0.15853\n"
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]
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}
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],
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"source": [
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"my_tree = readNewick('tyrosine_protein_kinase_fer.newick') # Read the newick file\n",
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"mynode1 = my_tree.findLabel(\"A0A1A8AU08\")\n",
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"print(mynode1) # Look at selected node after loading the tree\n",
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"mynode2 = my_tree.findLabel(\"G3PS36\")\n",
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"print(mynode2)"
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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": 25,
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"metadata": {
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"scrolled": true
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},
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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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"has-distance 0.0 from ancestor N_1O72YI\n",
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"has-distance 0.07799 from ancestor N_P3SJE1\n",
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"has-distance 0.02885 from ancestor N_6X5OCZ\n",
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"has-distance 0.13452 from ancestor N_LZTO3K\n",
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"has-distance 0.03481 from ancestor N_NN3PPW\n",
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"has-distance 0.18156 from ancestor N_73PQ48\n",
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"has-distance 0.08849 from ancestor N_IY4J2R\n",
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"has-distance 0.12177 from ancestor N_G5HCJJ\n",
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"has-distance 0.21528 from ancestor N_4RGOI5\n",
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"has-distance 0.01235 from ancestor N_HS73OU\n",
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"has-distance 0.01859 from ancestor N_KHKD4J\n",
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"has-distance 0.12479 from ancestor N_NP656I\n",
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"has-distance 0.01038 from ancestor N_A7C7F3\n",
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"has-distance 0.00261 from ancestor N_01RRZV\n"
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]
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}
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],
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"source": [
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"# print all the ancestor of the node A0A1A8AU08 with distance\n",
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"mynode1 = my_tree.findLabel(\"A0A1A8AU08\") # Get the node with the same name as the sequence\n",
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"a_node1 = my_tree.getAncestorsOf(mynode1, transitive = True) # Get the direct ancestor for the node\n",
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"for i in a_node1:\n",
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" print('has-distance', i.dist, 'from ancestor', i.label) # Print the evolutionary distance"
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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": 26,
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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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"has-distance 0.0 from ancestor N_1O72YI\n",
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"has-distance 0.07799 from ancestor N_P3SJE1\n",
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"has-distance 0.02885 from ancestor N_6X5OCZ\n",
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"has-distance 0.02773 from ancestor N_9M57YW\n",
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"has-distance 0.02666 from ancestor N_4VRM75\n",
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"has-distance 0.09947 from ancestor N_4VYY4L\n",
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"has-distance 0.0897 from ancestor N_0NESZ0\n",
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"has-distance 0.12596 from ancestor N_NMAIEZ\n",
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"has-distance 0.17501 from ancestor N_M5VDPE\n",
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"has-distance 0.03378 from ancestor N_8H3LJ6\n",
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"has-distance 0.09747 from ancestor N_5W280K\n",
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"has-distance 0.02613 from ancestor N_MY3XJW\n",
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"has-distance 0.08731 from ancestor N_6VA4CW\n"
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]
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}
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],
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"source": [
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"# print all the ancestor of the node G3PS36 with distance\n",
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"mynode2 = my_tree.findLabel(\"G3PS36\") # Get the node with the same name as the sequence\n",
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"a_node2 = my_tree.getAncestorsOf(mynode2, transitive = True) # Get the direct ancestor for the node\n",
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"for i in a_node2:\n",
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" print('has-distance', i.dist, 'from ancestor', i.label) # Print the evolutionary distance"
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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": 35,
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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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"[<phylo.PhyloNode object at 0x0000025EC4BD9C10>, <phylo.PhyloNode object at 0x0000025EC4BA5BB0>, <phylo.PhyloNode object at 0x0000025EC4BA5FD0>]\n",
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"nearest: N_6X5OCZ\n"
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]
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}
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],
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"source": [
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"# find all common ancestors\n",
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"common_ancestors = []\n",
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"for x in a_node1:\n",
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" for y in a_node2:\n",
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" if x.label == y.label:\n",
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" common_ancestors.append(x)\n",
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"print(common_ancestors)\n",
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"# find the nearest one\n",
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"nearest_dis = 100\n",
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"nearest = ''\n",
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"for i in common_ancestors:\n",
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" if i.dist < nearest_dis:\n",
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" nearest = i\n",
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"print(\"nearest: \", nearest.label)"
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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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"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": "3.8.3"
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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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