diff --git a/erbb_gold_standard/erbb_edges_gold_standard.txt b/erbb_gold_standard/erbb_edges_gold_standard.txt new file mode 100644 index 0000000..efa52cf --- /dev/null +++ b/erbb_gold_standard/erbb_edges_gold_standard.txt @@ -0,0 +1,237 @@ +P10398 Q02750 1.0 D +P10398 P36507 1.0 D +P04049 Q02750 1.0 D +P04049 P36507 1.0 D +P15056 Q02750 1.0 D +P15056 P36507 1.0 D +O14511 Q15303 1.0 D +Q02750 P28482 1.0 D +Q02750 P27361 1.0 D +P36507 P28482 1.0 D +P36507 P27361 1.0 D +P56975 P04626 1.0 D +P28482 P01106 1.0 D +P27361 P01106 1.0 D +P56975 Q15303 1.0 D +P28482 P19419 1.0 D +P27361 P19419 1.0 D +Q8WWG1 P04626 1.0 D +Q15303 P42229 1.0 D +Q15303 P51692 1.0 D +Q8WWG1 Q15303 1.0 D +P62993 Q13480 1.0 D +P04626 P19174 1.0 D +P04626 P16885 1.0 D +Q13480 P42336 1.0 D +Q13480 P42338 1.0 D +Q13480 O00329 1.0 D +Q13480 P27986 1.0 D +Q13480 O00459 1.0 D +Q13480 Q92569 1.0 D +P04626 P22681 1.0 D +P04626 Q13191 1.0 D +Q9Y243 P42345 1.0 D +P31749 P42345 1.0 D +P31751 P42345 1.0 D +P04626 P42229 1.0 D 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+hsa:994 up:Q6MZW8 equivalent +hsa:9940 up:Q9Y238 equivalent +hsa:9941 up:Q9Y2C4 equivalent +hsa:9942 up:O75191 equivalent +hsa:9943 up:O95747 equivalent +hsa:9945 up:A0A0S2Z4X9 equivalent +hsa:9945 up:B3KMR8 equivalent +hsa:9945 up:O94808 equivalent +hsa:9946 up:O95825 equivalent +hsa:9947 up:O60732 equivalent +hsa:9948 up:O75083 equivalent +hsa:9948 up:V9HWG7 equivalent +hsa:9949 up:A0A0S2Z4X0 equivalent +hsa:9949 up:Q9Y4X0 equivalent +hsa:995 up:P30307 equivalent +hsa:9950 up:Q8TBA6 equivalent +hsa:9951 up:Q9Y661 equivalent +hsa:9953 up:Q9Y662 equivalent +hsa:9955 up:Q9Y663 equivalent +hsa:9956 up:Q9Y278 equivalent +hsa:9957 up:O14792 equivalent +hsa:9958 up:Q9Y4E8 equivalent +hsa:996 up:P30260 equivalent +hsa:9960 up:Q9Y6I4 equivalent +hsa:9961 up:Q14764 equivalent +hsa:9961 up:X5D2M8 equivalent +hsa:9962 up:A0A140VK48 equivalent +hsa:9962 up:Q9UGH3 equivalent +hsa:9963 up:Q9UHI7 equivalent +hsa:9965 up:A0A7U3L4E7 equivalent +hsa:9965 up:O95750 equivalent +hsa:9966 up:A0A0U5JA19 equivalent +hsa:9966 up:O95150 equivalent +hsa:9967 up:Q9Y2W1 equivalent +hsa:9968 up:Q93074 equivalent +hsa:9969 up:Q9UHV7 equivalent +hsa:997 up:P49427 equivalent +hsa:9970 up:Q14994 equivalent +hsa:9971 up:Q96RI1 equivalent +hsa:9972 up:P49790 equivalent +hsa:9973 up:O14618 equivalent +hsa:9975 up:F1D8P2 equivalent +hsa:9975 up:Q14995 equivalent +hsa:9976 up:Q92478 equivalent +hsa:9978 up:P62877 equivalent +hsa:998 up:P60953 equivalent +hsa:9980 up:Q9Y3R5 equivalent +hsa:9982 up:Q14512 equivalent +hsa:9984 up:Q96FV9 equivalent +hsa:9985 up:O95072 equivalent +hsa:9986 up:Q0P5W4 equivalent +hsa:9986 up:Q9Y256 equivalent +hsa:9987 up:O14979 equivalent +hsa:9988 up:B3KMJ8 equivalent +hsa:9988 up:Q9Y222 equivalent +hsa:9989 up:Q8TF05 equivalent +hsa:999 up:A0A0U2ZQU7 equivalent +hsa:999 up:B3GN61 equivalent +hsa:999 up:P12830 equivalent +hsa:9990 up:Q9UHW9 equivalent +hsa:9991 up:O95758 equivalent +hsa:9992 up:Q9Y6J6 equivalent +hsa:9993 up:P98153 equivalent +hsa:9993 up:Q8IWC8 equivalent +hsa:9994 up:Q9UKL3 equivalent +hsa:9997 up:O43819 equivalent diff --git a/erbb_gold_standard/parse_kegg_egfr.ipynb b/erbb_gold_standard/parse_kegg_egfr.ipynb new file mode 100644 index 0000000..4a53287 --- /dev/null +++ b/erbb_gold_standard/parse_kegg_egfr.ipynb @@ -0,0 +1,1613 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "from Bio.KEGG.KGML.KGML_parser import read, parse\n", + "import pandas as pd\n", + "import requests\n", + "import itertools" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Load KEGG xml file**" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Pathway: ErbB signaling pathway\n", + "KEGG ID: path:hsa04012\n", + "Image file: https://www.kegg.jp/kegg/pathway/hsa/hsa04012.png\n", + "Organism: hsa\n", + "Entries: 80\n", + "Entry types:\n", + "\tgene: 60\n", + "\tgroup: 6\n", + "\tcompound: 4\n", + "\tmap: 10\n", + "\n" + ] + } + ], + "source": [ + "pathway = read(open(\"hiv_raw_data/hsa04012.xml\", 'r'))\n", + "print(pathway)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Function to extract relations (i.e. edges) from KGML file**" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "def extract_relations(kgml_file):\n", + "\n", + " with open(kgml_file, 'r') as f:\n", + " pathway = read(f)\n", + "\n", + " relations_data = []\n", + "\n", + " # iterate over all relations in the pathway\n", + " for relation in pathway.relations:\n", + " entry1 = relation.entry1.id\n", + " entry2 = relation.entry2.id\n", + " relation_type = relation.type # Type of interaction (e.g., PPrel, GErel, etc.)\n", + "\n", + " relations_data.append((entry1, entry2, relation_type))\n", + "\n", + " return relations_data" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Parse KGML file to extract relations**" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "85\n" + ] + } + ], + "source": [ + "kgml_file_path = \"hiv_raw_data/hsa04012.xml\" \n", + "relations = extract_relations(kgml_file_path)\n", + "\n", + "# for node1, node2, rel_type in relations:\n", + "# print(f\"Relation: Node1={node1}, Node2={node2}, Type={rel_type}\")\n", + "\n", + "print(len(relations))" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
Node1Node2RelationType
07877PPrel
14510PPrel
27776PPrel
344178PPrel
47671PPrel
\n", + "
" + ], + "text/plain": [ + " Node1 Node2 RelationType\n", + "0 78 77 PPrel\n", + "1 45 10 PPrel\n", + "2 77 76 PPrel\n", + "3 44 178 PPrel\n", + "4 76 71 PPrel" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "relations_df = pd.DataFrame(relations, columns=['Node1', 'Node2', 'RelationType'])\n", + "relations_df.head()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Get entries i.e. nodes from KGML file**" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "80" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "entries_data = []\n", + "for entry in pathway.entries.values():\n", + " entries_data.append({\n", + " 'id': entry.id,\n", + " 'name': entry.name,\n", + " 'type': entry.type,\n", + " 'link': entry.link,\n", + " 'reaction': entry.reaction,\n", + " })\n", + "entries_df = pd.DataFrame(entries_data)\n", + "len(entries_df)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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idnametypelinkreaction
07path:hsa05223maphttps://www.kegg.jp/dbget-bin/www_bget?hsa05223
18hsa:2885genehttps://www.kegg.jp/dbget-bin/www_bget?hsa:2885
29hsa:2002genehttps://www.kegg.jp/dbget-bin/www_bget?hsa:2002
310hsa:2066genehttps://www.kegg.jp/dbget-bin/www_bget?hsa:2066
411hsa:2066genehttps://www.kegg.jp/dbget-bin/www_bget?hsa:2066
\n", + "
" + ], + "text/plain": [ + " id name type link \\\n", + "0 7 path:hsa05223 map https://www.kegg.jp/dbget-bin/www_bget?hsa05223 \n", + "1 8 hsa:2885 gene https://www.kegg.jp/dbget-bin/www_bget?hsa:2885 \n", + "2 9 hsa:2002 gene https://www.kegg.jp/dbget-bin/www_bget?hsa:2002 \n", + "3 10 hsa:2066 gene https://www.kegg.jp/dbget-bin/www_bget?hsa:2066 \n", + "4 11 hsa:2066 gene https://www.kegg.jp/dbget-bin/www_bget?hsa:2066 \n", + "\n", + " reaction \n", + "0 \n", + "1 \n", + "2 \n", + "3 \n", + "4 " + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "entries_df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'compound', 'gene', 'group', 'map'}" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "set(entries_df['type'])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Map the entry IDs in the relations to NodeIDs**" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
Node1Node2RelationTypeNode1_Name
07877PPrelhsa:369 hsa:5894 hsa:673
14510PPrelhsa:9542
27776PPrelhsa:5604 hsa:5605
344178PPrelhsa:10718
47671PPrelhsa:5594 hsa:5595
\n", + "
" + ], + "text/plain": [ + " Node1 Node2 RelationType Node1_Name\n", + "0 78 77 PPrel hsa:369 hsa:5894 hsa:673\n", + "1 45 10 PPrel hsa:9542\n", + "2 77 76 PPrel hsa:5604 hsa:5605\n", + "3 44 178 PPrel hsa:10718\n", + "4 76 71 PPrel hsa:5594 hsa:5595" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# replace Node1 with Name\n", + "relations_df = relations_df.merge(entries_df[['id', 'name']], left_on='Node1', right_on='id', how='left').drop(columns=['id'])\n", + "relations_df.rename(columns={'name': 'Node1_Name'}, inplace=True)\n", + "relations_df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
Node1Node2RelationTypeNode1_NameNode2_Name
07877PPrelhsa:369 hsa:5894 hsa:673hsa:5604 hsa:5605
14510PPrelhsa:9542hsa:2066
27776PPrelhsa:5604 hsa:5605hsa:5594 hsa:5595
344178PPrelhsa:10718undefined
47671PPrelhsa:5594 hsa:5595hsa:4609
\n", + "
" + ], + "text/plain": [ + " Node1 Node2 RelationType Node1_Name Node2_Name\n", + "0 78 77 PPrel hsa:369 hsa:5894 hsa:673 hsa:5604 hsa:5605\n", + "1 45 10 PPrel hsa:9542 hsa:2066\n", + "2 77 76 PPrel hsa:5604 hsa:5605 hsa:5594 hsa:5595\n", + "3 44 178 PPrel hsa:10718 undefined\n", + "4 76 71 PPrel hsa:5594 hsa:5595 hsa:4609" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# replace Node2 with Name\n", + "relations_df = relations_df.merge(entries_df[['id', 'name']], left_on='Node2', right_on='id', how='left').drop(columns=['id'])\n", + "relations_df.rename(columns={'name': 'Node2_Name'}, inplace=True)\n", + "relations_df.head()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Replace all `undefined` with ErbB-2 ID**" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [], + "source": [ + "relations_df = relations_df.replace('undefined', 'hsa:2064', regex=True)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Get cartesian product of all proteins in each ro - i.e. get all pairs**" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "85\n" + ] + }, + { + "data": { + "text/html": [ + "
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0123456
0hsa:369hsa:5894hsa:673NoneNoneNoneNone
1hsa:9542NoneNoneNoneNoneNoneNone
2hsa:5604hsa:5605NoneNoneNoneNoneNone
3hsa:10718NoneNoneNoneNoneNoneNone
4hsa:5594hsa:5595NoneNoneNoneNoneNone
\n", + "
" + ], + "text/plain": [ + " 0 1 2 3 4 5 6\n", + "0 hsa:369 hsa:5894 hsa:673 None None None None\n", + "1 hsa:9542 None None None None None None\n", + "2 hsa:5604 hsa:5605 None None None None None\n", + "3 hsa:10718 None None None None None None\n", + "4 hsa:5594 hsa:5595 None None None None None" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "split_node1_df = relations_df['Node1_Name'].str.split(' ', expand=True)\n", + "print(len(split_node1_df))\n", + "split_node1_df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "85\n" + ] + }, + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
0123456
0hsa:5604hsa:5605NoneNoneNoneNoneNone
1hsa:2066NoneNoneNoneNoneNoneNone
2hsa:5594hsa:5595NoneNoneNoneNoneNone
3hsa:2064NoneNoneNoneNoneNoneNone
4hsa:4609NoneNoneNoneNoneNoneNone
\n", + "
" + ], + "text/plain": [ + " 0 1 2 3 4 5 6\n", + "0 hsa:5604 hsa:5605 None None None None None\n", + "1 hsa:2066 None None None None None None\n", + "2 hsa:5594 hsa:5595 None None None None None\n", + "3 hsa:2064 None None None None None None\n", + "4 hsa:4609 None None None None None None" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "split_node2_df = relations_df['Node2_Name'].str.split(' ', expand=True)\n", + "print(len(split_node2_df))\n", + "split_node2_df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "def cartesian_product_rows(df1, df2):\n", + " result = []\n", + " for row1, row2 in zip(df1.values, df2.values):\n", + " # remove None vals\n", + " values1 = [x for x in row1 if x is not None]\n", + " values2 = [x for x in row2 if x is not None]\n", + " \n", + " # get the cartesian prod\n", + " for pair in itertools.product(values1, values2):\n", + " result.append(pair)\n", + " \n", + " return pd.DataFrame(result)" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
Node1Node2
0hsa:369hsa:5604
1hsa:369hsa:5605
2hsa:5894hsa:5604
3hsa:5894hsa:5605
4hsa:673hsa:5604
\n", + "
" + ], + "text/plain": [ + " Node1 Node2\n", + "0 hsa:369 hsa:5604\n", + "1 hsa:369 hsa:5605\n", + "2 hsa:5894 hsa:5604\n", + "3 hsa:5894 hsa:5605\n", + "4 hsa:673 hsa:5604" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "all_reaction_pairs = cartesian_product_rows(df1=split_node1_df, df2=split_node2_df)\n", + "all_reaction_pairs.columns = ['Node1', 'Node2']\n", + "all_reaction_pairs.head()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**ID Mapping using LinkDB + keep only SwissProt reviewed proteins**" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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HSAUniprotlink_category
0hsa:1up:P04217equivalent
1hsa:1up:V9HWD8equivalent
2hsa:10up:A4Z6T7equivalent
3hsa:10up:P11245equivalent
4hsa:100up:A0A0S2Z381equivalent
\n", + "
" + ], + "text/plain": [ + " HSA Uniprot link_category\n", + "0 hsa:1 up:P04217 equivalent\n", + "1 hsa:1 up:V9HWD8 equivalent\n", + "2 hsa:10 up:A4Z6T7 equivalent\n", + "3 hsa:10 up:P11245 equivalent\n", + "4 hsa:100 up:A0A0S2Z381 equivalent" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "hsa_uniprot_df = pd.read_csv(\"hiv_raw_data/hsa_uniprot_03122025.list\", sep='\\t', header=None)\n", + "hsa_uniprot_df.columns = ['HSA','Uniprot','link_category']\n", + "hsa_uniprot_df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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Node1Node2Node1_Uniprot
0hsa:369hsa:5604up:A0A024R178
1hsa:369hsa:5604up:P10398
2hsa:369hsa:5605up:A0A024R178
3hsa:369hsa:5605up:P10398
4hsa:5894hsa:5604up:L7RRS6
\n", + "
" + ], + "text/plain": [ + " Node1 Node2 Node1_Uniprot\n", + "0 hsa:369 hsa:5604 up:A0A024R178\n", + "1 hsa:369 hsa:5604 up:P10398\n", + "2 hsa:369 hsa:5605 up:A0A024R178\n", + "3 hsa:369 hsa:5605 up:P10398\n", + "4 hsa:5894 hsa:5604 up:L7RRS6" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# replace Node1 with UniprotID\n", + "all_reaction_pairs = all_reaction_pairs.merge(hsa_uniprot_df[['HSA', 'Uniprot']], left_on='Node1', right_on='HSA', how='left').drop(columns=['HSA'])\n", + "all_reaction_pairs.rename(columns={'Uniprot': 'Node1_Uniprot'}, inplace=True)\n", + "all_reaction_pairs.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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Node1Node2Node1_UniprotNode2_Uniprot
0hsa:369hsa:5604up:A0A024R178up:A4QPA9
1hsa:369hsa:5604up:A0A024R178up:Q02750
2hsa:369hsa:5604up:P10398up:A4QPA9
3hsa:369hsa:5604up:P10398up:Q02750
4hsa:369hsa:5605up:A0A024R178up:P36507
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" + ], + "text/plain": [ + " Node1 Node2 Node1_Uniprot Node2_Uniprot\n", + "0 hsa:369 hsa:5604 up:A0A024R178 up:A4QPA9\n", + "1 hsa:369 hsa:5604 up:A0A024R178 up:Q02750\n", + "2 hsa:369 hsa:5604 up:P10398 up:A4QPA9\n", + "3 hsa:369 hsa:5604 up:P10398 up:Q02750\n", + "4 hsa:369 hsa:5605 up:A0A024R178 up:P36507" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# replace Node1 with UniprotID\n", + "all_reaction_pairs = all_reaction_pairs.merge(hsa_uniprot_df[['HSA', 'Uniprot']], left_on='Node2', right_on='HSA', how='left').drop(columns=['HSA'])\n", + "all_reaction_pairs.rename(columns={'Uniprot': 'Node2_Uniprot'}, inplace=True)\n", + "all_reaction_pairs.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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Node1_UniprotNode2_Uniprot
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" + ], + "text/plain": [ + " Node1_Uniprot Node2_Uniprot\n", + "0 up:A0A024R178 up:A4QPA9\n", + "1 up:A0A024R178 up:Q02750\n", + "2 up:P10398 up:A4QPA9\n", + "3 up:P10398 up:Q02750\n", + "4 up:A0A024R178 up:P36507" + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "all_reaction_pairs_uniprot = all_reaction_pairs.drop(columns=['Node1', 'Node2'])\n", + "all_reaction_pairs_uniprot.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\sumed\\AppData\\Local\\Temp\\ipykernel_21620\\578247303.py:2: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " all_reaction_pairs_uniprot = all_reaction_pairs_uniprot.applymap(lambda x: x.replace(\"up:\", \"\") if isinstance(x, str) else x)\n" + ] + }, + { + "data": { + "text/html": [ + "
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Node1_UniprotNode2_Uniprot
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" + ], + "text/plain": [ + " Node1_Uniprot Node2_Uniprot\n", + "0 A0A024R178 A4QPA9\n", + "1 A0A024R178 Q02750\n", + "2 P10398 A4QPA9\n", + "3 P10398 Q02750\n", + "4 A0A024R178 P36507" + ] + }, + "execution_count": 25, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Remove 'up:' from all strings excluding NaN\n", + "all_reaction_pairs_uniprot = all_reaction_pairs_uniprot.applymap(lambda x: x.replace(\"up:\", \"\") if isinstance(x, str) else x)\n", + "all_reaction_pairs_uniprot.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [], + "source": [ + "def filter_dataframe(df):\n", + " base_url = \"https://www.genome.jp/entry/sp:\"\n", + " # list to keep track of rows to keep\n", + " rows_to_keep = []\n", + " df = df.dropna()\n", + " for index, row in df.iterrows():\n", + " n1_uniprot = row['Node1_Uniprot']\n", + " n2_uniprot = row['Node2_Uniprot']\n", + " url_n1 = f\"{base_url}{n1_uniprot}\"\n", + " response_n1 = requests.get(url_n1)\n", + " url_n2 = f\"{base_url}{n2_uniprot}\"\n", + " response_n2 = requests.get(url_n2)\n", + " if \"No such data was found.\" not in response_n1.text and \"No such data was found.\" not in response_n2.text:\n", + " rows_to_keep.append(index)\n", + " # print(df.loc[index])\n", + " # filter the DataFrame to keep only the desired rows\n", + " filtered_df = df.loc[rows_to_keep].reset_index(drop=True)\n", + " return filtered_df" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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Node1_UniprotNode2_Uniprot
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" + ], + "text/plain": [ + " Node1_Uniprot Node2_Uniprot\n", + "0 P10398 Q02750\n", + "1 P10398 P36507\n", + "2 P04049 Q02750\n", + "3 P04049 P36507\n", + "4 P15056 Q02750" + ] + }, + "execution_count": 27, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "copy = all_reaction_pairs_uniprot.copy()\n", + "all_reaction_pairs_swissprot = filter_dataframe(copy)\n", + "all_reaction_pairs_swissprot.head()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Add directionality and edge weights**" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [], + "source": [ + "directionality = 'D'\n", + "edge_weight = 1.0" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "all_reaction_pairs_swissprot['Prize'] = edge_weight\n", + "all_reaction_pairs_swissprot['Directionality'] = directionality" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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Node1_UniprotNode2_UniprotDirectionalityPrize
0P10398Q02750D1.0
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" + ], + "text/plain": [ + " Node1_Uniprot Node2_Uniprot Directionality Prize\n", + "0 P10398 Q02750 D 1.0\n", + "1 P10398 P36507 D 1.0\n", + "2 P04049 Q02750 D 1.0\n", + "3 P04049 P36507 D 1.0\n", + "4 P15056 Q02750 D 1.0" + ] + }, + "execution_count": 30, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "all_reaction_pairs_swissprot.head()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Save file**" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [], + "source": [ + "all_reaction_pairs_swissprot.to_csv('erbb_edges_gold_standard.txt',sep='\\t',header=None, index=False)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "base", + "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": "3.11.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/hiv-benchmarking/build_protein_dummy_prize_file.ipynb b/hiv-benchmarking/build_protein_dummy_prize_file.ipynb new file mode 100644 index 0000000..306244e --- /dev/null +++ b/hiv-benchmarking/build_protein_dummy_prize_file.ipynb @@ -0,0 +1,504 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import numpy as np" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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NODEIDprize
0B0YIW2_HUMAN5.029366
1HTF4_HUMAN4.582688
2FETUA_HUMAN4.027456
3HBA_HUMAN3.955817
4KCRM_HUMAN3.885428
.........
1118AXIN1_HUMAN1.005809
1119RTN4_HUMAN1.005192
1120J3KR72_HUMAN1.003755
1121PARP6_HUMAN1.003196
1122T184C_HUMAN1.002288
\n", + "

1123 rows × 2 columns

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" + ], + "text/plain": [ + " NODEID prize\n", + "0 B0YIW2_HUMAN 5.029366\n", + "1 HTF4_HUMAN 4.582688\n", + "2 FETUA_HUMAN 4.027456\n", + "3 HBA_HUMAN 3.955817\n", + "4 KCRM_HUMAN 3.885428\n", + "... ... ...\n", + "1118 AXIN1_HUMAN 1.005809\n", + "1119 RTN4_HUMAN 1.005192\n", + "1120 J3KR72_HUMAN 1.003755\n", + "1121 PARP6_HUMAN 1.003196\n", + "1122 T184C_HUMAN 1.002288\n", + "\n", + "[1123 rows x 2 columns]" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "modified_prize_05 = pd.read_csv('hiv_processed_data/modified_prize_05.txt', sep='\\t')\n", + "modified_prize_05" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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NODEID
0CGT_HUMAN
1ACHA_HUMAN
2ACHB_HUMAN
3A1AG1_HUMAN
4A1AG2_HUMAN
\n", + "
" + ], + "text/plain": [ + " NODEID\n", + "0 CGT_HUMAN\n", + "1 ACHA_HUMAN\n", + "2 ACHB_HUMAN\n", + "3 A1AG1_HUMAN\n", + "4 A1AG2_HUMAN" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "human_dummy_nodes = pd.read_csv('hiv_processed_data/human_dummy_proteins_uniprotkb.txt', header=None)\n", + "human_dummy_nodes.rename(columns={0:'NODEID'}, inplace=True)\n", + "human_dummy_nodes.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "1.8057502788094812" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "prizes_list = modified_prize_05['prize']\n", + "prizes_mean = prizes_list.mean()\n", + "prizes_mean" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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NODEIDprize
0CGT_HUMAN1.80575
1ACHA_HUMAN1.80575
2ACHB_HUMAN1.80575
3A1AG1_HUMAN1.80575
4A1AG2_HUMAN1.80575
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" + ], + "text/plain": [ + " NODEID prize\n", + "0 CGT_HUMAN 1.80575\n", + "1 ACHA_HUMAN 1.80575\n", + "2 ACHB_HUMAN 1.80575\n", + "3 A1AG1_HUMAN 1.80575\n", + "4 A1AG2_HUMAN 1.80575" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "human_dummy_nodes['prize']=prizes_mean\n", + "human_dummy_nodes.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['LSM12_HUMAN', 'MK14_HUMAN', 'CAF1A_HUMAN', 'CH60_HUMAN', 'DCAF1_HUMAN', 'COF1_HUMAN', 'STML2_HUMAN', 'VTNC_HUMAN', 'ARHG1_HUMAN', 'CO9_HUMAN', 'PML_HUMAN', 'P53_HUMAN', 'EPN1_HUMAN', 'PLIN3_HUMAN', 'SEC62_HUMAN', 'ANT3_HUMAN', 'ZAP70_HUMAN', 'KAPCB_HUMAN', 'TBB4A_HUMAN', 'TBA1B_HUMAN', 'ALBU_HUMAN', 'CD3E_HUMAN', 'PSD11_HUMAN', 'TSP1_HUMAN', 'ACTB_HUMAN', 'TRFL_HUMAN', 'EVL_HUMAN', 'CO3_HUMAN', 'LCK_HUMAN', 'RAF1_HUMAN', 'LEUK_HUMAN', 'HS105_HUMAN', 'PHB2_HUMAN']\n" + ] + }, + { + "data": { + "text/plain": [ + "33" + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "intersection = list(set(list(modified_prize_05['NODEID'])) & set(list(human_dummy_nodes['NODEID'])))\n", + "print(intersection)\n", + "len(intersection)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Merge dataframes on NODEID, using outer join to include all unique NODEIDs\n", + "merged_df = pd.merge(modified_prize_05, human_dummy_nodes, on=\"NODEID\", how=\"outer\", suffixes=('_og', '_dummy'))\n", + "# Calculate the max prize for each NODEID, filling NaN values with available data\n", + "merged_df['prize'] = merged_df[['prize_og', 'prize_dummy']].max(axis=1)\n", + "# Drop the old prize columns from both dataframes\n", + "merged_df = merged_df[['NODEID', 'prize']]" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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NODEIDprize
0B0YIW2_HUMAN5.029366
1HTF4_HUMAN4.582688
2FETUA_HUMAN4.027456
3HBA_HUMAN3.955817
4KCRM_HUMAN3.885428
.........
1546K2013_HUMAN1.805750
1547HACD3_HUMAN1.805750
1548VTI1A_HUMAN1.805750
1549VAPA_HUMAN1.805750
1550VDAC3_HUMAN1.805750
\n", + "

1551 rows × 2 columns

\n", + "
" + ], + "text/plain": [ + " NODEID prize\n", + "0 B0YIW2_HUMAN 5.029366\n", + "1 HTF4_HUMAN 4.582688\n", + "2 FETUA_HUMAN 4.027456\n", + "3 HBA_HUMAN 3.955817\n", + "4 KCRM_HUMAN 3.885428\n", + "... ... ...\n", + "1546 K2013_HUMAN 1.805750\n", + "1547 HACD3_HUMAN 1.805750\n", + "1548 VTI1A_HUMAN 1.805750\n", + "1549 VAPA_HUMAN 1.805750\n", + "1550 VDAC3_HUMAN 1.805750\n", + "\n", + "[1551 rows x 2 columns]" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "merged_df" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [], + "source": [ + "merged_df.to_csv(\"hiv_processed_data/modified_prize_dummy_05.txt\", index=False, sep='\\t')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "base", + "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": "3.11.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/hiv-benchmarking/hiv_processed_data/modified_prize_dummy_05.txt b/hiv-benchmarking/hiv_processed_data/modified_prize_dummy_05.txt new file mode 100644 index 0000000..f12707e --- /dev/null +++ b/hiv-benchmarking/hiv_processed_data/modified_prize_dummy_05.txt @@ -0,0 +1,1552 @@ +NODEID prize +B0YIW2_HUMAN 5.029365599650682 +HTF4_HUMAN 4.582688156260696 +FETUA_HUMAN 4.027455886706566 +HBA_HUMAN 3.955817065609741 +KCRM_HUMAN 3.885427876677981 +B7ZKJ8_HUMAN 3.885427876677981 +H4_HUMAN 3.885427876677981 +FBLN1_HUMAN 3.885427876677981 +H3BLZ8_HUMAN 3.737659276683696 +MMTA2_HUMAN 3.645611351503717 +CL16A_HUMAN 3.645611351503717 +ALBU_HUMAN 3.495543593199523 +UBAC2_HUMAN 3.4400540448812222 +H37_HUMAN 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