{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "19a33b01-d8d4-49de-9e05-302c14fb7c42",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2023-01-25 21:33\n"
]
}
],
"source": [
"from datetime import datetime, timezone\n",
"import pandas as pd\n",
"import pytz\n",
"\n",
"utc_dt = datetime.now(timezone.utc) # UTC time\n",
"dt = utc_dt.astimezone()\n",
"tz = pytz.timezone('Europe/Berlin')\n",
"berlin_now = datetime.now(tz)\n",
"print(f'{berlin_now:%Y-%m-%d %H:%M}')"
]
},
{
"cell_type": "markdown",
"id": "55f808fc-0a34-48d5-96b9-659d27f16f13",
"metadata": {},
"source": [
"The reviewers challenged us to look for the HGT candidates in the nearest non-metazoan outgroup, choanoflagellates. We are using _Salpingoeca rosetta_ and _Monosiga brevicollis_, two model choanoflagellates with publically available genomes."
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "c4ad4dc2-a115-4679-8947-c6ed78582bbd",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" % Total % Received % Xferd Average Speed Time Time Time Current\n",
" Dload Upload Total Spent Left Speed\n",
"100 9376k 0 9376k 0 0 789k 0 --:--:-- 0:00:11 --:--:-- 321k\n",
" % Total % Received % Xferd Average Speed Time Time Time Current\n",
" Dload Upload Total Spent Left Speed\n",
"100 6562k 0 6562k 0 0 1575k 0 --:--:-- 0:00:04 --:--:-- 1577k0 1460k 0 --:--:-- 0:00:03 --:--:-- 1462k\n"
]
}
],
"source": [
"!curl \"https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28proteome%3AUP000007799%29%29\" -o salpingoeca.faa\n",
"!curl \"https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28proteome%3AUP000001357%29%29\" -o monosiga.faa\n",
"!rm -rf tmp/"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "aae09518-9f38-4c3e-90e0-f8595589e748",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"%%bash --out salpingoeca.out --err salpingoeca.err\n",
"hgt_candidates=\"/Users/npapadop/Documents/data/coffe/hgt.pep\"\n",
"mmseqs easy-search ${hgt_candidates} \"./salpingoeca.faa\" salpingoeca.m8 tmp --search-type 2 -s 7.0"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "9f1aa456-1f6f-4523-b923-763b603b649c",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"%%bash --out monosiga.out --err monosiga.err\n",
"hgt_candidates=\"/Users/npapadop/Documents/data/coffe/hgt.pep\"\n",
"mmseqs easy-search ${hgt_candidates} \"./monosiga.faa\" monosiga.m8 tmp --search-type 2 -s 7.0"
]
},
{
"cell_type": "markdown",
"id": "80982650-856c-4b18-be0e-501b240533ab",
"metadata": {},
"source": [
"Let's have a look at the results:"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "169716b0-3ce2-4eb7-8e53-915c99ec5122",
"metadata": {},
"outputs": [
{
"data": {
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" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>c103983_g1_i1_m.71422,</td>\n",
" <td>A9V527</td>\n",
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" <td>505</td>\n",
" <td>370</td>\n",
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" <td>3.201000e-14</td>\n",
" <td>76</td>\n",
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" <tr>\n",
" <th>1</th>\n",
" <td>c97022_g1_i1_m.29482,</td>\n",
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" <td>9.888000e-05</td>\n",
" <td>44</td>\n",
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" <tr>\n",
" <th>2</th>\n",
" <td>c97022_g1_i1_m.29482,</td>\n",
" <td>A9V989</td>\n",
" <td>0.233</td>\n",
" <td>255</td>\n",
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" <td>61</td>\n",
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" <td>684</td>\n",
" <td>933</td>\n",
" <td>1.727000e-04</td>\n",
" <td>43</td>\n",
" </tr>\n",
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"</table>\n",
"</div>"
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" 0 1 2 3 4 5 6 7 8 9 \\\n",
"0 c103983_g1_i1_m.71422, A9V527 0.251 505 370 0 65 569 66 560 \n",
"1 c97022_g1_i1_m.29482, A9V324 0.302 135 91 0 93 224 114 248 \n",
"2 c97022_g1_i1_m.29482, A9V989 0.233 255 191 0 61 315 684 933 \n",
"\n",
" 10 11 \n",
"0 3.201000e-14 76 \n",
"1 9.888000e-05 44 \n",
"2 1.727000e-04 43 "
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pd.read_csv(\"monosiga.m8\", sep=\"\\t\", header=None)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "8c324422-faed-4249-89da-cb1dafeac4d1",
"metadata": {},
"outputs": [
{
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" <td>F2UGB0</td>\n",
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" <td>63</td>\n",
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" <tr>\n",
" <th>1</th>\n",
" <td>c97022_g1_i1_m.29482,</td>\n",
" <td>F2TZ54</td>\n",
" <td>0.262</td>\n",
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" 0 1 2 3 4 5 6 7 8 9 \\\n",
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"2 c97022_g1_i1_m.29482, F2UQL9 0.319 135 89 0 93 224 111 245 \n",
"\n",
" 10 11 \n",
"0 2.262000e-16 83 \n",
"1 5.263000e-07 52 \n",
"2 8.588000e-06 48 "
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pd.read_csv(\"salpingoeca.m8\", sep=\"\\t\", header=None)"
]
},
{
"cell_type": "markdown",
"id": "8184c03c-4741-4499-a346-a31f4e4ed61c",
"metadata": {},
"source": [
"In both cases the only relevant hit that is found is c103983_g1, the gene EggNOG v5.0 identifies as \"metal-dependent hydrolase - Proteobacteria\" and MorF putatively identifies as an aminohydrolase."
]
}
],
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