diff --git a/analysis/revision-hgt-outgroup.ipynb b/analysis/revision-hgt-outgroup.ipynb
index 0856d479a0dfb8f2d19bf6ad73ef1d9b0a428c3b..63c0689c976195fe0523ee3f0c0e882be48de001 100644
--- a/analysis/revision-hgt-outgroup.ipynb
+++ b/analysis/revision-hgt-outgroup.ipynb
@@ -10,7 +10,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "2023-01-24 16:43\n"
+ "2023-01-25 21:33\n"
]
}
],
@@ -46,10 +46,10 @@
"text": [
" % Total % Received % Xferd Average Speed Time Time Time Current\n",
" Dload Upload Total Spent Left Speed\n",
- "100 9376k 0 9376k 0 0 1607k 0 --:--:-- 0:00:05 --:--:-- 1472k\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 2390k 0 --:--:-- 0:00:02 --:--:-- 2394k\n"
+ "100 6562k 0 6562k 0 0 1575k 0 --:--:-- 0:00:04 --:--:-- 1577k0 1460k 0 --:--:-- 0:00:03 --:--:-- 1462k\n"
]
}
],
@@ -70,7 +70,7 @@
"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"
+ "mmseqs easy-search ${hgt_candidates} \"./salpingoeca.faa\" salpingoeca.m8 tmp --search-type 2 -s 7.0"
]
},
{
@@ -84,7 +84,7 @@
"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"
+ "mmseqs easy-search ${hgt_candidates} \"./monosiga.faa\" monosiga.m8 tmp --search-type 2 -s 7.0"
]
},
{
@@ -152,16 +152,50 @@
" <td>3.201000e-14</td>\n",
" <td>76</td>\n",
" </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>c97022_g1_i1_m.29482,</td>\n",
+ " <td>A9V324</td>\n",
+ " <td>0.302</td>\n",
+ " <td>135</td>\n",
+ " <td>91</td>\n",
+ " <td>0</td>\n",
+ " <td>93</td>\n",
+ " <td>224</td>\n",
+ " <td>114</td>\n",
+ " <td>248</td>\n",
+ " <td>9.888000e-05</td>\n",
+ " <td>44</td>\n",
+ " </tr>\n",
+ " <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",
+ " <td>191</td>\n",
+ " <td>0</td>\n",
+ " <td>61</td>\n",
+ " <td>315</td>\n",
+ " <td>684</td>\n",
+ " <td>933</td>\n",
+ " <td>1.727000e-04</td>\n",
+ " <td>43</td>\n",
+ " </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
- " 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",
+ " 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 "
+ "0 3.201000e-14 76 \n",
+ "1 9.888000e-05 44 \n",
+ "2 1.727000e-04 43 "
]
},
"execution_count": 5,
@@ -230,6 +264,36 @@
" <td>2.262000e-16</td>\n",
" <td>83</td>\n",
" </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>c97022_g1_i1_m.29482,</td>\n",
+ " <td>F2TZ54</td>\n",
+ " <td>0.262</td>\n",
+ " <td>260</td>\n",
+ " <td>185</td>\n",
+ " <td>0</td>\n",
+ " <td>56</td>\n",
+ " <td>315</td>\n",
+ " <td>19</td>\n",
+ " <td>270</td>\n",
+ " <td>5.263000e-07</td>\n",
+ " <td>52</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>c97022_g1_i1_m.29482,</td>\n",
+ " <td>F2UQL9</td>\n",
+ " <td>0.319</td>\n",
+ " <td>135</td>\n",
+ " <td>89</td>\n",
+ " <td>0</td>\n",
+ " <td>93</td>\n",
+ " <td>224</td>\n",
+ " <td>111</td>\n",
+ " <td>245</td>\n",
+ " <td>8.588000e-06</td>\n",
+ " <td>48</td>\n",
+ " </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
@@ -237,9 +301,13 @@
"text/plain": [
" 0 1 2 3 4 5 6 7 8 9 \\\n",
"0 c103983_g1_i1_m.71422, F2UGB0 0.253 490 354 0 63 552 159 633 \n",
+ "1 c97022_g1_i1_m.29482, F2TZ54 0.262 260 185 0 56 315 19 270 \n",
+ "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 "
+ "0 2.262000e-16 83 \n",
+ "1 5.263000e-07 52 \n",
+ "2 8.588000e-06 48 "
]
},
"execution_count": 6,