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7f. KOG comparisons.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"kernel": "Python3"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Index(['MM_Percentage', 'XT_Percentage', 'DR_Percentage', 'LS_Percentage',\n",
" 'DM_Percentage', 'CE_Percentage', 'Category'],\n",
" dtype='object')\n"
]
}
],
"source": [
"import pandas as pd\n",
"import os\n",
"os.chdir(\"/home/zhanglab1/ndong/Lymnaea_CNS_transcriptome_files/7_Interspecies_comparison/7f_KOG_comparisons\")\n",
"\n",
"data = None\n",
"filelist = [\"MM_KOG_summary.txt\", \"XT_KOG_summary.txt\", \"DR_KOG_summary.txt\", \"LS_KOG_summary.txt\", \"DM_KOG_summary.txt\", \"CE_KOG_summary.txt\"]\n",
"for f in filelist:\n",
" if data is None:\n",
" data = pd.read_csv(f, sep='\\t', index_col='KOG')\n",
" else:\n",
" data = data.join(pd.read_csv(f, sep='\\t', index_col='KOG'))\n",
" \n",
"data[\"Category\"] = [\"A\", \"B\", \"C\", \"D\", \"E\", \"F\", \"G\", \"H\", \"I\", \"J\", \"K\", \"L\", \"M\", \"N\", \"O\", \"P\", \"Q\", \"R\", \"S\", \"T\", \"U\", \"V\", \"W\", \"Y\", \"Z\"]\n",
"\n",
"print(data.columns)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"kernel": "R"
},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>MM_Percentage</th><th scope=col>XT_Percentage</th><th scope=col>DR_Percentage</th><th scope=col>LS_Percentage</th><th scope=col>DM_Percentage</th><th scope=col>CE_Percentage</th><th scope=col>Category</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>RNA processing and modification</th><td> 3.6242961</td><td> 3.3408356</td><td> 3.1163875</td><td> 3.1594416</td><td> 3.9281110</td><td> 3.6816505</td><td>A </td></tr>\n",
"\t<tr><th scope=row>Chromatin structure and dynamics</th><td> 1.7940467</td><td> 1.5262344</td><td> 1.5016607</td><td> 1.6327863</td><td> 1.7365587</td><td> 1.8617913</td><td>B </td></tr>\n",
"\t<tr><th scope=row>Energy production and conversion</th><td> 2.0353982</td><td> 1.9623013</td><td> 2.0033920</td><td> 2.3348845</td><td> 3.3972852</td><td> 3.2371687</td><td>C </td></tr>\n",
"\t<tr><th scope=row>Cell cycle control</th><td> 2.5905068</td><td> 2.6375018</td><td> 2.4273903</td><td> 2.9390154</td><td> 2.2143020</td><td> 2.6165716</td><td>D </td></tr>\n",
"\t<tr><th scope=row>Amino acid transport and metabolism</th><td> 1.9951730</td><td> 2.0818681</td><td> 2.1376581</td><td> 2.8737040</td><td> 3.2987033</td><td> 2.4572291</td><td>E </td></tr>\n",
"\t<tr><th scope=row>Nucleotide transport and metabolism</th><td> 1.0257442</td><td> 1.1323674</td><td> 1.0105293</td><td> 1.0858029</td><td> 1.1223174</td><td> 0.9141228</td><td>F </td></tr>\n",
"\t<tr><th scope=row>Carbohydrate transport and metabolism</th><td> 2.1520515</td><td> 2.5320017</td><td> 2.3885238</td><td> 3.1594416</td><td> 3.1546220</td><td> 3.1197585</td><td>G </td></tr>\n",
"\t<tr><th scope=row>Coenzyme transport and metabolism</th><td> 0.6315366</td><td> 0.6259671</td><td> 0.5829977</td><td> 0.8408850</td><td> 0.8569045</td><td> 0.6205971</td><td>H </td></tr>\n",
"\t<tr><th scope=row>Lipid transport and metabolism</th><td> 2.8238134</td><td> 2.9469686</td><td> 2.5828563</td><td> 3.0696383</td><td> 3.5413665</td><td> 3.6564911</td><td>I </td></tr>\n",
"\t<tr><th scope=row>Translation, ribosomal structure and biogenesis</th><td> 2.9283990</td><td> 3.0102687</td><td> 2.4415236</td><td> 3.1920973</td><td> 4.0115265</td><td> 4.1932238</td><td>J </td></tr>\n",
"\t<tr><th scope=row>Transcription</th><td>10.0965406</td><td> 8.6791391</td><td>10.9356229</td><td> 8.1802596</td><td> 8.2278001</td><td> 8.0845354</td><td>K </td></tr>\n",
"\t<tr><th scope=row>Replication, recombination and repair</th><td> 1.5607401</td><td> 1.9552680</td><td> 1.5475938</td><td> 2.3348845</td><td> 1.7517252</td><td> 2.0966119</td><td>L </td></tr>\n",
"\t<tr><th scope=row>Cell wall/membrane/envelope biogenesis</th><td> 1.0418343</td><td> 1.1534674</td><td> 0.9822627</td><td> 2.1144583</td><td> 1.0844013</td><td> 0.7631667</td><td>M </td></tr>\n",
"\t<tr><th scope=row>Cell motility</th><td> 0.2131939</td><td> 0.1969335</td><td> 0.2261324</td><td> 0.1714426</td><td> 0.1819974</td><td> 0.1425696</td><td>N </td></tr>\n",
"\t<tr><th scope=row>Posttranslational modification</th><td> 7.6548673</td><td> 8.0531720</td><td> 7.1938379</td><td> 8.1149482</td><td> 7.8638053</td><td> 8.5625629</td><td>O </td></tr>\n",
"\t<tr><th scope=row>Inorganic ion transport and metabolism</th><td> 2.5905068</td><td> 2.9469686</td><td> 2.8584552</td><td> 2.5798024</td><td> 2.9119587</td><td> 3.5642402</td><td>P </td></tr>\n",
"\t<tr><th scope=row>Secondary metabolites</th><td> 0.7079646</td><td> 1.2519342</td><td> 1.0281959</td><td> 1.7144257</td><td> 1.4787291</td><td> 1.1153975</td><td>Q </td></tr>\n",
"\t<tr><th scope=row>General function prediction only</th><td>12.3209976</td><td>12.3224082</td><td>11.8896191</td><td>13.2582252</td><td>13.2099795</td><td>11.8584368</td><td>R </td></tr>\n",
"\t<tr><th scope=row>Function unknown</th><td> 6.8664521</td><td> 6.5621044</td><td> 6.8546392</td><td> 6.7352437</td><td> 7.3784788</td><td> 7.0110701</td><td>S </td></tr>\n",
"\t<tr><th scope=row>Signal transduction mechanisms</th><td>20.8165728</td><td>20.6780138</td><td>21.9807787</td><td>18.3606825</td><td>16.9788428</td><td>17.4941295</td><td>T </td></tr>\n",
"\t<tr><th scope=row>Intracellular trafficking</th><td> 5.9493162</td><td> 5.7040371</td><td> 5.6992439</td><td> 4.9881623</td><td> 5.3234246</td><td> 4.9815498</td><td>U </td></tr>\n",
"\t<tr><th scope=row>Defense mechanisms</th><td> 0.8809332</td><td> 0.8721339</td><td> 0.8055968</td><td> 0.8408850</td><td> 0.6824903</td><td> 0.7967125</td><td>V </td></tr>\n",
"\t<tr><th scope=row>Extracellular structures</th><td> 1.6934835</td><td> 2.2366015</td><td> 2.1482581</td><td> 1.8450486</td><td> 1.2360658</td><td> 2.5327071</td><td>W </td></tr>\n",
"\t<tr><th scope=row>Nuclear structure</th><td> 0.5430410</td><td> 0.5978337</td><td> 0.6077309</td><td> 0.4735080</td><td> 0.3943277</td><td> 0.4780275</td><td>Y </td></tr>\n",
"\t<tr><th scope=row>Cytoskeleton</th><td> 5.4625905</td><td> 4.9936700</td><td> 5.0491131</td><td> 4.0003266</td><td> 4.0342762</td><td> 4.1596780</td><td>Z </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllllll}\n",
" & MM\\_Percentage & XT\\_Percentage & DR\\_Percentage & LS\\_Percentage & DM\\_Percentage & CE\\_Percentage & Category\\\\\n",
"\\hline\n",
"\tRNA processing and modification & 3.6242961 & 3.3408356 & 3.1163875 & 3.1594416 & 3.9281110 & 3.6816505 & A \\\\\n",
"\tChromatin structure and dynamics & 1.7940467 & 1.5262344 & 1.5016607 & 1.6327863 & 1.7365587 & 1.8617913 & B \\\\\n",
"\tEnergy production and conversion & 2.0353982 & 1.9623013 & 2.0033920 & 2.3348845 & 3.3972852 & 3.2371687 & C \\\\\n",
"\tCell cycle control & 2.5905068 & 2.6375018 & 2.4273903 & 2.9390154 & 2.2143020 & 2.6165716 & D \\\\\n",
"\tAmino acid transport and metabolism & 1.9951730 & 2.0818681 & 2.1376581 & 2.8737040 & 3.2987033 & 2.4572291 & E \\\\\n",
"\tNucleotide transport and metabolism & 1.0257442 & 1.1323674 & 1.0105293 & 1.0858029 & 1.1223174 & 0.9141228 & F \\\\\n",
"\tCarbohydrate transport and metabolism & 2.1520515 & 2.5320017 & 2.3885238 & 3.1594416 & 3.1546220 & 3.1197585 & G \\\\\n",
"\tCoenzyme transport and metabolism & 0.6315366 & 0.6259671 & 0.5829977 & 0.8408850 & 0.8569045 & 0.6205971 & H \\\\\n",
"\tLipid transport and metabolism & 2.8238134 & 2.9469686 & 2.5828563 & 3.0696383 & 3.5413665 & 3.6564911 & I \\\\\n",
"\tTranslation, ribosomal structure and biogenesis & 2.9283990 & 3.0102687 & 2.4415236 & 3.1920973 & 4.0115265 & 4.1932238 & J \\\\\n",
"\tTranscription & 10.0965406 & 8.6791391 & 10.9356229 & 8.1802596 & 8.2278001 & 8.0845354 & K \\\\\n",
"\tReplication, recombination and repair & 1.5607401 & 1.9552680 & 1.5475938 & 2.3348845 & 1.7517252 & 2.0966119 & L \\\\\n",
"\tCell wall/membrane/envelope biogenesis & 1.0418343 & 1.1534674 & 0.9822627 & 2.1144583 & 1.0844013 & 0.7631667 & M \\\\\n",
"\tCell motility & 0.2131939 & 0.1969335 & 0.2261324 & 0.1714426 & 0.1819974 & 0.1425696 & N \\\\\n",
"\tPosttranslational modification & 7.6548673 & 8.0531720 & 7.1938379 & 8.1149482 & 7.8638053 & 8.5625629 & O \\\\\n",
"\tInorganic ion transport and metabolism & 2.5905068 & 2.9469686 & 2.8584552 & 2.5798024 & 2.9119587 & 3.5642402 & P \\\\\n",
"\tSecondary metabolites & 0.7079646 & 1.2519342 & 1.0281959 & 1.7144257 & 1.4787291 & 1.1153975 & Q \\\\\n",
"\tGeneral function prediction only & 12.3209976 & 12.3224082 & 11.8896191 & 13.2582252 & 13.2099795 & 11.8584368 & R \\\\\n",
"\tFunction unknown & 6.8664521 & 6.5621044 & 6.8546392 & 6.7352437 & 7.3784788 & 7.0110701 & S \\\\\n",
"\tSignal transduction mechanisms & 20.8165728 & 20.6780138 & 21.9807787 & 18.3606825 & 16.9788428 & 17.4941295 & T \\\\\n",
"\tIntracellular trafficking & 5.9493162 & 5.7040371 & 5.6992439 & 4.9881623 & 5.3234246 & 4.9815498 & U \\\\\n",
"\tDefense mechanisms & 0.8809332 & 0.8721339 & 0.8055968 & 0.8408850 & 0.6824903 & 0.7967125 & V \\\\\n",
"\tExtracellular structures & 1.6934835 & 2.2366015 & 2.1482581 & 1.8450486 & 1.2360658 & 2.5327071 & W \\\\\n",
"\tNuclear structure & 0.5430410 & 0.5978337 & 0.6077309 & 0.4735080 & 0.3943277 & 0.4780275 & Y \\\\\n",
"\tCytoskeleton & 5.4625905 & 4.9936700 & 5.0491131 & 4.0003266 & 4.0342762 & 4.1596780 & Z \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | MM_Percentage | XT_Percentage | DR_Percentage | LS_Percentage | DM_Percentage | CE_Percentage | Category | \n",
"|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
"| RNA processing and modification | 3.6242961 | 3.3408356 | 3.1163875 | 3.1594416 | 3.9281110 | 3.6816505 | A | \n",
"| Chromatin structure and dynamics | 1.7940467 | 1.5262344 | 1.5016607 | 1.6327863 | 1.7365587 | 1.8617913 | B | \n",
"| Energy production and conversion | 2.0353982 | 1.9623013 | 2.0033920 | 2.3348845 | 3.3972852 | 3.2371687 | C | \n",
"| Cell cycle control | 2.5905068 | 2.6375018 | 2.4273903 | 2.9390154 | 2.2143020 | 2.6165716 | D | \n",
"| Amino acid transport and metabolism | 1.9951730 | 2.0818681 | 2.1376581 | 2.8737040 | 3.2987033 | 2.4572291 | E | \n",
"| Nucleotide transport and metabolism | 1.0257442 | 1.1323674 | 1.0105293 | 1.0858029 | 1.1223174 | 0.9141228 | F | \n",
"| Carbohydrate transport and metabolism | 2.1520515 | 2.5320017 | 2.3885238 | 3.1594416 | 3.1546220 | 3.1197585 | G | \n",
"| Coenzyme transport and metabolism | 0.6315366 | 0.6259671 | 0.5829977 | 0.8408850 | 0.8569045 | 0.6205971 | H | \n",
"| Lipid transport and metabolism | 2.8238134 | 2.9469686 | 2.5828563 | 3.0696383 | 3.5413665 | 3.6564911 | I | \n",
"| Translation, ribosomal structure and biogenesis | 2.9283990 | 3.0102687 | 2.4415236 | 3.1920973 | 4.0115265 | 4.1932238 | J | \n",
"| Transcription | 10.0965406 | 8.6791391 | 10.9356229 | 8.1802596 | 8.2278001 | 8.0845354 | K | \n",
"| Replication, recombination and repair | 1.5607401 | 1.9552680 | 1.5475938 | 2.3348845 | 1.7517252 | 2.0966119 | L | \n",
"| Cell wall/membrane/envelope biogenesis | 1.0418343 | 1.1534674 | 0.9822627 | 2.1144583 | 1.0844013 | 0.7631667 | M | \n",
"| Cell motility | 0.2131939 | 0.1969335 | 0.2261324 | 0.1714426 | 0.1819974 | 0.1425696 | N | \n",
"| Posttranslational modification | 7.6548673 | 8.0531720 | 7.1938379 | 8.1149482 | 7.8638053 | 8.5625629 | O | \n",
"| Inorganic ion transport and metabolism | 2.5905068 | 2.9469686 | 2.8584552 | 2.5798024 | 2.9119587 | 3.5642402 | P | \n",
"| Secondary metabolites | 0.7079646 | 1.2519342 | 1.0281959 | 1.7144257 | 1.4787291 | 1.1153975 | Q | \n",
"| General function prediction only | 12.3209976 | 12.3224082 | 11.8896191 | 13.2582252 | 13.2099795 | 11.8584368 | R | \n",
"| Function unknown | 6.8664521 | 6.5621044 | 6.8546392 | 6.7352437 | 7.3784788 | 7.0110701 | S | \n",
"| Signal transduction mechanisms | 20.8165728 | 20.6780138 | 21.9807787 | 18.3606825 | 16.9788428 | 17.4941295 | T | \n",
"| Intracellular trafficking | 5.9493162 | 5.7040371 | 5.6992439 | 4.9881623 | 5.3234246 | 4.9815498 | U | \n",
"| Defense mechanisms | 0.8809332 | 0.8721339 | 0.8055968 | 0.8408850 | 0.6824903 | 0.7967125 | V | \n",
"| Extracellular structures | 1.6934835 | 2.2366015 | 2.1482581 | 1.8450486 | 1.2360658 | 2.5327071 | W | \n",
"| Nuclear structure | 0.5430410 | 0.5978337 | 0.6077309 | 0.4735080 | 0.3943277 | 0.4780275 | Y | \n",
"| Cytoskeleton | 5.4625905 | 4.9936700 | 5.0491131 | 4.0003266 | 4.0342762 | 4.1596780 | Z | \n",
"\n",
"\n"
],
"text/plain": [
" MM_Percentage XT_Percentage\n",
"RNA processing and modification 3.6242961 3.3408356 \n",
"Chromatin structure and dynamics 1.7940467 1.5262344 \n",
"Energy production and conversion 2.0353982 1.9623013 \n",
"Cell cycle control 2.5905068 2.6375018 \n",
"Amino acid transport and metabolism 1.9951730 2.0818681 \n",
"Nucleotide transport and metabolism 1.0257442 1.1323674 \n",
"Carbohydrate transport and metabolism 2.1520515 2.5320017 \n",
"Coenzyme transport and metabolism 0.6315366 0.6259671 \n",
"Lipid transport and metabolism 2.8238134 2.9469686 \n",
"Translation, ribosomal structure and biogenesis 2.9283990 3.0102687 \n",
"Transcription 10.0965406 8.6791391 \n",
"Replication, recombination and repair 1.5607401 1.9552680 \n",
"Cell wall/membrane/envelope biogenesis 1.0418343 1.1534674 \n",
"Cell motility 0.2131939 0.1969335 \n",
"Posttranslational modification 7.6548673 8.0531720 \n",
"Inorganic ion transport and metabolism 2.5905068 2.9469686 \n",
"Secondary metabolites 0.7079646 1.2519342 \n",
"General function prediction only 12.3209976 12.3224082 \n",
"Function unknown 6.8664521 6.5621044 \n",
"Signal transduction mechanisms 20.8165728 20.6780138 \n",
"Intracellular trafficking 5.9493162 5.7040371 \n",
"Defense mechanisms 0.8809332 0.8721339 \n",
"Extracellular structures 1.6934835 2.2366015 \n",
"Nuclear structure 0.5430410 0.5978337 \n",
"Cytoskeleton 5.4625905 4.9936700 \n",
" DR_Percentage LS_Percentage\n",
"RNA processing and modification 3.1163875 3.1594416 \n",
"Chromatin structure and dynamics 1.5016607 1.6327863 \n",
"Energy production and conversion 2.0033920 2.3348845 \n",
"Cell cycle control 2.4273903 2.9390154 \n",
"Amino acid transport and metabolism 2.1376581 2.8737040 \n",
"Nucleotide transport and metabolism 1.0105293 1.0858029 \n",
"Carbohydrate transport and metabolism 2.3885238 3.1594416 \n",
"Coenzyme transport and metabolism 0.5829977 0.8408850 \n",
"Lipid transport and metabolism 2.5828563 3.0696383 \n",
"Translation, ribosomal structure and biogenesis 2.4415236 3.1920973 \n",
"Transcription 10.9356229 8.1802596 \n",
"Replication, recombination and repair 1.5475938 2.3348845 \n",
"Cell wall/membrane/envelope biogenesis 0.9822627 2.1144583 \n",
"Cell motility 0.2261324 0.1714426 \n",
"Posttranslational modification 7.1938379 8.1149482 \n",
"Inorganic ion transport and metabolism 2.8584552 2.5798024 \n",
"Secondary metabolites 1.0281959 1.7144257 \n",
"General function prediction only 11.8896191 13.2582252 \n",
"Function unknown 6.8546392 6.7352437 \n",
"Signal transduction mechanisms 21.9807787 18.3606825 \n",
"Intracellular trafficking 5.6992439 4.9881623 \n",
"Defense mechanisms 0.8055968 0.8408850 \n",
"Extracellular structures 2.1482581 1.8450486 \n",
"Nuclear structure 0.6077309 0.4735080 \n",
"Cytoskeleton 5.0491131 4.0003266 \n",
" DM_Percentage CE_Percentage\n",
"RNA processing and modification 3.9281110 3.6816505 \n",
"Chromatin structure and dynamics 1.7365587 1.8617913 \n",
"Energy production and conversion 3.3972852 3.2371687 \n",
"Cell cycle control 2.2143020 2.6165716 \n",
"Amino acid transport and metabolism 3.2987033 2.4572291 \n",
"Nucleotide transport and metabolism 1.1223174 0.9141228 \n",
"Carbohydrate transport and metabolism 3.1546220 3.1197585 \n",
"Coenzyme transport and metabolism 0.8569045 0.6205971 \n",
"Lipid transport and metabolism 3.5413665 3.6564911 \n",
"Translation, ribosomal structure and biogenesis 4.0115265 4.1932238 \n",
"Transcription 8.2278001 8.0845354 \n",
"Replication, recombination and repair 1.7517252 2.0966119 \n",
"Cell wall/membrane/envelope biogenesis 1.0844013 0.7631667 \n",
"Cell motility 0.1819974 0.1425696 \n",
"Posttranslational modification 7.8638053 8.5625629 \n",
"Inorganic ion transport and metabolism 2.9119587 3.5642402 \n",
"Secondary metabolites 1.4787291 1.1153975 \n",
"General function prediction only 13.2099795 11.8584368 \n",
"Function unknown 7.3784788 7.0110701 \n",
"Signal transduction mechanisms 16.9788428 17.4941295 \n",
"Intracellular trafficking 5.3234246 4.9815498 \n",
"Defense mechanisms 0.6824903 0.7967125 \n",
"Extracellular structures 1.2360658 2.5327071 \n",
"Nuclear structure 0.3943277 0.4780275 \n",
"Cytoskeleton 4.0342762 4.1596780 \n",
" Category\n",
"RNA processing and modification A \n",
"Chromatin structure and dynamics B \n",
"Energy production and conversion C \n",
"Cell cycle control D \n",
"Amino acid transport and metabolism E \n",
"Nucleotide transport and metabolism F \n",
"Carbohydrate transport and metabolism G \n",
"Coenzyme transport and metabolism H \n",
"Lipid transport and metabolism I \n",
"Translation, ribosomal structure and biogenesis J \n",
"Transcription K \n",
"Replication, recombination and repair L \n",
"Cell wall/membrane/envelope biogenesis M \n",
"Cell motility N \n",
"Posttranslational modification O \n",
"Inorganic ion transport and metabolism P \n",
"Secondary metabolites Q \n",
"General function prediction only R \n",
"Function unknown S \n",
"Signal transduction mechanisms T \n",
"Intracellular trafficking U \n",
"Defense mechanisms V \n",
"Extracellular structures W \n",
"Nuclear structure Y \n",
"Cytoskeleton Z "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"%get data --from Python3\n",
"\n",
"data\n",
"\n",
"write.table(data, file=\"KOG_summary.tsv\", sep=\"\\t\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "SoS",
"language": "sos",
"name": "sos"
},
"language_info": {
"codemirror_mode": "sos",
"file_extension": ".sos",
"mimetype": "text/x-sos",
"name": "sos",
"nbconvert_exporter": "sos_notebook.converter.SoS_Exporter",
"pygments_lexer": "sos"
},
"sos": {
"kernels": [
[
"Python3",
"python3",
"Python3",
"#FFD91A"
],
[
"R",
"ir",
"R",
"#DCDCDA"
]
],
"version": "0.9.15.8"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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