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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| >SEMA4A,38.4 | ||
| LAAQQSYWPHFVTVTVLFALVLSGALIILVASPLRALRARG | ||
| >SEMA4B,47.0 | ||
| WGADRSYWKEFLVMCTLFVLAVLLPVLFLLYRHRNSMKVFL | ||
| >SEMA4C,86.6 | ||
| EARAPLENLGLVWLAVVALGAVCLVLLLLVLSLRRRLREEL | ||
| >SEMA4D,19.1 | ||
| TMYLKSSDNRLLMSLFLFFFVLFLCLFFYNCYKGYLPRQCL | ||
| >SEMA4F,88.5 | ||
| RDAPSRAHTVGAGLAGFFLGILAASLTLILIGRRQQRRRQR | ||
| >SEMA4G,49.9 | ||
| GAQLAPDVRLLYVLAIAALGGLCLILASSLLYVACLREGRR | ||
| >SEMA5A,28.1 | ||
| EEKRCGEFNMFHMIAVGLSSSILGCLLTLLVYTYCQRYQQQ | ||
| >SEMA5B,30.0 | ||
| TDCAGFNLIHLVATGISCFLGSGLLTLAVYLSCQHCQRQSQ | ||
| >SEMA6A,21.1 | ||
| KGHDQLVPVTLLAIAVILAFVMGAVFSGITVYCVCDHRRKD | ||
| >SEMA6B,80.0 | ||
| VSVNLLVTSSVAAFVVGAVVSGFSVGWFVGLRERRELARRK | ||
| >SEMA6C,46.8 | ||
| ASASRSVPIPLLLASVAAAFALGASVSGLLVSCACRRAHRR | ||
| >SEMA6D,37.7 | ||
| GESNQMVHMNVLITCVFAAFVLGAFIAGVAVYCYRDMFVRK |
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,145 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "You can read FASTA files using the ``read_fasta()`` function:" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "f204a08b42e761b5" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": "<IPython.core.display.HTML object>", | ||
| "text/html": "<style type=\"text/css\">\n#T_1d975 thead th {\n background-color: white;\n color: black;\n}\n#T_1d975 tbody tr:nth-child(odd) {\n background-color: #f2f2f2;\n}\n#T_1d975 tbody tr:nth-child(even) {\n background-color: white;\n}\n#T_1d975 th {\n padding: 5px;\n white-space: nowrap;\n}\n#T_1d975 td {\n padding: 5px;\n white-space: nowrap;\n}\n</style>\n<table id=\"T_1d975\" style='display:block; max-height: 300px; max-width: 100%; overflow-x: auto; overflow-y: auto;'>\n <thead>\n <tr>\n <th class=\"blank level0\" > </th>\n <th id=\"T_1d975_level0_col0\" class=\"col_heading level0 col0\" >entry</th>\n <th id=\"T_1d975_level0_col1\" class=\"col_heading level0 col1\" >sequence</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th id=\"T_1d975_level0_row0\" class=\"row_heading level0 row0\" >1</th>\n <td id=\"T_1d975_row0_col0\" class=\"data row0 col0\" >SEMA4A,38.4</td>\n <td id=\"T_1d975_row0_col1\" class=\"data row0 col1\" >LAAQQSYWPHFVTVT...IILVASPLRALRARG</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row1\" class=\"row_heading level0 row1\" >2</th>\n <td id=\"T_1d975_row1_col0\" class=\"data row1 col0\" >SEMA4B,47.0</td>\n <td id=\"T_1d975_row1_col1\" class=\"data row1 col1\" >WGADRSYWKEFLVMC...LFLLYRHRNSMKVFL</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row2\" class=\"row_heading level0 row2\" >3</th>\n <td id=\"T_1d975_row2_col0\" class=\"data row2 col0\" >SEMA4C,86.6</td>\n <td id=\"T_1d975_row2_col1\" class=\"data row2 col1\" >EARAPLENLGLVWLA...LLLVLSLRRRLREEL</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row3\" class=\"row_heading level0 row3\" >4</th>\n <td id=\"T_1d975_row3_col0\" class=\"data row3 col0\" >SEMA4D,19.1</td>\n <td id=\"T_1d975_row3_col1\" class=\"data row3 col1\" >TMYLKSSDNRLLMSL...FFYNCYKGYLPRQCL</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row4\" class=\"row_heading level0 row4\" >5</th>\n <td id=\"T_1d975_row4_col0\" class=\"data row4 col0\" >SEMA4F,88.5</td>\n <td id=\"T_1d975_row4_col1\" class=\"data row4 col1\" >RDAPSRAHTVGAGLA...TLILIGRRQQRRRQR</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row5\" class=\"row_heading level0 row5\" >6</th>\n <td id=\"T_1d975_row5_col0\" class=\"data row5 col0\" >SEMA4G,49.9</td>\n <td id=\"T_1d975_row5_col1\" class=\"data row5 col1\" >GAQLAPDVRLLYVLA...ASSLLYVACLREGRR</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row6\" class=\"row_heading level0 row6\" >7</th>\n <td id=\"T_1d975_row6_col0\" class=\"data row6 col0\" >SEMA5A,28.1</td>\n <td id=\"T_1d975_row6_col1\" class=\"data row6 col1\" >EEKRCGEFNMFHMIA...LTLLVYTYCQRYQQQ</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row7\" class=\"row_heading level0 row7\" >8</th>\n <td id=\"T_1d975_row7_col0\" class=\"data row7 col0\" >SEMA5B,30.0</td>\n <td id=\"T_1d975_row7_col1\" class=\"data row7 col1\" >TDCAGFNLIHLVATG...LAVYLSCQHCQRQSQ</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row8\" class=\"row_heading level0 row8\" >9</th>\n <td id=\"T_1d975_row8_col0\" class=\"data row8 col0\" >SEMA6A,21.1</td>\n <td id=\"T_1d975_row8_col1\" class=\"data row8 col1\" >KGHDQLVPVTLLAIA...SGITVYCVCDHRRKD</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row9\" class=\"row_heading level0 row9\" >10</th>\n <td id=\"T_1d975_row9_col0\" class=\"data row9 col0\" >SEMA6B,80.0</td>\n <td id=\"T_1d975_row9_col1\" class=\"data row9 col1\" >VSVNLLVTSSVAAFV...WFVGLRERRELARRK</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row10\" class=\"row_heading level0 row10\" >11</th>\n <td id=\"T_1d975_row10_col0\" class=\"data row10 col0\" >SEMA6C,46.8</td>\n <td id=\"T_1d975_row10_col1\" class=\"data row10 col1\" >ASASRSVPIPLLLAS...SGLLVSCACRRAHRR</td>\n </tr>\n <tr>\n <th id=\"T_1d975_level0_row11\" class=\"row_heading level0 row11\" >12</th>\n <td id=\"T_1d975_row11_col0\" class=\"data row11 col0\" >SEMA6D,37.7</td>\n <td id=\"T_1d975_row11_col1\" class=\"data row11 col1\" >GESNQMVHMNVLITC...AGVAVYCYRDMFVRK</td>\n </tr>\n </tbody>\n</table>\n" | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "import aaanalysis as aa\n", | ||
| "file_path = \"data/example_FASTA.fasta\"\n", | ||
| "df_seq = aa.read_fasta(file_path)\n", | ||
| "aa.display_df(df_seq)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-02T21:28:50.165467820Z", | ||
| "start_time": "2024-05-02T21:28:50.048853581Z" | ||
| } | ||
| }, | ||
| "id": "6221c1f3f94b587" | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "To adjust the names of the columns for the primary FASTA file information, use ``col_id`` and ``col_seq``:" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "6195ed555b5e7680" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": "<IPython.core.display.HTML object>", | ||
| "text/html": "<style type=\"text/css\">\n#T_6c442 thead th {\n background-color: white;\n color: black;\n}\n#T_6c442 tbody tr:nth-child(odd) {\n background-color: #f2f2f2;\n}\n#T_6c442 tbody tr:nth-child(even) {\n background-color: white;\n}\n#T_6c442 th {\n padding: 5px;\n white-space: nowrap;\n}\n#T_6c442 td {\n padding: 5px;\n white-space: nowrap;\n}\n</style>\n<table id=\"T_6c442\" style='display:block; max-height: 300px; max-width: 100%; overflow-x: auto; overflow-y: auto;'>\n <thead>\n <tr>\n <th class=\"blank level0\" > </th>\n <th id=\"T_6c442_level0_col0\" class=\"col_heading level0 col0\" >ENTRY</th>\n <th id=\"T_6c442_level0_col1\" class=\"col_heading level0 col1\" >SQUENCE</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th id=\"T_6c442_level0_row0\" class=\"row_heading level0 row0\" >1</th>\n <td id=\"T_6c442_row0_col0\" class=\"data row0 col0\" >SEMA4A,38.4</td>\n <td id=\"T_6c442_row0_col1\" class=\"data row0 col1\" >LAAQQSYWPHFVTVT...IILVASPLRALRARG</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row1\" class=\"row_heading level0 row1\" >2</th>\n <td id=\"T_6c442_row1_col0\" class=\"data row1 col0\" >SEMA4B,47.0</td>\n <td id=\"T_6c442_row1_col1\" class=\"data row1 col1\" >WGADRSYWKEFLVMC...LFLLYRHRNSMKVFL</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row2\" class=\"row_heading level0 row2\" >3</th>\n <td id=\"T_6c442_row2_col0\" class=\"data row2 col0\" >SEMA4C,86.6</td>\n <td id=\"T_6c442_row2_col1\" class=\"data row2 col1\" >EARAPLENLGLVWLA...LLLVLSLRRRLREEL</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row3\" class=\"row_heading level0 row3\" >4</th>\n <td id=\"T_6c442_row3_col0\" class=\"data row3 col0\" >SEMA4D,19.1</td>\n <td id=\"T_6c442_row3_col1\" class=\"data row3 col1\" >TMYLKSSDNRLLMSL...FFYNCYKGYLPRQCL</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row4\" class=\"row_heading level0 row4\" >5</th>\n <td id=\"T_6c442_row4_col0\" class=\"data row4 col0\" >SEMA4F,88.5</td>\n <td id=\"T_6c442_row4_col1\" class=\"data row4 col1\" >RDAPSRAHTVGAGLA...TLILIGRRQQRRRQR</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row5\" class=\"row_heading level0 row5\" >6</th>\n <td id=\"T_6c442_row5_col0\" class=\"data row5 col0\" >SEMA4G,49.9</td>\n <td id=\"T_6c442_row5_col1\" class=\"data row5 col1\" >GAQLAPDVRLLYVLA...ASSLLYVACLREGRR</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row6\" class=\"row_heading level0 row6\" >7</th>\n <td id=\"T_6c442_row6_col0\" class=\"data row6 col0\" >SEMA5A,28.1</td>\n <td id=\"T_6c442_row6_col1\" class=\"data row6 col1\" >EEKRCGEFNMFHMIA...LTLLVYTYCQRYQQQ</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row7\" class=\"row_heading level0 row7\" >8</th>\n <td id=\"T_6c442_row7_col0\" class=\"data row7 col0\" >SEMA5B,30.0</td>\n <td id=\"T_6c442_row7_col1\" class=\"data row7 col1\" >TDCAGFNLIHLVATG...LAVYLSCQHCQRQSQ</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row8\" class=\"row_heading level0 row8\" >9</th>\n <td id=\"T_6c442_row8_col0\" class=\"data row8 col0\" >SEMA6A,21.1</td>\n <td id=\"T_6c442_row8_col1\" class=\"data row8 col1\" >KGHDQLVPVTLLAIA...SGITVYCVCDHRRKD</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row9\" class=\"row_heading level0 row9\" >10</th>\n <td id=\"T_6c442_row9_col0\" class=\"data row9 col0\" >SEMA6B,80.0</td>\n <td id=\"T_6c442_row9_col1\" class=\"data row9 col1\" >VSVNLLVTSSVAAFV...WFVGLRERRELARRK</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row10\" class=\"row_heading level0 row10\" >11</th>\n <td id=\"T_6c442_row10_col0\" class=\"data row10 col0\" >SEMA6C,46.8</td>\n <td id=\"T_6c442_row10_col1\" class=\"data row10 col1\" >ASASRSVPIPLLLAS...SGLLVSCACRRAHRR</td>\n </tr>\n <tr>\n <th id=\"T_6c442_level0_row11\" class=\"row_heading level0 row11\" >12</th>\n <td id=\"T_6c442_row11_col0\" class=\"data row11 col0\" >SEMA6D,37.7</td>\n <td id=\"T_6c442_row11_col1\" class=\"data row11 col1\" >GESNQMVHMNVLITC...AGVAVYCYRDMFVRK</td>\n </tr>\n </tbody>\n</table>\n" | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "df_seq = aa.read_fasta(file_path, col_id=\"ENTRY\", col_seq=\"SQUENCE\")\n", | ||
| "aa.display_df(df_seq)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-02T21:28:50.965212794Z", | ||
| "start_time": "2024-05-02T21:28:50.944687925Z" | ||
| } | ||
| }, | ||
| "id": "8d4c33fedb070859" | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "source": [ | ||
| "The ``col_id`` column should only contain the unique identifier. If the FASTA file comprises additional information, use the ``sep`` (default='|') argument to save them in additional columns:" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "d0ed30c599bcde82" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": "<IPython.core.display.HTML object>", | ||
| "text/html": "<style type=\"text/css\">\n#T_a7bf4 thead th {\n background-color: white;\n color: black;\n}\n#T_a7bf4 tbody tr:nth-child(odd) {\n background-color: #f2f2f2;\n}\n#T_a7bf4 tbody tr:nth-child(even) {\n background-color: white;\n}\n#T_a7bf4 th {\n padding: 5px;\n white-space: nowrap;\n}\n#T_a7bf4 td {\n padding: 5px;\n white-space: nowrap;\n}\n</style>\n<table id=\"T_a7bf4\" style='display:block; max-height: 300px; max-width: 100%; overflow-x: auto; overflow-y: auto;'>\n <thead>\n <tr>\n <th class=\"blank level0\" > </th>\n <th id=\"T_a7bf4_level0_col0\" class=\"col_heading level0 col0\" >entry</th>\n <th id=\"T_a7bf4_level0_col1\" class=\"col_heading level0 col1\" >sequence</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th id=\"T_a7bf4_level0_row0\" class=\"row_heading level0 row0\" >1</th>\n <td id=\"T_a7bf4_row0_col0\" class=\"data row0 col0\" >SEMA4A</td>\n <td id=\"T_a7bf4_row0_col1\" class=\"data row0 col1\" >LAAQQSYWPHFVTVT...IILVASPLRALRARG</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row1\" class=\"row_heading level0 row1\" >2</th>\n <td id=\"T_a7bf4_row1_col0\" class=\"data row1 col0\" >SEMA4B</td>\n <td id=\"T_a7bf4_row1_col1\" class=\"data row1 col1\" >WGADRSYWKEFLVMC...LFLLYRHRNSMKVFL</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row2\" class=\"row_heading level0 row2\" >3</th>\n <td id=\"T_a7bf4_row2_col0\" class=\"data row2 col0\" >SEMA4C</td>\n <td id=\"T_a7bf4_row2_col1\" class=\"data row2 col1\" >EARAPLENLGLVWLA...LLLVLSLRRRLREEL</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row3\" class=\"row_heading level0 row3\" >4</th>\n <td id=\"T_a7bf4_row3_col0\" class=\"data row3 col0\" >SEMA4D</td>\n <td id=\"T_a7bf4_row3_col1\" class=\"data row3 col1\" >TMYLKSSDNRLLMSL...FFYNCYKGYLPRQCL</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row4\" class=\"row_heading level0 row4\" >5</th>\n <td id=\"T_a7bf4_row4_col0\" class=\"data row4 col0\" >SEMA4F</td>\n <td id=\"T_a7bf4_row4_col1\" class=\"data row4 col1\" >RDAPSRAHTVGAGLA...TLILIGRRQQRRRQR</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row5\" class=\"row_heading level0 row5\" >6</th>\n <td id=\"T_a7bf4_row5_col0\" class=\"data row5 col0\" >SEMA4G</td>\n <td id=\"T_a7bf4_row5_col1\" class=\"data row5 col1\" >GAQLAPDVRLLYVLA...ASSLLYVACLREGRR</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row6\" class=\"row_heading level0 row6\" >7</th>\n <td id=\"T_a7bf4_row6_col0\" class=\"data row6 col0\" >SEMA5A</td>\n <td id=\"T_a7bf4_row6_col1\" class=\"data row6 col1\" >EEKRCGEFNMFHMIA...LTLLVYTYCQRYQQQ</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row7\" class=\"row_heading level0 row7\" >8</th>\n <td id=\"T_a7bf4_row7_col0\" class=\"data row7 col0\" >SEMA5B</td>\n <td id=\"T_a7bf4_row7_col1\" class=\"data row7 col1\" >TDCAGFNLIHLVATG...LAVYLSCQHCQRQSQ</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row8\" class=\"row_heading level0 row8\" >9</th>\n <td id=\"T_a7bf4_row8_col0\" class=\"data row8 col0\" >SEMA6A</td>\n <td id=\"T_a7bf4_row8_col1\" class=\"data row8 col1\" >KGHDQLVPVTLLAIA...SGITVYCVCDHRRKD</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row9\" class=\"row_heading level0 row9\" >10</th>\n <td id=\"T_a7bf4_row9_col0\" class=\"data row9 col0\" >SEMA6B</td>\n <td id=\"T_a7bf4_row9_col1\" class=\"data row9 col1\" >VSVNLLVTSSVAAFV...WFVGLRERRELARRK</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row10\" class=\"row_heading level0 row10\" >11</th>\n <td id=\"T_a7bf4_row10_col0\" class=\"data row10 col0\" >SEMA6C</td>\n <td id=\"T_a7bf4_row10_col1\" class=\"data row10 col1\" >ASASRSVPIPLLLAS...SGLLVSCACRRAHRR</td>\n </tr>\n <tr>\n <th id=\"T_a7bf4_level0_row11\" class=\"row_heading level0 row11\" >12</th>\n <td id=\"T_a7bf4_row11_col0\" class=\"data row11 col0\" >SEMA6D</td>\n <td id=\"T_a7bf4_row11_col1\" class=\"data row11 col1\" >GESNQMVHMNVLITC...AGVAVYCYRDMFVRK</td>\n </tr>\n </tbody>\n</table>\n" | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "df_seq = aa.read_fasta(file_path, sep=\",\")\n", | ||
| "aa.display_df(df_seq)\n" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2024-05-02T21:28:51.741497271Z", | ||
| "start_time": "2024-05-02T21:28:51.718363188Z" | ||
| } | ||
| }, | ||
| "id": "c63b0719186b520e" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "12c40961e7f22ae4" | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 2 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython2", | ||
| "version": "2.7.6" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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Learn more about bidirectional Unicode characters