{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/alexsha/miniconda3/envs/seq_tools/lib/python3.6/site-packages/Bio/SearchIO/__init__.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.\n",
      "  BiopythonExperimentalWarning)\n"
     ]
    }
   ],
   "source": [
    "import seq_tools.plot4seq as p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio.Align import MultipleSeqAlignment\n",
    "from Bio.Seq import Seq\n",
    "from Bio.SeqRecord import SeqRecord\n",
    "import seq_tools.hist_ss as st\n",
    "import numpy as np\n",
    "#import get_hist_ss_in_aln_for_shade\n",
    "\n",
    "human_h2a_z_core=Seq('SRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLI-KATIAGGGVIPHIHKSLIG')\n",
    "xenopus_h2a_core=Seq('TRSSRAGLQFPVGRVHRLLRKGNYAE-RVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP')\n",
    "  \n",
    "msa=MultipleSeqAlignment([SeqRecord(xenopus_h2a_core,id='H2A',name='H2A'),SeqRecord(human_h2a_z_core,id='H2Ah',name='H2Ah')])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<module 'seq_tools.hist_ss' from '/Users/alexsha/work_HD/seq_tools/seq_tools/hist_ss.py'>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from importlib import reload \n",
    "reload(st)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SingleLetterAlphabet() alignment with 2 rows and 129 columns\n",
      "SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHR-LLRKGNYAERV...KSK H2A\n",
      "---------------XRSXRAGLQFPVGRXHRXLXXXXXXXXRV...--- Query\n",
      "Type detected= H2A\n"
     ]
    }
   ],
   "source": [
    "reload(st)\n",
    "features=st.get_hist_ss_in_aln_for_shade(msa,below=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Chosen splitting parameters\n",
      "2 20\n",
      "Launcning Latex:\n",
      "pdflatex --file-line-error --synctex=1 -output-directory=/tmp --save-size=10000  /tmp/align.tex > /dev/null\n",
      "mv /tmp/align.pdf /tmp/tempshade.pdf\n",
      "Converting PDF to PNG\n",
      "convert -density 150 /tmp/tempshade.pdf -trim -bordercolor White -border 0.000%x0% /tmp/tempprofseq.png\n"
     ]
    }
   ],
   "source": [
    "reload(p)\n",
    "p.plot_prof4seq('default',list(map(np.abs,map(np.sin,range(len(msa[0]))))),msa,features,axis='conservation')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<img src=\"default.png\" alt=\"Plot\" >\n"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%%HTML\n",
    "<img src=\"default.png\" alt=\"Plot\" >"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "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": "3.6.7"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}