assemblies code

07_draft_assemblies/README.txt

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+# Code for analysing translocation using draft assemblies
+
+
+Jean-Talon.contigs.fasta	# canu draft assembly contigs from reads >8kb
+Jean-Talon.contigs.fasta.coords	# mummer output from alignment of the draft assembly against the wtdbg2 polished assembly
+Jean-Talon.unitigs.fasta	# canu draft assembly unitigs from reads >8kb
+Jean-Talon.unitigs.fasta.coords	# mummer output from alignment of the draft assembly against the wtdbg2 polished assembly
+Jean-Talon_reordered.fasta	# wtdbg2 polished assembly
+S288c.genome.fa			# Genome of the S.cerevisiae strain S288C produced by Yue et al. Nat. Genet. 2017.
+				# Downloaded from https://yjx1217.github.io/Yeast_PacBio_2016/data/
+S288c.genome.fa.coords		# mummer output from alignment of the draft assembly against the wtdbg2 polished assembly
+assemblies.ipynb		# main script
+barcode11.cns.fa		# wtdbg2 draft assembly from reads >8kb
+barcode11.cns.fa.coords		# mummer output from alignment of the draft assembly against the wtdbg2 polished assembly
+tig00000035.fasta		# canu unitig corresponding to the uncertain translocation junction

07_draft_assemblies/assemblies.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# author: Mathieu Hénault\n",
+    "from Bio import SeqIO\n",
+    "from Bio import SeqRecord as SeqRecord\n",
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "import itertools\n",
+    "from matplotlib import pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Analysis of the alignments of draft assemblies using mummer"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "DELTA = {}\n",
+    "ASSEMBLIES = {}\n",
+    "tig_order = {}\n",
+    "cum_len = {}\n",
+    "for s in ['Jean-Talon_reordered.fasta','S288c.genome.fa','barcode11.cns.fa', 'Jean-Talon.unitigs.fasta', 'Jean-Talon.contigs.fasta']:\n",
+    "    ASSEMBLIES[s] = {}\n",
+    "    tig_order[s] = []\n",
+    "    cl = []\n",
+    "    with open(f'/Volumes/MacintoshHD/Dropbox/Jean_Talon/assemblies/{s}') as fi:\n",
+    "        for seq in SeqIO.parse(fi, 'fasta'):\n",
+    "            ASSEMBLIES[s][seq.id] = seq\n",
+    "            tig_order[s].append(seq.id)\n",
+    "            cl.append(len(seq.seq))\n",
+    "    \n",
+    "    cl = pd.Series([0]+list(np.cumsum(cl)[:-1]), index=tig_order[s])\n",
+    "    cum_len[s] = cl\n",
+    "\n",
+    "    if s!='Jean-Talon_reordered.fasta':\n",
+    "        delta = pd.read_csv(f'/Volumes/MacintoshHD/Dropbox/Jean_Talon/mummer/{s}.coords', sep='\\t', skiprows=range(4), index_col=None, header=None)\n",
+    "        delta = delta.loc[(delta[4]>=1e4) & (delta[5]>=1e4)].astype({1:int,2:int,2:int,2:int}).sort_values(by=4)\n",
+    "        \n",
+    "        delta['s1'] = delta[0]+cum_len['Jean-Talon_reordered.fasta'].loc[delta[7].values].values\n",
+    "        delta['e1'] = delta[1]+cum_len['Jean-Talon_reordered.fasta'].loc[delta[7].values].values\n",
+    "        delta['s2'] = delta[2]+cum_len[s].loc[delta[8].values].values\n",
+    "        delta['e2'] = delta[3]+cum_len[s].loc[delta[8].values].values\n",
+    "        \n",
+    "        DELTA[s] = delta        "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig = plt.figure(figsize=[32,8])\n",
+    "gs = plt.GridSpec(ncols=4, nrows=1, wspace=0.3, left=0.03, bottom=0.08, right=0.96, top=0.9)\n",
+    "\n",
+    "assembly_alias = {'Jean-Talon_reordered.fasta': 'Jean-Talon wtdbg2 polished',\n",
+    "                  'S288c.genome.fa': 'S288C',\n",
+    "                  'barcode11.cns.fa': 'Jean-Talon wtdbg2 draft (>8kb reads)', \n",
+    "                  'Jean-Talon.unitigs.fasta': 'Jean-Talon Canu draft unitigs (>8kb reads)', \n",
+    "                  'Jean-Talon.contigs.fasta': 'Jean-Talon Canu draft contigs (>8kb reads)'}\n",
+    "coord_translocation = np.mean(np.array([1.4e5, 1.47e5])+cum_len['Jean-Talon_reordered.fasta'].loc['ctg6_pilon'])\n",
+    "\n",
+    "for ax_idx, s in enumerate(['S288c.genome.fa', 'barcode11.cns.fa', 'Jean-Talon.contigs.fasta', 'Jean-Talon.unitigs.fasta']):\n",
+    "    ax = fig.add_subplot(gs[ax_idx])\n",
+    "    delta = DELTA[s]\n",
+    "    for i in delta.index:\n",
+    "        s1, e1, s2, e2 = delta.loc[i, ['s1','e1','s2','e2']]\n",
+    "        c = str(1-delta.loc[i,6]/100)\n",
+    "        ax.plot([s1,e1], [s2,e2], color=c, lw=1)\n",
+    "    for i in cum_len[s]:\n",
+    "        ax.axhline(i, lw=0.5, ls=':', color='k')\n",
+    "    for i in cum_len['Jean-Talon_reordered.fasta']:\n",
+    "        ax.axvline(i, lw=0.5, ls=':', color='k')\n",
+    "    ax.margins(0)\n",
+    "    ax.axvline(coord_translocation, color='red', ls='-', lw=3, alpha=0.3)\n",
+    "    \n",
+    "    assembly_size = ax.axis()\n",
+    "    ax.set_xticks(np.arange(0, assembly_size[1], 1e6))\n",
+    "    ax.set_xticklabels(np.arange(0, assembly_size[1]*1e-6, 1).astype(int))\n",
+    "    ax.set_yticks(np.arange(0, assembly_size[3], 1e6))\n",
+    "    ax.set_yticklabels(np.arange(0, assembly_size[3]*1e-6, 1).astype(int))\n",
+    "    \n",
+    "    #if s=='S288c.genome.fa':\n",
+    "    for tig, df in delta.groupby(8):\n",
+    "        if len(ASSEMBLIES[s][tig].seq)>2e5:\n",
+    "            ax.text(assembly_size[1]*1.02, np.mean([df['s2'].min(), df['e2'].max()]), s=tig, va='center', ha='left', size=7)\n",
+    "            \n",
+    "    for tig, df in delta.groupby(7):\n",
+    "        if len(ASSEMBLIES['Jean-Talon_reordered.fasta'][tig].seq)>2e5:\n",
+    "            ax.text(np.mean([df['s1'].min(), df['e1'].max()]), assembly_size[3]*1.02, s=tig, va='bottom', ha='center', rotation=90, size=7)\n",
+    "            \n",
+    "    ax.set_xlabel(assembly_alias['Jean-Talon_reordered.fasta'], size=14)\n",
+    "    ax.set_ylabel(assembly_alias[s], size=14)\n",
+    "    \n",
+    "plt.savefig('/Volumes/MacintoshHD/Dropbox/Jean_Talon/fig/FigS7.svg')\n",
+    "#plt.show()\n",
+    "plt.close()"
+   ]
+  }
+ ],
+ "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": "3.6.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}