notebooks/GRCz11.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from collections import defaultdict, OrderedDict\n",
    "import warnings\n",
    "import gffutils\n",
    "import pybedtools\n",
    "import pandas as pd\n",
    "import copy\n",
    "import os\n",
    "import re\n",
    "from gffutils.pybedtools_integration import tsses\n",
    "from copy import deepcopy\n",
    "from collections import OrderedDict, Callable\n",
    "import errno\n",
    "\n",
    "def mkdir_p(path):\n",
    "    try:\n",
    "        os.makedirs(path)\n",
    "    except OSError as exc:  # Python >2.5\n",
    "        if exc.errno == errno.EEXIST and os.path.isdir(path):\n",
    "            pass\n",
    "        else:\n",
    "            raise\n",
    "            \n",
    "class DefaultOrderedDict(OrderedDict):\n",
    "    # Source: http://stackoverflow.com/a/6190500/562769\n",
    "    def __init__(self, default_factory=None, *a, **kw):\n",
    "        if (default_factory is not None and\n",
    "           not isinstance(default_factory, Callable)):\n",
    "            raise TypeError('first argument must be callable')\n",
    "        OrderedDict.__init__(self, *a, **kw)\n",
    "        self.default_factory = default_factory\n",
    "\n",
    "    def __getitem__(self, key):\n",
    "        try:\n",
    "            return OrderedDict.__getitem__(self, key)\n",
    "        except KeyError:\n",
    "            return self.__missing__(key)\n",
    "\n",
    "    def __missing__(self, key):\n",
    "        if self.default_factory is None:\n",
    "            raise KeyError(key)\n",
    "        self[key] = value = self.default_factory()\n",
    "        return value\n",
    "\n",
    "    def __reduce__(self):\n",
    "        if self.default_factory is None:\n",
    "            args = tuple()\n",
    "        else:\n",
    "            args = self.default_factory,\n",
    "        return type(self), args, None, None, self.items()\n",
    "\n",
    "    def copy(self):\n",
    "        return self.__copy__()\n",
    "\n",
    "    def __copy__(self):\n",
    "        return type(self)(self.default_factory, self)\n",
    "\n",
    "    def __deepcopy__(self, memo):\n",
    "        import copy\n",
    "        return type(self)(self.default_factory,\n",
    "                          copy.deepcopy(self.items()))\n",
    "\n",
    "    def __repr__(self):\n",
    "        return 'OrderedDefaultDict(%s, %s)' % (self.default_factory,\n",
    "                                               OrderedDict.__repr__(self))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "gtf = '/home/cmb-panasas2/skchoudh/genomes/GRCz11/annotation/Danio_rerio.GRCz11.96.chr.gtf'\n",
    "gtf_db = '/home/cmb-panasas2/skchoudh/genomes/GRCz11/annotation/Danio_rerio.GRCz11.96.chr.gtf'\n",
    "prefix = '/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/GRCz11/v96/'\n",
    "chr_sizes = '/home/cmb-panasas2/skchoudh/genomes/GRCz11/fasta/Danio_rerio.GRCz11.dna.primary_assembly.sizes'\n",
    "mkdir_p(prefix)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_gene_dict(db):\n",
    "    '''\n",
    "    Store each feature line db.all_features() as a dict of dicts\n",
    "    '''\n",
    "    gene_dict = DefaultOrderedDict(lambda: DefaultOrderedDict(lambda: DefaultOrderedDict(list)))\n",
    "    for line_no, feature in enumerate(db.all_features()):\n",
    "        gene_ids = feature.attributes['gene_id']\n",
    "        feature_type = feature.featuretype\n",
    "        if feature_type == 'gene':\n",
    "            if len(gene_ids)!=1:\n",
    "                logging.warning('Found multiple gene_ids on line {} in gtf'.format(line_no))\n",
    "                break\n",
    "            else:\n",
    "                gene_id = gene_ids[0]\n",
    "                gene_dict[gene_id]['gene'] = feature\n",
    "        else:\n",
    "            transcript_ids = feature.attributes['transcript_id']\n",
    "\n",
    "            for gene_id in gene_ids:\n",
    "                for transcript_id in transcript_ids:\n",
    "                    gene_dict[gene_id][transcript_id][feature_type].append(feature)\n",
    "    return gene_dict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "db = gffutils.create_db(gtf, dbfn=gtf_db, merge_strategy='merge', force=True, disable_infer_transcripts=True, disable_infer_genes=True)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "db = gffutils.FeatureDB(gtf_db, keep_order=True)\n",
    "gene_dict = create_gene_dict(db)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CDS\n",
      "Selenocysteine\n",
      "exon\n",
      "five_prime_utr\n",
      "gene\n",
      "start_codon\n",
      "stop_codon\n",
      "three_prime_utr\n",
      "transcript\n"
     ]
    }
   ],
   "source": [
    "for x in db.featuretypes():\n",
    "    print(x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_gene_list(gene_dict):\n",
    "    return list(set(gene_dict.keys()))\n",
    "\n",
    "def get_UTR_regions(gene_dict, gene_id, transcript, cds):\n",
    "    if len(cds)==0:\n",
    "        return [], []\n",
    "    utr5_regions = []\n",
    "    utr3_regions = []\n",
    "    utrs = gene_dict[gene_id][transcript]['UTR']\n",
    "    first_cds = cds[0]\n",
    "    last_cds = cds[-1]\n",
    "    for utr in utrs:\n",
    "        ## Push all cds at once\n",
    "        ## Sort later to remove duplicates\n",
    "        strand = utr.strand\n",
    "        if strand == '+':\n",
    "            if utr.stop < first_cds.start:\n",
    "                utr.feature_type = 'five_prime_UTR'\n",
    "                utr5_regions.append(utr)\n",
    "            elif utr.start > last_cds.stop:\n",
    "                utr.feature_type = 'three_prime_UTR'\n",
    "                utr3_regions.append(utr)\n",
    "            else:\n",
    "                raise RuntimeError('Error with cds')\n",
    "        elif strand == '-':\n",
    "            if utr.stop < first_cds.start:\n",
    "                utr.feature_type = 'three_prime_UTR'\n",
    "                utr3_regions.append(utr)\n",
    "            elif utr.start > last_cds.stop:\n",
    "                utr.feature_type = 'five_prime_UTR'\n",
    "                utr5_regions.append(utr)                \n",
    "            else:\n",
    "                raise RuntimeError('Error with cds')    \n",
    "    return utr5_regions, utr3_regions\n",
    "    \n",
    "def create_bed(regions, bedtype='0'):\n",
    "    '''Create bed from list of regions\n",
    "    bedtype: 0 or 1\n",
    "        0-Based or 1-based coordinate of the BED\n",
    "    '''\n",
    "    bedstr = ''\n",
    "    for region in regions:\n",
    "        assert len(region.attributes['gene_id']) == 1\n",
    "        ## GTF start is 1-based, so shift by one while writing \n",
    "        ## to 0-based BED format\n",
    "        if bedtype == '0':\n",
    "            start = region.start - 1\n",
    "        else:\n",
    "            start = region.start\n",
    "        bedstr += '{}\\t{}\\t{}\\t{}\\t{}\\t{}\\n'.format(region.chrom,\n",
    "                                             start,\n",
    "                                             region.stop,\n",
    "                                             re.sub('\\.\\d+', '', region.attributes['gene_id'][0]),\n",
    "                                             '.',\n",
    "                                             region.strand)\n",
    "    return bedstr\n",
    "\n",
    "def rename_regions(regions, gene_id):\n",
    "    regions = list(regions)\n",
    "    if len(regions) == 0:\n",
    "        return []\n",
    "    for region in regions:\n",
    "        region.attributes['gene_id'] = gene_id\n",
    "    return regions\n",
    "\n",
    "def merge_regions(db, regions):\n",
    "    if len(regions) == 0:\n",
    "        return []\n",
    "    merged = db.merge(sorted(list(regions), key=lambda x: x.start))\n",
    "    return merged\n",
    "\n",
    "def merge_regions_nostrand(db, regions):\n",
    "    if len(regions) == 0:\n",
    "        return []\n",
    "    merged = db.merge(sorted(list(regions), key=lambda x: x.start), ignore_strand=True)\n",
    "    return merged"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<BedTool(/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/GRCz11/v96/cds.bed.gz)>"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "utr5_bed = ''\n",
    "utr3_bed = ''\n",
    "gene_bed = ''\n",
    "exon_bed = ''\n",
    "intron_bed = ''\n",
    "start_codon_bed = ''\n",
    "stop_codon_bed = ''\n",
    "cds_bed = ''\n",
    "\n",
    "gene_list = []\n",
    "\n",
    "for gene_id in get_gene_list(gene_dict):\n",
    "    gene_list.append(gene_dict[gene_id]['gene'])\n",
    "    \n",
    "    utr5_regions, utr3_regions = [], []\n",
    "    exon_regions, intron_regions = [], []\n",
    "    star_codon_regions, stop_codon_regions = [], []\n",
    "    cds_regions = []\n",
    "    \n",
    "    for feature in gene_dict[gene_id].keys():\n",
    "        if feature == 'gene':\n",
    "            continue\n",
    "        cds = list(gene_dict[gene_id][feature]['CDS'])\n",
    "        exons = list(gene_dict[gene_id][feature]['exon'])\n",
    "        merged_exons = merge_regions(db, exons)\n",
    "        introns = db.interfeatures(merged_exons)\n",
    "        #utr5_region, utr3_region = get_UTR_regions(gene_dict, gene_id, feature, cds)\n",
    "        utr5_region = list(gene_dict[gene_id][feature]['five_prime_utr'])\n",
    "        utr3_region = list(gene_dict[gene_id][feature]['three_prime_utr'])\n",
    "        utr5_regions += utr5_region\n",
    "        utr3_regions += utr3_region\n",
    "        exon_regions += exons\n",
    "        intron_regions += introns\n",
    "        cds_regions += cds\n",
    "        \n",
    "    merged_utr5 = merge_regions(db, utr5_regions)\n",
    "    renamed_utr5 = rename_regions(merged_utr5, gene_id)\n",
    "    \n",
    "    merged_utr3 = merge_regions(db, utr3_regions)\n",
    "    renamed_utr3 = rename_regions(merged_utr3, gene_id)\n",
    "    \n",
    "    merged_exons = merge_regions(db, exon_regions)\n",
    "    renamed_exons = rename_regions(merged_exons, gene_id)\n",
    "    \n",
    "    merged_introns = merge_regions(db, intron_regions)\n",
    "    renamed_introns = rename_regions(merged_introns, gene_id)\n",
    "    \n",
    "    merged_cds = merge_regions(db, cds_regions)\n",
    "    renamed_cds = rename_regions(merged_cds, gene_id)\n",
    "    \n",
    "    utr3_bed += create_bed(renamed_utr3)\n",
    "    utr5_bed += create_bed(renamed_utr5)\n",
    "    exon_bed += create_bed(renamed_exons)\n",
    "    intron_bed += create_bed(renamed_introns)\n",
    "    cds_bed += create_bed(renamed_cds)\n",
    "    \n",
    "    \n",
    "gene_bed = create_bed(gene_list)\n",
    "gene_bedtool = pybedtools.BedTool(gene_bed, from_string=True)\n",
    "utr5_bedtool = pybedtools.BedTool(utr5_bed, from_string=True)\n",
    "utr3_bedtool = pybedtools.BedTool(utr3_bed, from_string=True)\n",
    "exon_bedtool = pybedtools.BedTool(exon_bed, from_string=True)\n",
    "intron_bedtool = pybedtools.BedTool(intron_bed, from_string=True)\n",
    "cds_bedtool = pybedtools.BedTool(cds_bed, from_string=True)\n",
    "\n",
    "utr5_cds_subtracted = utr5_bedtool.subtract(cds_bedtool)\n",
    "utr3_cds_subtracted = utr3_bedtool.subtract(cds_bedtool)\n",
    "utr5_cds_subtracted.remove_invalid().sort().saveas(os.path.join(prefix, 'utr5.bed.gz'))\n",
    "utr3_cds_subtracted.remove_invalid().sort().saveas(os.path.join(prefix, 'utr3.bed.gz'))\n",
    "gene_bedtool.remove_invalid().sort().saveas(os.path.join(prefix, 'gene.bed.gz'))\n",
    "exon_bedtool.remove_invalid().sort().saveas(os.path.join(prefix, 'exon.bed.gz'))\n",
    "intron_bedtool.remove_invalid().sort().saveas(os.path.join(prefix, 'intron.bed.gz'))\n",
    "cds_bedtool.remove_invalid().sort().saveas(os.path.join(prefix, 'cds.bed.gz'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<BedTool(/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/GRCz11/v96/stop_codon.bed.gz)>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "for gene_id in get_gene_list(gene_dict):\n",
    "    start_codons = []\n",
    "    stop_codons = []\n",
    "    for start_codon in db.children(gene_id, featuretype='start_codon'):\n",
    "        ## 1 -based stop\n",
    "        ## 0-based start handled while converting to bed\n",
    "        start_codon.stop = start_codon.start\n",
    "        start_codons.append(start_codon)\n",
    "    for stop_codon in db.children(gene_id, featuretype='stop_codon'):\n",
    "        stop_codon.start = stop_codon.stop\n",
    "        stop_codon.stop = stop_codon.stop+1\n",
    "        stop_codons.append(stop_codon)\n",
    "    merged_start_codons = merge_regions(db, start_codons)\n",
    "    renamed_start_codons = rename_regions(merged_start_codons, gene_id)\n",
    "    merged_stop_codons = merge_regions(db, stop_codons)\n",
    "    renamed_stop_codons = rename_regions(merged_stop_codons, gene_id)\n",
    "    \n",
    "    start_codon_bed += create_bed(renamed_start_codons)    \n",
    "    stop_codon_bed += create_bed(renamed_stop_codons)\n",
    "\n",
    "    \n",
    "start_codon_bedtool = pybedtools.BedTool(start_codon_bed, from_string=True)\n",
    "stop_codon_bedtool = pybedtools.BedTool(stop_codon_bed, from_string=True)\n",
    "start_codon_bedtool.remove_invalid().sort().saveas(os.path.join(prefix, 'start_codon.bed.gz'))\n",
    "stop_codon_bedtool.remove_invalid().sort().saveas(os.path.join(prefix, 'stop_codon.bed.gz'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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