PFB2017 Nick Gladman.ipynb

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   "source": [
    "# Nick Gladman Peak-Parser Code"
   ]
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   "source": [
    "###import re"
   ]
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   "source": [
    "###Will make our own Bedfile class"
   ]
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   "source": [
    "```class Bedfile(object):\n",
    "\t'''\n",
    "\tClass to read a bedfile type file.\n",
    "\t'''"
   ]
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   "metadata": {},
   "source": [
    "```def __init__(self, path=None): #standard idiom when defining classes"
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   "source": [
    "###set dictionary to be used in lower script and filepath designation"
   ]
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   "source": [
    "```self.chromosomes = dict() # key=chromosome name, value=Chromosome object\n",
    "\t\tself.filepath = path"
   ]
  },
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   "metadata": {},
   "source": [
    "###opening file from script or argparse and reading in line by line"
   ]
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   "source": [
    "```with open(path) as bedfile:\n",
    "\t\t\tfor line in bedfile:\n",
    "\t\t\t\tline = line.rstrip()\n",
    "                fields = line.split(\"\\t\")\n",
    "\t\t\t\tchr_name = fields[0]"
   ]
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   "source": [
    "### get existing or create new chromosome\t"
   ]
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   "source": [
    "```if chr_name in self.chromosomes:\n",
    "\t\t\t\t\tchromosome =  self.chromosomes[chr_name] #chromosome_name is associated with the chromosome value, which in the else statement below we turn into a Chromosome object list\n",
    "\t\t\t\telse:\n",
    "\t\t\t\t\tchromosome = Chromosome(name=chr_name) # we creating a new object in our dictionary, chromosome, and that object is of the Class Chromosome and its name is chr_name\n",
    "\t\t\t\t\tself.chromosomes[chr_name.lower()] = chromosome"
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