Cythoning of parse fasta

parse_fasta.ipynb

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      "%load_ext cythonmagic"
     ],
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      "%%cython\n",
      "cimport cython\n",
      "from cpython cimport bool\n",
      "from string import strip\n",
      "\n",
      "cdef bool is_fasta_label(str x):\n",
      "    \"\"\"Checks if x looks like a FASTA label line.\"\"\"\n",
      "    return x.startswith('>')\n",
      "\n",
      "cdef bool is_blank_or_comment(str x):\n",
      "    \"\"\"Checks if x is blank or a FASTA comment line.\"\"\"\n",
      "    return (not x) or x.startswith('#') or x.isspace()\n",
      "\n",
      "\n",
      "cdef bool is_blank(str x):\n",
      "    \"\"\"Checks if x is blank.\"\"\"\n",
      "    return (not x) or x.isspace()\n",
      "\n",
      "cdef bool is_empty(str line):\n",
      "    \"\"\"Returns True empty lines and lines consisting only of whitespace.\"\"\"\n",
      "    return (not line) or line.isspace()\n",
      "\n",
      "def FastaFinder():\n",
      "    \"\"\"Returns function that returns successive labeled records from file.\n",
      "    \"\"\"\n",
      "    def parser(lines):\n",
      "        curr = []\n",
      "        for l in lines:\n",
      "            \n",
      "            line = strip(l)\n",
      "            \n",
      "            if is_blank_or_comment(line):\n",
      "                continue\n",
      "            # if we find the label, return the previous record\n",
      "            if is_fasta_label(line):\n",
      "                if curr:\n",
      "                    yield curr\n",
      "                    curr = []\n",
      "            curr.append(line)\n",
      "        # don't forget to return the last record in the file\n",
      "        if curr:\n",
      "            yield curr\n",
      "    return parser\n",
      "\n",
      "def parse_fasta(object infile,        \n",
      "                str label_characters='>'):\n",
      "    finder = FastaFinder()\n",
      "    for rec in finder(infile):\n",
      "        # first line must be a label line\n",
      "        if not rec[0][0] in label_characters:    \n",
      "            raise ValueError(\"Found Fasta record without label line: %s\" %\n",
      "                                  rec)\n",
      "        # record must have at least one sequence\n",
      "        if len(rec) < 2:\n",
      "            raise ValueError(\"Found label line without sequences: %s\" %\n",
      "                                  rec)\n",
      "            \n",
      "        label = rec[0][1:].strip()\n",
      "        seq = ''.join(rec[1:])\n",
      "    \n",
      "        yield label, seq"
     ],
     "language": "python",
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     "prompt_number": 41
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     "cell_type": "code",
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     "input": [
      "f = '/Users/mcdonadt/not_backed_up/gg_13_5.fasta'\n",
      "from gzip import open as gzopen\n",
      "def unroll_parser(f, parser):\n",
      "    for rec in parser(f):\n",
      "        pass\n",
      "%time unroll_parser(open(f), parse_fasta)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "CPU times: user 4.56 s, sys: 472 ms, total: 5.03 s\n",
        "Wall time: 5.03 s\n"
       ]
      }
     ],
     "prompt_number": 42
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from skbio.parse.sequences import parse_fasta as skbio_parse_fasta\n",
      "%time unroll_parser(open(f), skbio_parse_fasta)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "CPU times: user 8.19 s, sys: 502 ms, total: 8.7 s\n",
        "Wall time: 8.7 s\n"
       ]
      }
     ],
     "prompt_number": 43
    },
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