finding_a_protein_motif.ipynb

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    "## Finding a protein motif\n",
    "\n",
    "### Problem:\n",
    "\n",
    "**Given:** At most 15 UniProt Protein Database access IDs\n",
    "\n",
    "**Return:** For each protein posessing the N-glycosylation motif, output its given access ID followed by a list of locations in the protein string where the motif can be found.\n",
    "\n",
    "\n",
    "------------\n",
    "\n",
    "A protein motif is represented by a shorthand as follows:\n",
    "- [XY] means 'either X or Y'\n",
    "- {X} means 'any amino acid except X'\n",
    "\n",
    "The N-glycosylation motif is written as N{P}[ST]{P}"
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    "import urllib2\n",
    "from Bio import SeqIO\n",
    "import re\n",
    "\n",
    "def id_to_fasta(ID):\n",
    "    url = \"http://www.uniprot.org/uniprot/%s.fasta\" % ID.strip()\n",
    "    url_out = urllib2.urlopen(url)\n",
    "    fasta = SeqIO.parse(url_out, \"fasta\")\n",
    "    return(fasta)\n",
    "\n",
    "def is_motif(s):\n",
    "    s = s.upper()\n",
    "    assert len(s) is int(4)\n",
    "    pattern = re.compile('N[^P][ST][^P]')\n",
    "    return bool(pattern.match(s))\n",
    "\n",
    "def name_and_position(ID):\n",
    "    fasta_gen = id_to_fasta(ID)\n",
    "    positions = []\n",
    "    for fasta in fasta_gen:\n",
    "        sequence =  str(fasta.seq)\n",
    "        for i in xrange(len(sequence) - 4):\n",
    "            if is_motif(sequence[i:i + 4]):\n",
    "                positions.append(i + 1)    \n",
    "    if len(positions) > 0:\n",
    "        print ID,\n",
    "        print ' '.join(str(num) for num in positions), \"\\n\""
   ]
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      "B5ZC00\n",
      "85 118 142 306 395 \n",
      "\n",
      "P07204_TRBM_HUMAN\n",
      "47 115 116 382 409 \n",
      "\n",
      "P20840_SAG1_YEAST\n",
      "79 109 135 248 306 348 364 402 485 501 614 \n",
      "\n"
     ]
    }
   ],
   "source": [
    "for line in open(\"/home/scott/Dropbox/rosalind/mprt.txt\"):\n",
    "    name_and_position(line)"
   ]
  }
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finding_a_shared_motif.ipynb