Introduction to loops for biologists

introduction_to_loops_for_biologists.ipynb

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      "# Introduction to loops for biologists\n",
      "\n",
      "![Introduction to loops](http://www.kelloggs.ie/content/dam/workarea/assetpushqueue/images/web-raw-approved/eng%20IE/38/56/prod_img-253856.jpg/jcr:content/renditions/cq5dam.thumbnail.319.319.png \"Introduction to loops\")\n",
      "\n",
      "## Background\n",
      "\n",
      "* **This introduction assumes a very basic knowledge of programming, such as variable usage, assignment, and list indexing.**\n",
      "* We can use programming languages to solve problems that require a defined, logical approach.\n",
      "* Programming languages have different structures such as semantics, grammar and syntax, just as spoken languages do.\n",
      "* In the same way spoken languages share common lexical terms and grammar, so do different programming languages.\n",
      "* One type of structure shared between programming languages is the control of the flow of a program.\n",
      "\n",
      "## Control flow\n",
      "\n",
      "* Generally the instructions (code) of a program are executed in a stepwise manner from the beginning to the end.\n",
      "* It is possible to add statements that change the flow of the program.\n",
      "* Loops are one such way of controlling the flow of a program.\n",
      "* Loops, as the name suggests, allow one to repeat a certain portion of code - generally based on certain conditions.\n",
      "* There are a number of different ways of implementing loops, most of which are shared across programming languages.\n",
      "\n",
      "## Loop types\n",
      "\n",
      "* Some languages, such as the Perl programming language have a detailed repertoire of different loop types that are beyond the scope of this introduction.\n",
      "* I will use Python here, as it has a very simple syntax for beginners, and only implements **for** loops and **while** loops."
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     "source": [
      "### for loop"
     ]
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     "cell_type": "code",
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     "input": [
      "# for loop\n",
      "for i in range(1, 11):\n",
      "        print i"
     ],
     "language": "python",
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       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "1\n",
        "2\n",
        "3\n",
        "4\n",
        "5\n",
        "6\n",
        "7\n",
        "8\n",
        "9\n",
        "10\n"
       ]
      }
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     "prompt_number": 30
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     "source": [
      "### while loop"
     ]
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     "input": [
      "# while loop\n",
      "i = 1\n",
      "while i <= 10:\n",
      "    print i\n",
      "    i += 1"
     ],
     "language": "python",
     "metadata": {},
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       "stream": "stdout",
       "text": [
        "1\n",
        "2\n",
        "3\n",
        "4\n",
        "5\n",
        "6\n",
        "7\n",
        "8\n",
        "9\n",
        "10\n"
       ]
      }
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     "source": [
      "### for loops for biologists\n",
      "\n",
      "* The for loop allows you to iterate over a list of items\n",
      "* This may be useful to iterate over all GenBank IDs in a list in order to fetch the FASTA formatted sequence corresponding to each ID."
     ]
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     "input": [
      "# import modules required\n",
      "from Bio import Entrez, SeqIO\n",
      "\n",
      "# set email so Entrez can tell us off if we send too many queries\n",
      "Entrez.email = \"gawbul@gmail.com\"\n",
      "\n",
      "# set a list of genbank ids\n",
      "genbank_ids = [\"119395733\", \"568974803\", \"110626132\", \"347446670\", \"442628803\"]\n",
      "\n",
      "# iterate over gebank ids\n",
      "for id in genbank_ids:\n",
      "    print \"Fetching data for id %s\" % id\n",
      "    print\n",
      "    handle = Entrez.efetch(db=\"nucleotide\", id=id, rettype=\"fasta\", retmode=\"text\")\n",
      "    record = SeqIO.read(handle, \"fasta\")\n",
      "    handle.close()\n",
      "    print record\n",
      "    print"
     ],
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       "text": [
        "Fetching data for id 119395733\n",
        "\n",
        "ID: gi|119395733|ref|NM_000059.3|\n",
        "Name: gi|119395733|ref|NM_000059.3|\n",
        "Description: gi|119395733|ref|NM_000059.3| Homo sapiens breast cancer 2, early onset (BRCA2), mRNA\n",
        "Number of features: 0\n",
        "Seq('GTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTGTGGCACTGCT...ATT', SingleLetterAlphabet())"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "\n",
        "Fetching data for id 568974803\n",
        "\n",
        "ID: gi|568974803|ref|XM_006533728.1|\n",
        "Name: gi|568974803|ref|XM_006533728.1|\n",
        "Description: gi|568974803|ref|XM_006533728.1| PREDICTED: Mus musculus contactin associated protein-like 1 (Cntnap1), transcript variant X1, mRNA\n",
        "Number of features: 0\n",
        "Seq('TCATCGTACCCGGAGTAAAGTCCCCAGGAGACCTGGTGGCATCAAAATGAGAAG...CCC', SingleLetterAlphabet())"
       ]
      },
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       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "\n",
        "Fetching data for id 110626132\n",
        "\n",
        "ID: gi|110626132|ref|NM_001030280.1|\n",
        "Name: gi|110626132|ref|NM_001030280.1|\n",
        "Description: gi|110626132|ref|NM_001030280.1| Danio rerio solute carrier family 24, member 5 (slc24a5), mRNA\n",
        "Number of features: 0\n",
        "Seq('GTAAGCCGCGGCGGTGTGTGTGTGTGTGTGTGTTCTCCGTCATCTGTGTTCTGC...CCT', SingleLetterAlphabet())"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "\n",
        "Fetching data for id 347446670\n",
        "\n",
        "ID: gi|347446670|ref|NM_001244612.1|\n",
        "Name: gi|347446670|ref|NM_001244612.1|\n",
        "Description: gi|347446670|ref|NM_001244612.1| Bos taurus insulin-like growth factor 1 receptor (IGF1R), mRNA\n",
        "Number of features: 0\n",
        "Seq('GAGAAAGGGGAATTTGGTCCCAAATAAAAGGAATGAAGTCTAGCTCCGGAGGAG...AAC', SingleLetterAlphabet())"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "\n",
        "Fetching data for id 442628803\n",
        "\n",
        "ID: gi|442628803|ref|NM_165390.2|\n",
        "Name: gi|442628803|ref|NM_165390.2|\n",
        "Description: gi|442628803|ref|NM_165390.2| Drosophila melanogaster Cullin-2 (Cul-2), transcript variant A, mRNA\n",
        "Number of features: 0\n",
        "Seq('CGATAGATTATATCGATATCGTCTTCGTCTGACAAACCATTTCACGATACCAAA...ATT', SingleLetterAlphabet())"
       ]
      },
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       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "\n"
       ]
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     "source": [
      "### while loops for biologists\n",
      "\n",
      "* The while loop allows you to repeat a task while a certain condition is true\n",
      "* This can be useful when you need to run something only a given number of times or until you break the condition"
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      "# set a list of genbank ids\n",
      "spp_names = [\"homo_sapiens\", \"mus_musculus\", \"bos_taurus\", \"danio_rerio\", \"drosophila_melanogaster\"]\n",
      "\n",
      "# search through list\n",
      "found = False\n",
      "list_index = 0\n",
      "while found == False:\n",
      "    name = spp_names[list_index]\n",
      "    if name == \"danio_rerio\":\n",
      "        print \"Found %s at list position %d.\" % (name, list_index + 1)\n",
      "        found = True\n",
      "    else:\n",
      "        print name\n",
      "    list_index += 1"
     ],
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       "text": [
        "homo_sapiens\n",
        "mus_musculus\n",
        "bos_taurus\n",
        "Found danio_rerio at list position 4.\n"
       ]
      }
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     "source": [
      "## Summary\n",
      "\n",
      "* Loops allow you to alter the flow of a program.\n",
      "* These can loop (iterate) over a list of items or repeat at task based on certain conditions.\n",
      "* Different types of loops evaluate the conditions at different times in the execution of the program.\n",
      "* It is wise to be certain exactly how the loop is executing your code in order to minimalise the need for debugging."
     ]
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     "source": [
      "## Further information\n",
      "\n",
      "* [Python for Biologists](http://pythonforbiologists.com)\n",
      "* [A Primer on Python for Life Science Researchers](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030199)\n",
      "* [Rosalind: Python Village](http://rosalind.info/problems/list-view/?location=python-village)"
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