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BjornFJohansson/Filipa.ipynb

Created January 14, 2016 17:22
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Filipa.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"import pydna"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from Bio.SeqRecord import SeqRecord"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from Bio.Seq import Seq"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"pRSO13 = pydna.read('''\n",
"\n",
"LOCUS pROS13_sequence 5877 bp ds-DNA circular 14-JAN-2016\n",
"DEFINITION \n",
"ACCESSION P30790\n",
"KEYWORDS .\n",
"SOURCE Unknown.\n",
" ORGANISM Unknown Unclassified.\n",
"REFERENCE 1 (bases 1 to 5877)\n",
" AUTHORS Self\n",
" JOURNAL Notebook \n",
"COMMENT Robert Mans, Harmen M. van Rossum, Melanie Wijsman, Antoon Backx,\n",
" Niels G. Kuijpers, Marcel van den Broek, Pascale Daran-Lapujade,\n",
" Jack T. Pronk, Antonius J.A. van Maris and Jean-Marc G. Daran\n",
" (2015) CRISPR/Cas9: a molecular Swiss army knife for simultaneous\n",
" introduction of multiple genetic modifications in Saccharomyces\n",
" cerevisiae. FEMS Yeast Research\n",
"COMMENT ApEinfo:methylated:1\n",
"FEATURES Location/Qualifiers\n",
" misc_feature 197..292\n",
" /gene=\"ori\"\n",
" /product=\"E.coli origin of replication\"\n",
" /SECDrawAs=\"Region\"\n",
" /label=E.coli origin of replication\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" CDS 973..1833\n",
" /gene=\"AmpR\"\n",
" /product=\"beta-lactamase\"\n",
" /SECDrawAs=\"Gene\"\n",
" /label=beta-lactamase\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 2141..2529\n",
" /gene=\"pAgTEF\"\n",
" /product=\"Ashbya gossypii TEF promoter\"\n",
" /SECDrawAs=\"Region\"\n",
" /label=Ashbya gossypii TEF promoter\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" CDS 2530..3339\n",
" /gene=\"kanMX\"\n",
" /SECDrawAs=\"Gene\"\n",
" /label=kanMX\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 3344..3579\n",
" /gene=\"tAgTEF\"\n",
" /product=\"Ashbya gossypii TEF terminator\"\n",
" /SECDrawAs=\"Region\"\n",
" /label=Ashbya gossypii TEF terminator\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 3761..4029\n",
" /gene=\"pSNR52 \"\n",
" /product=\"SNR52 promoter\"\n",
" /SECDrawAs=\"Region\"\n",
" /label=SNR52 promoter\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 4030..4124\n",
" /gene=\"gRNA-ADE2.Y\"\n",
" /product=\"structural guiding RNA-ADE2.Y\"\n",
" /SECDrawAs=\"Gene\"\n",
" /label=structural guiding RNA-ADE2.Y\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" CDS 4129..4148\n",
" /gene=\"tSUP4\"\n",
" /product=\"SUP4 terminator\"\n",
" /SECDrawAs=\"Region\"\n",
" /label=SUP4 terminator\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature complement(4194..5356)\n",
" /gene=\"2 æm\"\n",
" /SECDrawAs=\"Region\"\n",
" /label=2 æm\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" CDS complement(5400..5419)\n",
" /gene=\"tSUP4\"\n",
" /product=\"SUP4 terminator\"\n",
" /SECDrawAs=\"Region\"\n",
" /label=SUP4 terminator(1)\n",
" /ApEinfo_label=SUP4 terminator\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature complement(5420..5518)\n",
" /gene=\"gRNA-CAN1.Y\"\n",
" /product=\"structural guiding RNA-CAN1.Y\"\n",
" /SECDrawAs=\"Gene\"\n",
" /label=structural guiding RNA-CAN1.Y\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature complement(5519..5787)\n",
" /gene=\"pSNR52 \"\n",
" /product=\"SNR52 promoter\"\n",
" /SECDrawAs=\"Region\"\n",
" /label=SNR52 promoter(1)\n",
" /ApEinfo_label=SNR52 promoter\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 4125..4148\n",
" /label=match\n",
" /ApEinfo_fwdcolor=cyan\n",
" /ApEinfo_revcolor=green\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 4050..4124\n",
" /label=befmatch@ \n",
" /ApEinfo_fwdcolor=#ffbaa4\n",
" /ApEinfo_revcolor=green\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 5400..5423\n",
" /label=New Featurematchrev\n",
" /ApEinfo_fwdcolor=cyan\n",
" /ApEinfo_revcolor=green\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 5424..5498\n",
" /label=match22\n",
" /ApEinfo_fwdcolor=#ffccad\n",
" /ApEinfo_revcolor=green\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 3980..4000\n",
" /label=begin primer\n",
" /ApEinfo_fwdcolor=#a6ffa6\n",
" /ApEinfo_revcolor=green\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 4066..4082\n",
" /label=finish primer\n",
" /ApEinfo_fwdcolor=#bfb4ff\n",
" /ApEinfo_revcolor=green\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 4003..4029\n",
" /label=6005\n",
" /ApEinfo_fwdcolor=#7771ff\n",
" /ApEinfo_revcolor=green\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 4125..4128\n",
" /gene=\"gRNA-ADE2.Y\"\n",
" /product=\"structural guiding RNA-ADE2.Y\"\n",
" /SECDrawAs=\"Gene\"\n",
" /label=structural guiding RNA-ADE2.Y(1)\n",
" /ApEinfo_label=structural guiding RNA-ADE2.Y\n",
" /ApEinfo_fwdcolor=pink\n",
" /ApEinfo_revcolor=pink\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
" misc_feature 5519..5545\n",
" /label=6005(1)\n",
" /ApEinfo_label=6005\n",
" /ApEinfo_fwdcolor=#2342ff\n",
" /ApEinfo_revcolor=green\n",
" /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}\n",
" width 5 offset 0\n",
"ORIGIN\n",
" 1 tctagagaga ggcggtttgc gtattgggcg ctcttccgct tcctcgctca ctgactcgct\n",
" 61 gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt\n",
" 121 atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc\n",
" 181 caggaaccgt aaaaaggccg cgttgctggc gtttttccat aggctccgcc cccctgacga\n",
" 241 gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata\n",
" 301 ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac\n",
" 361 cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg\n",
" 421 taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc\n",
" 481 cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag\n",
" 541 acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt\n",
" 601 aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaaggacagt\n",
" 661 atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg\n",
" 721 atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac\n",
" 781 gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca\n",
" 841 gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac\n",
" 901 ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac\n",
" 961 ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt\n",
" 1021 tcgttcatcc atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt\n",
" 1081 accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt\n",
" 1141 atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc\n",
" 1201 cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa\n",
" 1261 tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg\n",
" 1321 tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt\n",
" 1381 gtgcaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc\n",
" 1441 agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt\n",
" 1501 aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg\n",
" 1561 gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac\n",
" 1621 tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc\n",
" 1681 gctgttgaga tccagttcga tgtaacccac tcgtgcaccc aactgatctt cagcatcttt\n",
" 1741 tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg\n",
" 1801 aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag\n",
" 1861 catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa\n",
" 1921 acaaataggg gttccgcgca ctcgagacta tatgtgaagg catggctatg gcacggcaga\n",
" 1981 cattccgcca gatcatcaat aggcacacta tatgtgaagg catggctatg gcacggcaga\n",
" 2041 cattccgcca gatcatcaat aggcaccttc gtacgctgca ggtcgacaac ccttaatata\n",
" 2101 acttcgtata atgtatgcta tacgaagtta ttaggtctag agatctgttt agcttgcctc\n",
" 2161 gtccccgccg ggtcacccgg ccagcgacat ggaggcccag aataccctcc ttgacagtct\n",
" 2221 tgacgtgcgc agctcagggg catgatgtga ctgtcgcccg tacatttagc ccatacatcc\n",
" 2281 ccatgtataa tcatttgcat ccatacattt tgatggccgc acggcgcgaa gcaaaaatta\n",
" 2341 cggctcctcg ctgcagacct gcgagcaggg aaacgctccc ctcacagacg cgttgaattg\n",
" 2401 tccccacgcc gcgcccctgt agagaaatat aaaaggttag gatttgccac tgaggttctt\n",
" 2461 ctttcatata cttcctttta aaatcttgct aggatacagt tctcacatca catccgaaca\n",
" 2521 taaacaacca tgggtaagga aaagactcac gtttcgaggc cgcgattaaa ttccaacatg\n",
" 2581 gatgctgatt tatatgggta taaatgggct cgcgataatg tcgggcaatc aggtgcgaca\n",
" 2641 atctatcgat tgtatgggaa gcccgatgcg ccagagttgt ttctgaaaca tggcaaaggt\n",
" 2701 agcgttgcca atgatgttac agatgagatg gtcagactaa actggctgac ggaatttatg\n",
" 2761 cctcttccga ccatcaagca ttttatccgt actcctgatg atgcatggtt actcaccact\n",
" 2821 gcgatccccg gcaaaacagc attccaggta ttagaagaat atcctgattc aggtgaaaat\n",
" 2881 attgttgatg cgctggcagt gttcctgcgc cggttgcatt cgattcctgt ttgtaattgt\n",
" 2941 ccttttaaca gcgatcgcgt atttcgtctc gctcaggcgc aatcacgaat gaataacggt\n",
" 3001 ttggttgatg cgagtgattt tgatgacgag cgtaatggct ggcctgttga acaagtctgg\n",
" 3061 aaagaaatgc ataagctttt gccattctca ccggattcag tcgtcactca tggtgatttc\n",
" 3121 tcacttgata accttatttt tgacgagggg aaattaatag gttgtattga tgttggacga\n",
" 3181 gtcggaatcg cagaccgata ccaggatctt gccatcctat ggaactgcct cggtgagttt\n",
" 3241 tctccttcat tacagaaacg gctttttcaa aaatatggta ttgataatcc tgatatgaat\n",
" 3301 aaattgcagt ttcatttgat gctcgatgag tttttctaat cagtactgac aataaaaaga\n",
" 3361 ttcttgtttt caagaacttg tcatttgtat agttttttta tattgtagtt gttctatttt\n",
" 3421 aatcaaatgt tagcgtgatt tatatttttt ttcgcctcga catcatctgc ccagatgcga\n",
" 3481 agttaagtgc gcagaaagta atatcatgcg tcaatcgtat gtgaatgctg gtcgctatac\n",
" 3541 tgctgtcgat tcgatactaa cgccgccatc cagtgtcgaa aacgagctct cgagaaccct\n",
" 3601 taatataact tcgtataatg tatgctatac gaagttatta ggtgatatca gatccactag\n",
" 3661 tggcctatgc cacctttcga gaggacgatg cccgtgtcta aatgattcga ccagcctaag\n",
" 3721 aatgttcaac ccctcactaa agggaacaaa agctggagct tctttgaaaa gataatgtat\n",
" 3781 gattatgctt tcactcatat ttatacagaa acttgatgtt ttctttcgag tatatacaag\n",
" 3841 gtgattacat gtacgtttga agtacaactc tagattttgt agtgccctct tgggctagcg\n",
" 3901 gtaaaggtgc gcattttttc acaccctaca atgttctgtt caaaagattt tggtcaaacg\n",
" 3961 ctgtagaagt gaaagttggt gcgcatgttt cggcgttcga aacttctccg cagtgaaaga\n",
" 4021 taaatgatca cttgaagatt ctttagtgtg ttttagagct agaaatagca agttaaaata\n",
" 4081 aggctagtcc gttatcaact tgaaaaagtg gcaccgagtc ggtggtgctt tttttgtttt\n",
" 4141 ttatgtcttc gagtcatgta attagttatg tcacgcttac gttcacgccc tccacgcatt\n",
" 4201 taagcataaa cacgcactat gccgttcttc tcatgtatat atatatacag gcaacacgca\n",
" 4261 gatataggtg cgacgtgaac agtgagctgt atgtgcgcag ctcgcgttgc attttcggaa\n",
" 4321 gcgctcgttt tcggaaacgc tttgaagttc ctattccgaa gttcctattc tgtagaaagt\n",
" 4381 ataggaactt cagagcgctt ttgaaaacca aaagcgctct gaagacgcac tttcaaaaaa\n",
" 4441 ccaaaaacgc accggactgt aacgagctac taaaatattg cgaataccgc ttccacaaac\n",
" 4501 attgctcaaa agtatctctt tgctatatat ctctgtgcta tatccctata taacctaccc\n",
" 4561 atccaccttt cgctccttga acttgcatct aaactcgacc tctacatttt ttatgtttat\n",
" 4621 ctctagtatt actctttaga caaaaaaatt gtagtaagaa ctattcatag agtgaatcga\n",
" 4681 aaacaatacg aaaatgtaaa catttcctat acgtagtata tagagacaaa atagaagaaa\n",
" 4741 ccgttcataa ttttctgacc aatgaagaat catcaacgct atcactttct gttcacaaag\n",
" 4801 tatgcgcaat ccacatcggt atagaatata atcggggatg cctttatctt gaaaaaatgc\n",
" 4861 acccgcagct tcgctagtaa tcagtaaacg cgggaagtgg agtcaggctt tttttatgga\n",
" 4921 agagaaaata gacaccaaag tagccttctt ctaaccttaa cggacctaca gtgcaaaaag\n",
" 4981 ttatcaagag actgcattat agagcgcaca aaggagaaaa aaagtaatct aagatgcttt\n",
" 5041 gttagaaaaa tagcgctctc gggatgcatt tttgtagaac aaaaaagaag tatagattct\n",
" 5101 ttgttggtaa aatagcgctc tcgcgttgca tttctgttct gtaaaaatgc agctcagatt\n",
" 5161 ctttgtttga aaaattagcg ctctcgcgtt gcatttttgt tttacaaaaa tgaagcacag\n",
" 5221 attcttcgtt ggtaaaatag cgctttcgcg ttgcatttct gttctgtaaa aatgcagctc\n",
" 5281 agattctttg tttgaaaaat tagcgctctc gcgttgcatt tttgttctac aaaatgaagc\n",
" 5341 acagatgctt cgttggaggg cgtgaacgta agcgtgacat aactaattac atgactcgaa\n",
" 5401 gacataaaaa acaaaaaaag caccaccgac tcggtgccac tttttcaagt tgataacgga\n",
" 5461 ctagccttat tttaacttgc tatttctagc tctaaaactc ctccatagag aacgtatcga\n",
" 5521 tcatttatct ttcactgcgg agaagtttcg aacgccgaaa catgcgcacc aactttcact\n",
" 5581 tctacagcgt ttgaccaaaa tcttttgaac agaacattgt agggtgtgaa aaaatgcgca\n",
" 5641 cctttaccgc tagcccaaga gggcactaca aaatctagag ttgtacttca aacgtacatg\n",
" 5701 taatcacctt gtatatactc gaaagaaaac atcaagtttc tgtataaata tgagtgaaag\n",
" 5761 cataatcata cattatcttt tcaaagaagc tccagctttt gttcccttta gtgagggtat\n",
" 5821 tcacgtagac ggataggtat agccagacat cagcagcata cttcgggaac cgtaggc\n",
"//\n",
"\n",
"''')"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Dseqrecord\n",
"circular: True\n",
"size: 5877\n",
"ID: P30790\n",
"Name: pROS13_sequence\n",
"Number of features: 21\n",
"/comment=Robert Mans, Harmen M. van Rossum, Melanie Wijsman, Antoon Backx,\n",
"Niels G. Kuijpers, Marcel van den Broek, Pascale Daran-Lapujade,\n",
"Jack T. Pronk, Antonius J.A. van Maris and Jean-Marc G. Daran\n",
"(2015) CRISPR/Cas9: a molecular Swiss army knife for simultaneous\n",
"introduction of multiple genetic modifications in Saccharomyces\n",
"cerevisiae. FEMS Yeast Research\n",
"ApEinfo:methylated:1\n",
"/source=Unknown\n",
"/taxonomy=[]\n",
"/keywords=['']\n",
"/references=[Reference(title='', ...)]\n",
"/accessions=['P30790']\n",
"/data_file_division= \n",
"/date=14-JAN-2016\n",
"/organism=Unknown Unclassified.\n",
"Dseq(o5877)\n",
"TCTA..AGGC\n",
"AGAT..TCCG\n"
]
}
],
"source": [
"print pRSO13"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"f1, r1 = pydna.parse('''\n",
"\n",
">f1_6005\n",
"GATCATTTATCTTTCACTGCGGAGAAG\n",
"\n",
">r1_6005\n",
"GATCATTTATCTTTCACTGCGGAGAAG\n",
" \n",
" ''', ds=False)"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"result = pydna.Anneal((f1,r1), pRSO13)"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"Reaction(products = 4)"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"result"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Template pROS13_sequence 5877 nt circular:\n",
"Primer f1_6005 anneals forward at position 5545\n",
"Primer r1_6005 anneals forward at position 5545\n",
"\n",
"Primer f1_6005 anneals reverse at position 4002\n",
"Primer r1_6005 anneals reverse at position 4002\n"
]
}
],
"source": [
"print result.report()"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[Dseqrecord(-4388), Dseqrecord(-4388), Dseqrecord(-4388), Dseqrecord(-4388)]"
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"result.products"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"GATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCACCAACTTTCACTTCTACAGCGTTTGACCAAAATCTTTTGAACAGAACATTGTAGGGTGTGAAAAAATGCGCACCTTTACCGCTAGCCCAAGAGGGCACTACAAAATCTAGAGTTGTACTTCAAACGTACATGTAATCACCTTGTATATACTCGAAAGAAAACATCAAGTTTCTGTATAAATATGAGTGAAAGCATAATCATACATTATCTTTTCAAAGAAGCTCCAGCTTTTGTTCCCTTTAGTGAGGGTATTCACGTAGACGGATAGGTATAGCCAGACATCAGCAGCATACTTCGGGAACCGTAGGCTCTAGAGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACTCGAGACTATATGTGAAGGCATGGCTATGGCACGGCAGACATTCCGCCAGATCATCAATAGGCACACTATATGTGAAGGCATGGCTATGGCACGGCAGACATTCCGCCAGATCATCAATAGGCACCTTCGTACGCTGCAGGTCGACAACCCTTAATATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTCTAGAGATCTGTTTAGCTTGCCTCGTCCCCGCCGGGTCACCCGGCCAGCGACATGGAGGCCCAGAATACCCTCCTTGACAGTCTTGACGTGCGCAGCTCAGGGGCATGATGTGACTGTCGCCCGTACATTTAGCCCATACATCCCCATGTATAATCATTTGCATCCATACATTTTGATGGCCGCACGGCGCGAAGCAAAAATTACGGCTCCTCGCTGCAGACCTGCGAGCAGGGAAACGCTCCCCTCACAGACGCGTTGAATTGTCCCCACGCCGCGCCCCTGTAGAGAAATATAAAAGGTTAGGATTTGCCACTGAGGTTCTTCTTTCATATACTTCCTTTTAAAATCTTGCTAGGATACAGTTCTCACATCACATCCGAACATAAACAACCATGGGTAAGGAAAAGACTCACGTTTCGAGGCCGCGATTAAATTCCAACATGGATGCTGATTTATATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGATTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGCGTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCTCTTCCGACCATCAAGCATTTTATCCGTACTCCTGATGATGCATGGTTACTCACCACTGCGATCCCCGGCAAAACAGCATTCCAGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCGCTGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCTTTTAACAGCGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAATAACGGTTTGGTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAAGAAATGCATAAGCTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAACCTTATTTTTGACGAGGGGAAATTAATAGGTTGTATTGATGTTGGACGAGTCGGAATCGCAGACCGATACCAGGATCTTGCCATCCTATGGAACTGCCTCGGTGAGTTTTCTCCTTCATTACAGAAACGGCTTTTTCAAAAATATGGTATTGATAATCCTGATATGAATAAATTGCAGTTTCATTTGATGCTCGATGAGTTTTTCTAATCAGTACTGACAATAAAAAGATTCTTGTTTTCAAGAACTTGTCATTTGTATAGTTTTTTTATATTGTAGTTGTTCTATTTTAATCAAATGTTAGCGTGATTTATATTTTTTTTCGCCTCGACATCATCTGCCCAGATGCGAAGTTAAGTGCGCAGAAAGTAATATCATGCGTCAATCGTATGTGAATGCTGGTCGCTATACTGCTGTCGATTCGATACTAACGCCGCCATCCAGTGTCGAAAACGAGCTCTCGAGAACCCTTAATATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTGATATCAGATCCACTAGTGGCCTATGCCACCTTTCGAGAGGACGATGCCCGTGTCTAAATGATTCGACCAGCCTAAGAATGTTCAACCCCTCACTAAAGGGAACAAAAGCTGGAGCTTCTTTGAAAAGATAATGTATGATTATGCTTTCACTCATATTTATACAGAAACTTGATGTTTTCTTTCGAGTATATACAAGGTGATTACATGTACGTTTGAAGTACAACTCTAGATTTTGTAGTGCCCTCTTGGGCTAGCGGTAAAGGTGCGCATTTTTTCACACCCTACAATGTTCTGTTCAAAAGATTTTGGTCAAACGCTGTAGAAGTGAAAGTTGGTGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATC\n"
]
}
],
"source": [
"print result.products[0].seq"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.11"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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