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protein-clustering.html
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<title>Protein clustering process — Overview of datasets</title>
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Intro
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<a class="reference internal" href="bindingdb-overview.html">
BindingDB overview
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BioLiP overview
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Protein clustering process
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Ligand clustering process
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BindingDB clusters
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BioLiP clusters
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Combined clusters
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Overview
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Cluster statistics
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<h1>Protein clustering process</h1>
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Setup
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Overview
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Cluster statistics
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<div class="tex2jax_ignore mathjax_ignore section" id="protein-clustering-process">
<h1>Protein clustering process<a class="headerlink" href="#protein-clustering-process" title="Permalink to this headline">¶</a></h1>
<div class="section" id="setup">
<h2>Setup<a class="headerlink" href="#setup" title="Permalink to this headline">¶</a></h2>
<p>Add user’s current working directory to search path:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">sys</span>
<span class="n">sys</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="p">[</span><span class="sa">r</span><span class="s2">"C:\sw\plb"</span><span class="p">]</span> <span class="o">+</span> <span class="n">sys</span><span class="o">.</span><span class="n">path</span>
</pre></div>
</div>
</div>
</div>
<p>Also change current working directory:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="sa">r</span><span class="s2">"C:\sw\plb"</span><span class="p">)</span>
</pre></div>
</div>
</div>
</div>
<p>Imports:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">Counter</span>
<span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
<span class="kn">import</span> <span class="nn">myst_nb</span>
<span class="kn">from</span> <span class="nn">src.config</span> <span class="kn">import</span> <span class="n">get_config</span>
<span class="kn">from</span> <span class="nn">src.data_split.protein_clustering</span> <span class="kn">import</span> <span class="n">read_protein_cluster_labels</span>
<span class="kn">from</span> <span class="nn">src.data_structure_utils</span> <span class="kn">import</span> <span class="n">read_tsv</span>
<span class="kn">from</span> <span class="nn">src.stats_utils</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">get_stats_from_counter</span><span class="p">,</span>
<span class="n">print_counter_stats_df</span><span class="p">,</span>
<span class="p">)</span>
</pre></div>
</div>
</div>
</div>
<p>Set up document options:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># This import automatically sets seeds</span>
<span class="kn">import</span> <span class="nn">src.set_seed</span>
<span class="c1"># Nice pandas tables</span>
<span class="kn">import</span> <span class="nn">itables</span>
<span class="n">itables</span><span class="o">.</span><span class="n">init_notebook_mode</span><span class="p">(</span><span class="n">all_interactive</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">itables</span><span class="o">.</span><span class="n">options</span><span class="o">.</span><span class="n">maxColumns</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># unlimited columns</span>
<span class="n">itables</span><span class="o">.</span><span class="n">options</span><span class="o">.</span><span class="n">maxBytes</span> <span class="o">=</span> <span class="mi">32000000</span>
<span class="n">itables</span><span class="o">.</span><span class="n">options</span><span class="o">.</span><span class="n">classes</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"display"</span><span class="p">,</span> <span class="s2">"nowrap"</span><span class="p">]</span>
<span class="n">itables</span><span class="o">.</span><span class="n">options</span><span class="o">.</span><span class="n">order</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># disable auto-sorting</span>
</pre></div>
</div>
</div>
<div class="cell_output docutils container">
<script type="application/javascript">if (typeof require !== 'undefined')
require.config({
paths: {
jquery: 'https://code.jquery.com/jquery-3.5.1.min',
datatables: 'https://cdn.datatables.net/1.11.3/js/jquery.dataTables.min',
}
});
</script></div>
</div>
<p>Get filepaths of data directories:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">config</span> <span class="o">=</span> <span class="n">get_config</span><span class="p">()</span>
<span class="n">dir_data</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">config</span><span class="p">[</span><span class="s2">"data_directory"</span><span class="p">])</span>
<span class="n">dir_features</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">config</span><span class="p">[</span><span class="s2">"features_directory"</span><span class="p">])</span>
</pre></div>
</div>
</div>
</div>
</div>
<div class="section" id="overview">
<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
<p>The general process I used for clustering the protein sequences is:</p>
<ul class="simple">
<li><p>Get a combined list of all unique protein sequences present in the filtered
BindingDB and BioLiP dataframes</p></li>
<li><p>Cluster the sequences using <a class="reference external" href="https://github.com/soedinglab/MMseqs2">mmseqs cluster</a>
with a sequence identity threshold of >10% (otherwise, I used default options)</p></li>
</ul>
</div>
<div class="section" id="cluster-statistics">
<h2>Cluster statistics<a class="headerlink" href="#cluster-statistics" title="Permalink to this headline">¶</a></h2>
<p>Read the protein cluster assignments file:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">df_protein_clusters</span> <span class="o">=</span> <span class="n">read_protein_cluster_labels</span><span class="p">(</span>
<span class="n">proteins_fasta</span><span class="o">=</span><span class="n">dir_features</span> <span class="o">/</span> <span class="s2">"all_proteins_single.fasta"</span><span class="p">,</span>
<span class="n">clusters_tsv</span><span class="o">=</span><span class="n">dir_features</span> <span class="o">/</span> <span class="s2">"all_proteins_single_mmseqs_db_seqid_0.1/clusters.tsv"</span><span class="p">,</span>
<span class="p">)</span>
</pre></div>
</div>
</div>
</div>
<p>Print a sample of the clustering outputs:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">itables</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">df_protein_clusters</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">30</span><span class="p">))</span>
</pre></div>
</div>
</div>
<div class="cell_output docutils container">
<div class="output text_html"><table id="ea0ed983-2169-473a-8a06-4bc25b97ff5b" class="display nowrap"style="max-width:100%"><thead><th>cluster</th><th>protein_id</th><th>chain_sequence</th><th>is_representative_seq</th></thead><tbody><tr><td>Loading... (need <a href=https://mwouts.github.io/itables/troubleshooting.html>help</a>?)</td></tr></tbody></table>
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.11.3/css/jquery.dataTables.min.css">
<style> table td {
text-overflow: ellipsis;
overflow: hidden;
} </style>
<style> table th {
text-overflow: ellipsis;
overflow: hidden;
} </style>
<script type="module">
// Define the table data
const data = [["2275", "2275", "EKYQNLLVVIDPNQDDQPALRRAVYIVQRNGGRIKAFLPVYDLSYDMTTLLSPDERNAMRKGVINQKTAWIKQQARYYLEAGIQIDIKVIWHNRPYEAIIEEVITDKHDLLIKMAHQHDKLGSLIFTPLDWQLLRKCPAPVWMVKDKEWPEYGTIVVAANLSNEESYHDALNLKLIELTNDLSHRIQKDPDVHLLSAYPVAPINIAIELPDFDPNLYNNALRGQHLIAMKELRQKFSIPEEKTHVKEGLPEQVIPQVCEELNAGIVVLGILGRTGAAFLGNTAEQLIDHIKCDLLAIKPDGFTCPITV", true], ["2275", "6390", "MAMYQNMLVVIDPNQDDQPALRRAVYLHQRIGGKIKAFLPIYDFSYEMTTLLSPDERTAMRQGVISQRTAWIREQAKYYLEAGVPIEIKVVWHNRPFEAIIQEVIAGSHDLVLKMAHQADRLEAVIFTPTDWHLLRKCPSPVWMVKDQPWPEGGKALVAVNLASEEPYHNALNEKLVKETLQLAEQVNHTEVHLVGAYPVTPINIAIELPEFDPSVYNDAIRGQHLLAMKALRQKFSIDEKVTHVEKGLPEEVIPDLAEHLQAGIVVLGTVGRTGLSAAFLGNTAEQVIDHLRCDLLVIKPDEYQTPVELD", false], ["2403", "2403", "EPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE", true], ["2403", "3271", "GEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE", false], ["2595", "2595", "ESFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSAHTRCKLCYPFIMGIHIIDR", true], ["2595", "13445", "VESFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSAHTRCKLCYPMQPFIMGIHIIDRE", false], ["2659", "2659", "ETVQDCENKLPPSLKSRLCEIRRYEIIEGPEMDKHIHCVMRALDFVYEDGRGDYHKLYDPLNIIELDKRHDVNLEKCIGECVQVPTSERAHVFYKCLLKSTTGRTFKKVFDLMELKKAGKVPQHQRYTAEFVQIMKDYDKALNC", true], ["2659", "7092", "METVQDCENKLPPSLKSRLCEIRRYEIIEGPEMDKHIHCVMRALDFVYEDGRGDYHKLYDPLNIIELDKRHDVNLEKCIGECVQVPTSERAHVFYKCLLKSTTGRTFKKVFDLMELKKAGKVPQHQRYTAEFVQIMKDYDKALNC", false], ["2691", "2691", "EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGFQQWRGLSRYFKVQLRKRRVK", true], ["2723", "2723", "EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK", true], ["2723", "10089", "PTFYDIETLKVIDEEWQRTQCSPRETAVEVASELGKSTNTFFKPPCVNVFRCGGCCNEESLICMNTSTSYISKQLFEISVPLTSVPELVPVKVANHTGCKCLPT", false], ["2755", "2755", "EYQLVVNAVRKLQESGFYWSAVTGGEANLLLSAEPAGTFLIRDSSDQRHFFTLSVKTQSGTKNLRIQCEGGSFSLQSDPRSTQPVPRFDCVLKLVHHYMPPPGTPSFSLPPTEPSSEVPEQPPAQALPGSTPKRAYYIYSGGEKIPLVLSRPLSSN", true], ["2947", "2947", "FTGGDEYQKHFLPRDYLATYYSFDGSPSPEAEMLKFNLECLHKTFGPGGLQGDTLIDIGSGPTIYQVLAACDSFQDITLSDFTDRNREELEKWLKKEPGAYDWTPAVKFACELEGNSGRWEEKEEKLRAAVKRVLKCDVHLGNPLAPAVLPLADCVLTLLAMECACCSLDAYRAALCNLASLLKPGGHLVTTVTLRLPSYMVGKREFSCVALEKGEVEQAVLDAGFDIEQLLHSPQSYSVTNAANNGVCCIVARKKP", true], ["2947", "7488", "MKGGFTGGDEYQKHFLPRDYLATYYSFDGSPSPEAEMLKFNLECLHKTFGPGGLQGDTLIDIGSGPTIYQVLAACDSFQDITLSDFTDRNREELEKWLKKEPGAYDWTPAVKFACELEGNSGRWEEKEEKLRAAVKRVLKCDVHLGNPLAPAVLPLADCVLTLLAMECACCSLDAYRAALCNLASLLKPGGHLVTTVTLRLPSYMVGKREFSCVALEKEEVEQAVLDAGFDIEQLLHSPQSYSVTNAANNGVCFIVARKKPGP", false], ["2947", "11689", "SHFNPRDYLEKYYKFGSRHSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKKEPAAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSLPLGREAVEAAVKEAGYTIEWFEVIEGLFSLVARKL", false], ["2947", "7059", "MESGFTSKDTYLSHFNPRDYLEKYYKFGSRHSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKKEPEAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSSLPLGREAVEAAVKEAGYTIEWFEVISQSYSSTMANNEGLFSLVARKLSRPL", false], ["2947", "13367", "TYLSHFNPRDYLEKYYKFGSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKKEPAAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSSLPLGREAVEAAVKEAGYTIEWFEVISQSYSSTMANNEGLFSLVARKL", false], ["2947", "8399", "MSGADRSPNAGAAPDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVGL", false], ["2947", "8415", "MSGTDRSQAAGAVPDSDPGLAAVSSAYQRFEPRAYLRNNYAPPRGDLSCPDGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTIYQLLSACAHFEDITMTDFLEVNRQELRLWLREEPGAFDWSVYSQHVCLIEGKGESWQEKECQLRARVKRILPIDVHRPQPLGAGGLAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLAVVPVREEEVREALVRTATRCGICARTPMPAHLQTGVDDVKGIFFTRAQKKVGV", false], ["3299", "3299", "GFKGVGTYEIVPYQAPSLNLNAWEGKLEPGAVVRTYTRGDKPSDNAKWQVALVAGSGDSAEYLIINVHSGYFLTATKENHIVSTPQISPTDPSARWTIKPATTHQYEVFTINNKVSELGQLTVKDYSTHSGADVLSASAKTADNQKWYFDAK", true], ["3459", "3459", "GKEKSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDKTGGGGGGGG", true], ["3459", "3458", "GKEKSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK", false], ["3459", "2258", "EKSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK", false], ["3459", "2259", "EKSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDKTE", false], ["3459", "7205", "MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGITIDISLWKFETTKYYITIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVNKMDSTEPAYSEKRYDEIVKEVSAYIKKIGYNPATVPFVPISGWHGDNMLEPSPNMPWFKGWKVERKEGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGILRPGMVVTFAPVNITTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDIRRGNVCGDSKSDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACKFAELKEKIDRRSGKKLEDNPKSLKSGDAAIVEMVPGKPMCVESFSQYPPLGRFAVRDMRQTVAVGVIKNVEKKSGGAGKVTKSAQKAQKAGK", false], ["3459", "12808", "TEDATDLQNEVDQELLKDMYGKEHVNIVFIGHVDAGKSTLGGNILFLTGMVDKRTMEKIEREAKRAYFETEHRRFSLLDAPGASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMDEPSVQWSEERYKECVDKLSMFLRRVAGYNSKTDVKYMPVSAYTGQNVKDRVDSSVCPWYQGPSLLEYLDSMTHLERKVNAPFIMPIASKYKDLGTILEGKIEAGSIKKNSNVLVMPINQTLEVTAIYDEADEEISSSICGDQVRLRVRGDDSDVQTGYVLTSTKNPVHATTRFIAQIAILELPSILTTGYSCVMHIHTAVEEVSFAKLLHKLDKTNRKSKKPPMFATKGMKIIAELETQTPVCMERFEDYQYMGRFTLRDQGTTVAVGKVVKILD", false], ["3459", "12807", "TEDATDLQNEVDQELLKDMYGKEHVNIVFIGHVDAGKSTLGGNILFLTGMVDKRTMEKIEREAKERAYFETEHRRFSLLDAPGASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMDEPSVQWSEERYKECVDKLSMFLRRVAGYNSKTDVKYMPVSAYTGQNVKDRVDSSVCPWYQGPSLLEYLDSMTHLERKVNAPFIMPIASKYKDLGTILEGKIEAGSIKKNSNVLVMPINQTLEVTAIYDEADEEISSSICGDQVRLRVRGDDSDVQTGYVLTSTKNPVHATTRFIAQIAILELPSILTTGYSCVMHIHTAVEEVSFAKLLHKLDKTNRKSKKPPMFATKGMKIIAELETQTPVCMERFEDYQYMGRFTLRDQGTTVAVGKVVKILD", false], ["3459", "3338", "GGKDHVSLIFMGHVDAGKSTMGGNLLYLTGSVDKRTIEKYEREAKDAGRQGWYLSWVMDTNKEERNDGKTIEVGKAYFETEKRRYTILDAPGHKMYVSEMIGGASQADVGVLVISARKGEYETGFERGGQTREHALLAKTQGVNKMVVVVNKMDDPTVNWSKERYDQCVSNVSNFLRAIGYNIKTDVVFMPVSGYSGANLKDHVDPKECPWYTGPTLLEYLDTMNHVDRHINAPFMLPIAAKMKDLGTIVEGKIESGHIKKGQSTLLMPNKTAVEIQNIYNETENEVDMAMCGEQVKLRIKGVEEEDISPGFVLTSPKNPIKSVTKFVAQIAIVELKSIIAAGFSCVMHVHTAIEEVHIVKLLHKLEKGTNRKSKKPPAFAKKGMKVIAVLETEAPVCVETYQDYPQLGRFTLRDQGTTIAIGKIVKIAE", false], ["3459", "12956", "TKPHVNIGTIGHVDHGKTTLTAAITKVLAEKGQAEFKAYDQIDKAPEEKERGITISTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNKVDMVDDEELLELVEMEVRELLSSYDFPGDDIPIIKGSALKALEGDEEGEEAIMKLMDAVDSYIPEPERAIDKPFLMPIEDVFSIRGTVVTGRVERGIVKVGEEVEIVGIRDTQKTTCTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKPGSIKPHTKFKAEVYILTKEEGGRHTPFFNGYRPQFYFRTTDVTGVITLPEGVEMVMPGDNVTITVELIAPIAMEEGLRFAIREGGRTVGAGVVSEIIE", false], ["3459", "9068", "NKPHVNVGTIGHVDHGKTTLTAAIATICAKTYGGEAKDYSQIDSAPEEKARGITINTSHVEYDSPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVCAATDGPMPQTREHILLSRQVGVPYIIVFLNKCDLVDDEELLELVEMEVRELLSTYDFPGDDTPVIRGSALAALNGEAGPYGEESVLALVAALDSYIPEPERAIDKAFLMPIEDVFSISGRGTVVTGRVEAGIIKVGEEVEIVGIKDTVKTTVTGVEMFRKLLDEGRAGENCGILLRGTKREEVQRGQVLAKPGTIKPHTKFDAEVYVLSKEEGGRHTPFLNGYRPQFYFRTTDVTGAIQLKEGVEMVMPGDNVEMSVELIHPIAMDPGLRFAIREGGRTVGAGVVAKVTA", false]];
if (typeof require === 'undefined') {
// TODO: This should become the default (use a simple import)
// when the ESM version works independently of whether
// require.js is there or not, see
// https://datatables.net/forums/discussion/69066/esm-es6-module-support?
const {default: $} = await import("https://esm.sh/[email protected]");
const {default: initDataTables} = await import("https://esm.sh/[email protected][email protected]");
initDataTables();
// Define the dt_args
let dt_args = {"columnDefs": [{"width": "70px", "targets": "_all"}], "order": []};
dt_args["data"] = data;
// Display the table
$(document).ready(function () {
$('#ea0ed983-2169-473a-8a06-4bc25b97ff5b').DataTable(dt_args);
});
} else {
require(["jquery", "datatables"], ($, datatables) => {
// Define the dt_args
let dt_args = {"columnDefs": [{"width": "70px", "targets": "_all"}], "order": []};
dt_args["data"] = data;
// Display the table
$(document).ready(function () {
$('#ea0ed983-2169-473a-8a06-4bc25b97ff5b').DataTable(dt_args);
});
}
)
}
</script>
</div></div>
</div>
<p>Generate some statistics from the clustering outputs:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">protein_cluster_stats</span> <span class="o">=</span> <span class="n">get_stats_from_counter</span><span class="p">(</span>
<span class="n">counts</span><span class="o">=</span><span class="n">Counter</span><span class="p">(</span><span class="n">df_protein_clusters</span><span class="p">[</span><span class="s2">"cluster"</span><span class="p">]),</span>
<span class="n">ntop</span><span class="o">=</span><span class="mi">30</span><span class="p">,</span>
<span class="n">nbins</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span>
<span class="n">name_of_thing_being_counted</span><span class="o">=</span><span class="s2">"cluster_label"</span><span class="p">,</span>
<span class="n">xaxis_name</span><span class="o">=</span><span class="s2">"number of unique aa sequences in the cluster"</span><span class="p">,</span>
<span class="n">do_show</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="p">)</span>
</pre></div>
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Total number of entries: 14167
Total number of unique entries: 3230
Distribution of frequencies of individual entries, linear scale (left):
Distribution of frequencies of individual entries, log scale (right):
</pre></div>
</div>
<img alt="_images/protein-clustering_15_1.png" src="_images/protein-clustering_15_1.png" />
<img alt="_images/protein-clustering_15_2.png" src="_images/protein-clustering_15_2.png" />
</div>
</div>
<p>The most commonly occurring clusters are:</p>
<div class="cell docutils container">
<div class="cell_input docutils container">
<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">print_counter_stats_df</span><span class="p">(</span><span class="n">protein_cluster_stats</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="cell_output docutils container">
<div class="output text_html"><table id="6de70b48-6a00-47e8-87e3-c35f2dd922ca" class="display nowrap"style="max-width:100%"><thead><th>number_of_occurrences</th><th>cluster_label</th></thead><tbody><tr><td>Loading... (need <a href=https://mwouts.github.io/itables/troubleshooting.html>help</a>?)</td></tr></tbody></table>
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<style> table th {
text-overflow: ellipsis;
overflow: hidden;
} </style>
<script type="module">
// Define the table data
const data = [[949, "509"], [582, "12068"], [338, "10470"], [204, "3283"], [183, "4076"], [168, "7843"], [163, "9634"], [158, "8379"], [112, "9316"], [100, "10720"], [90, "11438"], [88, "9402"], [88, "13590"], [87, "11986"], [85, "1046"], [82, "6000"], [77, "2587"], [75, "8768"], [69, "5272"], [65, "4427"], [63, "7987"], [62, "4497"], [54, "6432"], [51, "7361"], [48, "14055"], [44, "11584"], [40, "420"], [40, "6070"], [40, "6801"], [38, "12212"]];
if (typeof require === 'undefined') {
// TODO: This should become the default (use a simple import)
// when the ESM version works independently of whether
// require.js is there or not, see
// https://datatables.net/forums/discussion/69066/esm-es6-module-support?
const {default: $} = await import("https://esm.sh/[email protected]");
const {default: initDataTables} = await import("https://esm.sh/[email protected][email protected]");
initDataTables();
// Define the dt_args
let dt_args = {"columnDefs": [{"width": "70px", "targets": "_all"}], "order": []};
dt_args["data"] = data;
// Display the table
$(document).ready(function () {
$('#6de70b48-6a00-47e8-87e3-c35f2dd922ca').DataTable(dt_args);
});
} else {
require(["jquery", "datatables"], ($, datatables) => {
// Define the dt_args
let dt_args = {"columnDefs": [{"width": "70px", "targets": "_all"}], "order": []};
dt_args["data"] = data;
// Display the table
$(document).ready(function () {
$('#6de70b48-6a00-47e8-87e3-c35f2dd922ca').DataTable(dt_args);
});
}
)
}
</script>
</div></div>
</div>
</div>
</div>
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binderOptions: {
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