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Mikado.dot
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Mikado.dot
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digraph G {
graph [rankdir=TB, clusterrank="local"];
subgraph cluster_G {
graph [style="filled,rounded",fillcolor="#80808018", label=""];
__init__ [label="__init__", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="0"];
_transcripts [label="_transcripts", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="1"];
_transcripts__clique_methods [label="_transcripts.clique_methods", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="2"];
_transcripts__scoring_configuration [label="_transcripts.scoring_configuration", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="3"];
_transcripts__transcript_base [label="_transcripts.transcript_base", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="4"];
_transcripts__transcript_methods [label="_transcripts.transcript_methods", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="5"];
_transcripts__transcript_methods__finalizing [label="_transcripts.transcript_methods.finalizing", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="6"];
_transcripts__transcript_methods__printing [label="_transcripts.transcript_methods.printing", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="7"];
configuration [label="configuration", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="8"];
configuration__configuration [label="configuration.configuration", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="9"];
configuration__configurator [label="configuration.configurator", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="10"];
configuration__daijin_configuration [label="configuration.daijin_configuration", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="11"];
configuration__daijin_configurator [label="configuration.daijin_configurator", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="12"];
configuration__picking_config [label="configuration.picking_config", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="13"];
configuration__prepare_config [label="configuration.prepare_config", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="14"];
configuration__serialise_config [label="configuration.serialise_config", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="15"];
daijin [label="daijin", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="16"];
daijin____main__ [label="daijin.__main__", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="17"];
loci [label="loci", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="18"];
loci__abstractlocus [label="loci.abstractlocus", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="19"];
loci__excluded [label="loci.excluded", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="20"];
loci__locus [label="loci.locus", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="21"];
loci__monosublocus [label="loci.monosublocus", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="22"];
loci__monosublocusholder [label="loci.monosublocusholder", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="23"];
loci__sublocus [label="loci.sublocus", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="24"];
loci__superlocus [label="loci.superlocus", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="25"];
parsers [label="parsers", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="26"];
parsers__GFF [label="parsers.GFF", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="27"];
parsers__GTF [label="parsers.GTF", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="28"];
parsers__bam_parser [label="parsers.bam_parser", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="29"];
parsers__bed12 [label="parsers.bed12", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="30"];
parsers__blast_utils [label="parsers.blast_utils", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="31"];
parsers__gfannotation [label="parsers.gfannotation", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="32"];
picking [label="picking", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="33"];
picking___loci_serialiser [label="picking._loci_serialiser", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="34"];
picking___locus_line_creator [label="picking._locus_line_creator", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="35"];
picking___locus_single_printer [label="picking._locus_single_printer", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="36"];
picking___merge_loci_utils [label="picking._merge_loci_utils", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="37"];
picking__loci_processer [label="picking.loci_processer", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="38"];
picking__picker [label="picking.picker", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="39"];
preparation [label="preparation", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="40"];
preparation__annotation_parser [label="preparation.annotation_parser", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="41"];
preparation__checking [label="preparation.checking", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="42"];
preparation__prepare [label="preparation.prepare", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="43"];
scales [label="scales", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="44"];
scales__accountant [label="scales.accountant", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="45"];
scales__assignment [label="scales.assignment", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="46"];
scales__assignment__assigner [label="scales.assignment.assigner", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="47"];
scales__assignment__distributed [label="scales.assignment.distributed", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="48"];
scales__calculator [label="scales.calculator", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="49"];
scales__class_codes [label="scales.class_codes", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="50"];
scales__compare [label="scales.compare", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="51"];
scales__prediction_parsers [label="scales.prediction_parsers", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="52"];
scales__prediction_parsers__parse_bam_prediction [label="scales.prediction_parsers.parse_bam_prediction", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="53"];
scales__prediction_parsers__parse_bed12 [label="scales.prediction_parsers.parse_bed12", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="54"];
scales__prediction_parsers__parse_gff3_prediction [label="scales.prediction_parsers.parse_gff3_prediction", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="55"];
scales__prediction_parsers__parse_gtf_prediction [label="scales.prediction_parsers.parse_gtf_prediction", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="56"];
scales__prediction_parsers__transmission [label="scales.prediction_parsers.transmission", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="57"];
scales__reference_preparation [label="scales.reference_preparation", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="58"];
scales__reference_preparation__gene_dict [label="scales.reference_preparation.gene_dict", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="59"];
scales__reference_preparation__indexing [label="scales.reference_preparation.indexing", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="60"];
scales__reference_preparation__prepare_reference [label="scales.reference_preparation.prepare_reference", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="61"];
scales__resultstorer [label="scales.resultstorer", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="62"];
serializers [label="serializers", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="63"];
serializers__blast_serializer [label="serializers.blast_serializer", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="64"];
serializers__blast_serializer__blast_serialiser [label="serializers.blast_serializer.blast_serialiser", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="65"];
serializers__blast_serializer__hit [label="serializers.blast_serializer.hit", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="66"];
serializers__blast_serializer__hsp [label="serializers.blast_serializer.hsp", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="67"];
serializers__blast_serializer__query [label="serializers.blast_serializer.query", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="68"];
serializers__blast_serializer__tab_serialiser [label="serializers.blast_serializer.tab_serialiser", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="69"];
serializers__blast_serializer__tabular_utils [label="serializers.blast_serializer.tabular_utils", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="70"];
serializers__blast_serializer__target [label="serializers.blast_serializer.target", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="71"];
serializers__blast_serializer__utils [label="serializers.blast_serializer.utils", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="72"];
serializers__blast_serializer__xml_serialiser [label="serializers.blast_serializer.xml_serialiser", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="73"];
serializers__blast_serializer__xml_utils [label="serializers.blast_serializer.xml_utils", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="74"];
serializers__external [label="serializers.external", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="75"];
serializers__junction [label="serializers.junction", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="76"];
serializers__orf [label="serializers.orf", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="77"];
subprograms [label="subprograms", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="78"];
subprograms____main__ [label="subprograms.__main__", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="79"];
subprograms__compare [label="subprograms.compare", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="80"];
subprograms__configure [label="subprograms.configure", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="81"];
subprograms__pick [label="subprograms.pick", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="82"];
subprograms__prepare [label="subprograms.prepare", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="83"];
subprograms__serialise [label="subprograms.serialise", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="84"];
subprograms__util [label="subprograms.util", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="85"];
subprograms__util__awk_gtf [label="subprograms.util.awk_gtf", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="86"];
subprograms__util__class_codes [label="subprograms.util.class_codes", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="87"];
subprograms__util__convert [label="subprograms.util.convert", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="88"];
subprograms__util__grep [label="subprograms.util.grep", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="89"];
subprograms__util__metrics [label="subprograms.util.metrics", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="90"];
subprograms__util__stats [label="subprograms.util.stats", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="91"];
subprograms__util__trim [label="subprograms.util.trim", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="92"];
transcripts [label="transcripts", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="93"];
transcripts__reference_gene [label="transcripts.reference_gene", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="94"];
transcripts__transcript [label="transcripts.transcript", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="95"];
transcripts__transcript_methods [label="transcripts.transcript_methods", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="96"];
transcripts__transcript_methods__retrieval [label="transcripts.transcript_methods.retrieval", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="97"];
transcripts__transcript_methods__splitting [label="transcripts.transcript_methods.splitting", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="98"];
transcripts__transcriptchecker [label="transcripts.transcriptchecker", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="99"];
transcripts__transcriptcomputer [label="transcripts.transcriptcomputer", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="100"];
utilities [label="utilities", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="101"];
utilities__dbutils [label="utilities.dbutils", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="102"];
utilities__file_type [label="utilities.file_type", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="103"];
utilities__log_utils [label="utilities.log_utils", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="104"];
utilities__namespace [label="utilities.namespace", style="filled", fillcolor="#ffffffb2", fontcolor="#000000", group="105"];
subgraph cluster__transcripts__clique_methods {
graph [style="filled,rounded",fillcolor="#80808018", label="_transcripts.clique_methods"];
_transcripts__clique_methods__define_graphX [label="define_graph\n(_transcripts/clique_methods.py:39)", style="filled", fillcolor="#ffa499b2", fontcolor="#000000", group="2"];
_transcripts__clique_methods__find_cliques [label="find_cliques\n(_transcripts/clique_methods.py:77)", style="filled", fillcolor="#ffa499b2", fontcolor="#000000", group="2"];
_transcripts__clique_methods__find_communities [label="find_communities\n(_transcripts/clique_methods.py:13)", style="filled", fillcolor="#ffa499b2", fontcolor="#000000", group="2"];
}
subgraph cluster__transcripts__scoring_configuration {
graph [style="filled,rounded",fillcolor="#80808018", label="_transcripts.scoring_configuration"];
_transcripts__scoring_configuration__InclusionFilter [label="InclusionFilter\n(_transcripts/scoring_configuration.py:34)", style="filled", fillcolor="#ffaa99b2", fontcolor="#000000", group="3"];
_transcripts__scoring_configuration__MinMaxScore [label="MinMaxScore\n(_transcripts/scoring_configuration.py:70)", style="filled", fillcolor="#ffaa99b2", fontcolor="#000000", group="3"];
_transcripts__scoring_configuration__NumBoolEqualityFilter [label="NumBoolEqualityFilter\n(_transcripts/scoring_configuration.py:25)", style="filled", fillcolor="#ffaa99b2", fontcolor="#000000", group="3"];
_transcripts__scoring_configuration__RangeFilter [label="RangeFilter\n(_transcripts/scoring_configuration.py:43)", style="filled", fillcolor="#ffaa99b2", fontcolor="#000000", group="3"];
_transcripts__scoring_configuration__Requirements [label="Requirements\n(_transcripts/scoring_configuration.py:96)", style="filled", fillcolor="#ffaa99b2", fontcolor="#000000", group="3"];
_transcripts__scoring_configuration__ScoringFile [label="ScoringFile\n(_transcripts/scoring_configuration.py:182)", style="filled", fillcolor="#ffaa99b2", fontcolor="#000000", group="3"];
_transcripts__scoring_configuration__SizeFilter [label="SizeFilter\n(_transcripts/scoring_configuration.py:16)", style="filled", fillcolor="#ffaa99b2", fontcolor="#000000", group="3"];
_transcripts__scoring_configuration__TargetScore [label="TargetScore\n(_transcripts/scoring_configuration.py:82)", style="filled", fillcolor="#ffaa99b2", fontcolor="#000000", group="3"];
subgraph cluster__transcripts__scoring_configuration__RangeFilter {
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