AUTHORS
CHANGELOG.md
DESCRIPTION.md
MANIFEST.in
README.md
requirements.txt
setup.py
./setup.py
./.eggs/ujson-1.35-py3.4-linux-x86_64.egg/ujson.py
./Mikado/__init__.py
./Mikado/exceptions.py
./Mikado/version.py
./Mikado/configuration/__init__.py
./Mikado/configuration/configurator.py
./Mikado/configuration/daijin_configurator.py
./Mikado/daijin/__init__.py
./Mikado/loci/__init__.py
./Mikado/loci/abstractlocus.py
./Mikado/loci/excluded.py
./Mikado/loci/locus.py
./Mikado/loci/monosublocus.py
./Mikado/loci/monosublocusholder.py
./Mikado/loci/reference_gene.py
./Mikado/loci/sublocus.py
./Mikado/loci/superlocus.py
./Mikado/parsers/GFF.py
./Mikado/parsers/GTF.py
./Mikado/parsers/__init__.py
./Mikado/parsers/bed12.py
./Mikado/parsers/blast_utils.py
./Mikado/parsers/blast_xml.py
./Mikado/parsers/gfannotation.py
./Mikado/picking/__init__.py
./Mikado/picking/loci_processer.py
./Mikado/picking/picker.py
./Mikado/preparation/__init__.py
./Mikado/preparation/annotation_parser.py
./Mikado/preparation/checking.py
./Mikado/preparation/prepare.py
./Mikado/scales/__init__.py
./Mikado/scales/accountant.py
./Mikado/scales/assigner.py
./Mikado/scales/class_codes.py
./Mikado/scales/compare.py
./Mikado/scales/resultstorer.py
./Mikado/serializers/__init__.py
./Mikado/serializers/external.py
./Mikado/serializers/junction.py
./Mikado/serializers/orf.py
./Mikado/serializers/blast_serializer/__init__.py
./Mikado/serializers/blast_serializer/hit.py
./Mikado/serializers/blast_serializer/hsp.py
./Mikado/serializers/blast_serializer/query.py
./Mikado/serializers/blast_serializer/target.py
./Mikado/serializers/blast_serializer/utils.py
./Mikado/serializers/blast_serializer/xml_serialiser.py
./Mikado/subprograms/__init__.py
./Mikado/subprograms/__main__.py
./Mikado/subprograms/compare.py
./Mikado/subprograms/configure.py
./Mikado/subprograms/pick.py
./Mikado/subprograms/prepare.py
./Mikado/subprograms/serialise.py
./Mikado/subprograms/util/__init__.py
./Mikado/subprograms/util/awk_gtf.py
./Mikado/subprograms/util/class_codes.py
./Mikado/subprograms/util/convert.py
./Mikado/subprograms/util/grep.py
./Mikado/subprograms/util/merge_blast.py
./Mikado/subprograms/util/metrics.py
./Mikado/subprograms/util/stats.py
./Mikado/subprograms/util/trim.py
./Mikado/tests/__init__.py
./Mikado/tests/assigner_tester.py
./Mikado/tests/intervaltree_tests.py
./Mikado/tests/locus_tester.py
./Mikado/tests/orf_tester.py
./Mikado/tests/parser_testing.py
./Mikado/tests/test_blast_related.py
./Mikado/tests/test_clique_methods.py
./Mikado/tests/test_db_utils.py
./Mikado/tests/test_external_scores.py
./Mikado/tests/test_gene.py
./Mikado/tests/test_invalid_orfs.py
./Mikado/tests/test_json.py
./Mikado/tests/test_metrics.py
./Mikado/tests/test_modifications.py
./Mikado/tests/test_serialisation.py
./Mikado/tests/test_splitting.py
./Mikado/tests/test_system_calls.py
./Mikado/tests/test_transcript_checker.py
./Mikado/tests/test_transcript_methods.py
./Mikado/tests/transcript_tester_negative.py
./Mikado/tests/transcript_tester_positive.py
./Mikado/tests/transcript_tester_single.py
./Mikado/tests/utilities_tester.py
./Mikado/transcripts/__init__.py
./Mikado/transcripts/clique_methods.py
./Mikado/transcripts/transcript.py
./Mikado/transcripts/transcriptchecker.py
./Mikado/transcripts/transcript_methods/__init__.py
./Mikado/transcripts/transcript_methods/finalizing.py
./Mikado/transcripts/transcript_methods/printing.py
./Mikado/transcripts/transcript_methods/retrieval.py
./Mikado/transcripts/transcript_methods/splitting.py
./Mikado/utilities/__init__.py
./Mikado/utilities/dbutils.py
./Mikado/utilities/log_utils.py
./Reference/filter_human.py
./Reference/get_biotype_source.py
./build/lib.linux-x86_64-3.4/Mikado/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/exceptions.py
./build/lib.linux-x86_64-3.4/Mikado/version.py
./build/lib.linux-x86_64-3.4/Mikado/configuration/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/configuration/configurator.py
./build/lib.linux-x86_64-3.4/Mikado/configuration/daijin_configurator.py
./build/lib.linux-x86_64-3.4/Mikado/daijin/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/loci/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/loci/abstractlocus.py
./build/lib.linux-x86_64-3.4/Mikado/loci/excluded.py
./build/lib.linux-x86_64-3.4/Mikado/loci/locus.py
./build/lib.linux-x86_64-3.4/Mikado/loci/monosublocus.py
./build/lib.linux-x86_64-3.4/Mikado/loci/monosublocusholder.py
./build/lib.linux-x86_64-3.4/Mikado/loci/reference_gene.py
./build/lib.linux-x86_64-3.4/Mikado/loci/sublocus.py
./build/lib.linux-x86_64-3.4/Mikado/loci/superlocus.py
./build/lib.linux-x86_64-3.4/Mikado/parsers/GFF.py
./build/lib.linux-x86_64-3.4/Mikado/parsers/GTF.py
./build/lib.linux-x86_64-3.4/Mikado/parsers/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/parsers/bed12.py
./build/lib.linux-x86_64-3.4/Mikado/parsers/blast_utils.py
./build/lib.linux-x86_64-3.4/Mikado/parsers/blast_xml.py
./build/lib.linux-x86_64-3.4/Mikado/parsers/gfannotation.py
./build/lib.linux-x86_64-3.4/Mikado/picking/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/picking/loci_processer.py
./build/lib.linux-x86_64-3.4/Mikado/picking/picker.py
./build/lib.linux-x86_64-3.4/Mikado/preparation/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/preparation/annotation_parser.py
./build/lib.linux-x86_64-3.4/Mikado/preparation/checking.py
./build/lib.linux-x86_64-3.4/Mikado/preparation/prepare.py
./build/lib.linux-x86_64-3.4/Mikado/scales/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/scales/accountant.py
./build/lib.linux-x86_64-3.4/Mikado/scales/assigner.py
./build/lib.linux-x86_64-3.4/Mikado/scales/class_codes.py
./build/lib.linux-x86_64-3.4/Mikado/scales/compare.py
./build/lib.linux-x86_64-3.4/Mikado/scales/resultstorer.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/external.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/junction.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/orf.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/blast_serializer/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/blast_serializer/hit.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/blast_serializer/hsp.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/blast_serializer/query.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/blast_serializer/target.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/blast_serializer/utils.py
./build/lib.linux-x86_64-3.4/Mikado/serializers/blast_serializer/xml_serialiser.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/__main__.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/compare.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/configure.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/pick.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/prepare.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/serialise.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/awk_gtf.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/class_codes.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/convert.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/grep.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/merge_blast.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/metrics.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/stats.py
./build/lib.linux-x86_64-3.4/Mikado/subprograms/util/trim.py
./build/lib.linux-x86_64-3.4/Mikado/tests/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/tests/assigner_tester.py
./build/lib.linux-x86_64-3.4/Mikado/tests/intervaltree_tests.py
./build/lib.linux-x86_64-3.4/Mikado/tests/locus_tester.py
./build/lib.linux-x86_64-3.4/Mikado/tests/orf_tester.py
./build/lib.linux-x86_64-3.4/Mikado/tests/parser_testing.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_blast_related.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_clique_methods.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_db_utils.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_external_scores.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_gene.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_invalid_orfs.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_json.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_metrics.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_modifications.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_serialisation.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_splitting.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_system_calls.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_transcript_checker.py
./build/lib.linux-x86_64-3.4/Mikado/tests/test_transcript_methods.py
./build/lib.linux-x86_64-3.4/Mikado/tests/transcript_tester_negative.py
./build/lib.linux-x86_64-3.4/Mikado/tests/transcript_tester_positive.py
./build/lib.linux-x86_64-3.4/Mikado/tests/transcript_tester_single.py
./build/lib.linux-x86_64-3.4/Mikado/tests/utilities_tester.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/clique_methods.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/transcript.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/transcriptchecker.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/transcript_methods/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/transcript_methods/finalizing.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/transcript_methods/printing.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/transcript_methods/retrieval.py
./build/lib.linux-x86_64-3.4/Mikado/transcripts/transcript_methods/splitting.py
./build/lib.linux-x86_64-3.4/Mikado/utilities/__init__.py
./build/lib.linux-x86_64-3.4/Mikado/utilities/dbutils.py
./build/lib.linux-x86_64-3.4/Mikado/utilities/log_utils.py
./build/lib.linux-x86_64-3.5/Mikado/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/exceptions.py
./build/lib.linux-x86_64-3.5/Mikado/version.py
./build/lib.linux-x86_64-3.5/Mikado/configuration/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/configuration/configurator.py
./build/lib.linux-x86_64-3.5/Mikado/configuration/daijin_configurator.py
./build/lib.linux-x86_64-3.5/Mikado/daijin/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/loci/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/loci/abstractlocus.py
./build/lib.linux-x86_64-3.5/Mikado/loci/excluded.py
./build/lib.linux-x86_64-3.5/Mikado/loci/locus.py
./build/lib.linux-x86_64-3.5/Mikado/loci/monosublocus.py
./build/lib.linux-x86_64-3.5/Mikado/loci/monosublocusholder.py
./build/lib.linux-x86_64-3.5/Mikado/loci/reference_gene.py
./build/lib.linux-x86_64-3.5/Mikado/loci/sublocus.py
./build/lib.linux-x86_64-3.5/Mikado/loci/superlocus.py
./build/lib.linux-x86_64-3.5/Mikado/parsers/GFF.py
./build/lib.linux-x86_64-3.5/Mikado/parsers/GTF.py
./build/lib.linux-x86_64-3.5/Mikado/parsers/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/parsers/bed12.py
./build/lib.linux-x86_64-3.5/Mikado/parsers/blast_utils.py
./build/lib.linux-x86_64-3.5/Mikado/parsers/blast_xml.py
./build/lib.linux-x86_64-3.5/Mikado/parsers/gfannotation.py
./build/lib.linux-x86_64-3.5/Mikado/picking/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/picking/loci_processer.py
./build/lib.linux-x86_64-3.5/Mikado/picking/picker.py
./build/lib.linux-x86_64-3.5/Mikado/preparation/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/preparation/annotation_parser.py
./build/lib.linux-x86_64-3.5/Mikado/preparation/checking.py
./build/lib.linux-x86_64-3.5/Mikado/preparation/prepare.py
./build/lib.linux-x86_64-3.5/Mikado/scales/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/scales/accountant.py
./build/lib.linux-x86_64-3.5/Mikado/scales/assigner.py
./build/lib.linux-x86_64-3.5/Mikado/scales/class_codes.py
./build/lib.linux-x86_64-3.5/Mikado/scales/compare.py
./build/lib.linux-x86_64-3.5/Mikado/scales/resultstorer.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/external.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/junction.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/orf.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/blast_serializer/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/blast_serializer/hit.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/blast_serializer/hsp.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/blast_serializer/query.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/blast_serializer/target.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/blast_serializer/utils.py
./build/lib.linux-x86_64-3.5/Mikado/serializers/blast_serializer/xml_serialiser.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/__main__.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/compare.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/configure.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/pick.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/prepare.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/serialise.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/awk_gtf.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/class_codes.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/convert.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/grep.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/merge_blast.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/metrics.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/stats.py
./build/lib.linux-x86_64-3.5/Mikado/subprograms/util/trim.py
./build/lib.linux-x86_64-3.5/Mikado/tests/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/tests/assigner_tester.py
./build/lib.linux-x86_64-3.5/Mikado/tests/intervaltree_tests.py
./build/lib.linux-x86_64-3.5/Mikado/tests/locus_tester.py
./build/lib.linux-x86_64-3.5/Mikado/tests/orf_tester.py
./build/lib.linux-x86_64-3.5/Mikado/tests/parser_testing.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_blast_related.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_clique_methods.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_db_utils.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_external_scores.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_gene.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_invalid_orfs.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_json.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_metrics.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_modifications.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_serialisation.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_splitting.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_system_calls.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_transcript_checker.py
./build/lib.linux-x86_64-3.5/Mikado/tests/test_transcript_methods.py
./build/lib.linux-x86_64-3.5/Mikado/tests/transcript_tester_negative.py
./build/lib.linux-x86_64-3.5/Mikado/tests/transcript_tester_positive.py
./build/lib.linux-x86_64-3.5/Mikado/tests/transcript_tester_single.py
./build/lib.linux-x86_64-3.5/Mikado/tests/utilities_tester.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/clique_methods.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/transcript.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/transcriptchecker.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/transcript_methods/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/transcript_methods/finalizing.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/transcript_methods/printing.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/transcript_methods/retrieval.py
./build/lib.linux-x86_64-3.5/Mikado/transcripts/transcript_methods/splitting.py
./build/lib.linux-x86_64-3.5/Mikado/utilities/__init__.py
./build/lib.linux-x86_64-3.5/Mikado/utilities/dbutils.py
./build/lib.linux-x86_64-3.5/Mikado/utilities/log_utils.py
./build/lib.linux-x86_64-3.6/Mikado/__init__.py
./build/lib.linux-x86_64-3.6/Mikado/exceptions.py
./build/lib.linux-x86_64-3.6/Mikado/version.py
./build/lib.linux-x86_64-3.6/Mikado/configuration/__init__.py
./build/lib.linux-x86_64-3.6/Mikado/configuration/configurator.py
./build/lib.linux-x86_64-3.6/Mikado/configuration/daijin_configurator.py
./build/lib.linux-x86_64-3.6/Mikado/daijin/__init__.py
./build/lib.linux-x86_64-3.6/Mikado/loci/__init__.py
./build/lib.linux-x86_64-3.6/Mikado/loci/abstractlocus.py
./build/lib.linux-x86_64-3.6/Mikado/loci/excluded.py
./build/lib.linux-x86_64-3.6/Mikado/loci/locus.py
./build/lib.linux-x86_64-3.6/Mikado/loci/monosublocus.py
./build/lib.linux-x86_64-3.6/Mikado/loci/monosublocusholder.py
./build/lib.linux-x86_64-3.6/Mikado/loci/reference_gene.py
./build/lib.linux-x86_64-3.6/Mikado/loci/sublocus.py
./build/lib.linux-x86_64-3.6/Mikado/loci/superlocus.py
./build/lib.linux-x86_64-3.6/Mikado/parsers/GFF.py
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util/calculate_distances.py
util/class_run.py
util/convert_cdna_match_gff3.py
util/extract_promoter_regions.py
util/getFastaFromIds.py
util/gffjunc_to_bed12.py
util/grep.py
util/merge_junction_bed12.py
util/remove_from_embl.py
util/remove_utrs.py
util/sanitize_blast_db.py
util/split_fasta.py
util/tease_maker_apart.py
util/trim_long_introns.py