AUTHORS
CHANGELOG.md
DESCRIPTION.md
MANIFEST.in
README.md
requirements.txt
setup.py
./setup.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_bed12.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
./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_bed12.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
./docs/conf.py
./util/add_transcript_feature_to_gtf.py
./util/align_collect.py
./util/analyse_metrics.py
./util/asm_collect.py
./util/bam2gtf.py
./util/calculate_distances.py
./util/class_run.py
./util/convert_cdna_match_gff3.py
./util/create_model.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/self_training.py
./util/split_fasta.py
./util/tease_maker_apart.py
./util/trim_long_introns.py
Mikado/__init__.py
Mikado/exceptions.py
Mikado/version.py
Mikado.egg-info/PKG-INFO
Mikado.egg-info/SOURCES.txt
Mikado.egg-info/dependency_links.txt
Mikado.egg-info/entry_points.txt
Mikado.egg-info/not-zip-safe
Mikado.egg-info/requires.txt
Mikado.egg-info/top_level.txt
Mikado/configuration/__init__.py
Mikado/configuration/configuration_blueprint.json
Mikado/configuration/configurator.py
Mikado/configuration/daijin_configurator.py
Mikado/configuration/daijin_schema.json
Mikado/configuration/requirements_blueprint.json
Mikado/configuration/scoring_blueprint.json
Mikado/configuration/scoring_files/athaliana_scoring.yaml
Mikado/configuration/scoring_files/celegans_scoring.yaml
Mikado/configuration/scoring_files/dmelanogaster_scoring.yaml
Mikado/configuration/scoring_files/hsapiens_scoring.yaml
Mikado/configuration/scoring_files/human.yaml
Mikado/configuration/scoring_files/insects.yaml
Mikado/configuration/scoring_files/plants.yaml
Mikado/configuration/scoring_files/scerevisiae.yaml
Mikado/configuration/scoring_files/worm.yaml
Mikado/daijin/__init__.py
Mikado/daijin/example_config.yaml
Mikado/daijin/hpc.json
Mikado/daijin/hpc.yaml
Mikado/daijin/mikado.snakefile
Mikado/daijin/tr.snakefile
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/contrast.c
Mikado/scales/contrast.pxd
Mikado/scales/contrast.pyx
Mikado/scales/f1.c
Mikado/scales/f1.pxd
Mikado/scales/f1.pyx
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/chr5.fas.gz
Mikado/tests/configuration.yaml
Mikado/tests/cufflinks.gtf
Mikado/tests/genome.fai
Mikado/tests/intervaltree_tests.py
Mikado/tests/junctions.bed
Mikado/tests/locus_tester.py
Mikado/tests/mikado.blast.asn.gz
Mikado/tests/mikado.blast.xml
Mikado/tests/mikado.db
Mikado/tests/mikado_prepared.gtf
Mikado/tests/orf_tester.py
Mikado/tests/parser_testing.py
Mikado/tests/plants.suspicious_requirement.yaml
Mikado/tests/scoring_only_cds.yaml
Mikado/tests/test_bed12.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/trinity.cDNA_match.gff3
Mikado/tests/trinity.gff3
Mikado/tests/trinity.gtf
Mikado/tests/trinity.match_matchpart.gff3
Mikado/tests/trinity_stats.txt
Mikado/tests/uniprot_sprot_plants.fasta.gz
Mikado/tests/utilities_tester.py
Mikado/tests/fusion_test/fusion_test_pred.gtf
Mikado/tests/fusion_test/fusion_test_ref.gff3
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/intervaltree.c
Mikado/utilities/intervaltree.pyx
Mikado/utilities/log_utils.py
Mikado/utilities/overlap.c
Mikado/utilities/overlap.pxd
Mikado/utilities/overlap.pyx
util/add_transcript_feature_to_gtf.py
util/align_collect.py
util/asm_collect.py
util/bam2gtf.py
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