AUTHORS
CHANGELOG.md
DESCRIPTION.md
LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.cfg
setup.py
Mikado/__init__.py
Mikado/__main__.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/_transcripts/__init__.py
Mikado/_transcripts/clique_methods.py
Mikado/_transcripts/scoring_configuration.py
Mikado/_transcripts/transcript_base.py
Mikado/_transcripts/transcript_methods/__init__.py
Mikado/_transcripts/transcript_methods/finalizing.py
Mikado/_transcripts/transcript_methods/printing.py
Mikado/configuration/__init__.py
Mikado/configuration/configuration.py
Mikado/configuration/configurator.py
Mikado/configuration/daijin_configuration.py
Mikado/configuration/daijin_configurator.py
Mikado/configuration/picking_config.py
Mikado/configuration/prepare_config.py
Mikado/configuration/serialise_config.py
Mikado/configuration/scoring_files/mammalian.yaml
Mikado/configuration/scoring_files/plant.yaml
Mikado/configuration/scoring_files/HISTORIC/athaliana_scoring.yaml
Mikado/configuration/scoring_files/HISTORIC/celegans_scoring.yaml
Mikado/configuration/scoring_files/HISTORIC/dmelanogaster_scoring.yaml
Mikado/configuration/scoring_files/HISTORIC/hsapiens_scoring.yaml
Mikado/configuration/scoring_files/HISTORIC/human.yaml
Mikado/configuration/scoring_files/HISTORIC/insects.yaml
Mikado/configuration/scoring_files/HISTORIC/mammalian.yaml
Mikado/configuration/scoring_files/HISTORIC/plant.yaml
Mikado/configuration/scoring_files/HISTORIC/plants.yaml
Mikado/configuration/scoring_files/HISTORIC/scerevisiae.yaml
Mikado/configuration/scoring_files/HISTORIC/worm.yaml
Mikado/daijin/__init__.py
Mikado/daijin/__main__.py
Mikado/daijin/assemble.py
Mikado/daijin/assemble.smk
Mikado/daijin/hpc.yaml
Mikado/daijin/mikado.py
Mikado/daijin/mikado.smk
Mikado/daijin/envs/blast.yaml
Mikado/daijin/envs/cufflinks.yaml
Mikado/daijin/envs/diamond.yaml
Mikado/daijin/envs/gmap.yaml
Mikado/daijin/envs/gnuplot.yaml
Mikado/daijin/envs/hisat2.yaml
Mikado/daijin/envs/portcullis.yaml
Mikado/daijin/envs/prodigal.yaml
Mikado/daijin/envs/samtools.yaml
Mikado/daijin/envs/scallop.yaml
Mikado/daijin/envs/star.yaml
Mikado/daijin/envs/stringtie.yaml
Mikado/daijin/envs/tophat2.yaml
Mikado/daijin/envs/transdecoder.yaml
Mikado/daijin/envs/trinity.yaml
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/sublocus.py
Mikado/loci/superlocus.py
Mikado/parsers/GFF.py
Mikado/parsers/GTF.py
Mikado/parsers/__init__.py
Mikado/parsers/bam_parser.py
Mikado/parsers/bed12.py
Mikado/parsers/blast_utils.py
Mikado/parsers/gfannotation.py
Mikado/parsers/parser.py
Mikado/picking/__init__.py
Mikado/picking/_loci_serialiser.py
Mikado/picking/_locus_line_creator.py
Mikado/picking/_locus_single_printer.py
Mikado/picking/_merge_loci_utils.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/calculator.py
Mikado/scales/class_codes.py
Mikado/scales/compare.py
Mikado/scales/contrast.cpp
Mikado/scales/contrast.pxd
Mikado/scales/contrast.pyx
Mikado/scales/resultstorer.py
Mikado/scales/assignment/__init__.py
Mikado/scales/assignment/assigner.py
Mikado/scales/assignment/distributed.py
Mikado/scales/prediction_parsers/__init__.py
Mikado/scales/prediction_parsers/parse_bam_prediction.py
Mikado/scales/prediction_parsers/parse_bed12.py
Mikado/scales/prediction_parsers/parse_gff3_prediction.py
Mikado/scales/prediction_parsers/parse_gtf_prediction.py
Mikado/scales/prediction_parsers/transmission.py
Mikado/scales/reference_preparation/__init__.py
Mikado/scales/reference_preparation/gene_dict.py
Mikado/scales/reference_preparation/indexing.py
Mikado/scales/reference_preparation/prepare_reference.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/aln_string_parser.cpp
Mikado/serializers/blast_serializer/aln_string_parser.pyx
Mikado/serializers/blast_serializer/blast_serialiser.py
Mikado/serializers/blast_serializer/btop_parser.cpp
Mikado/serializers/blast_serializer/btop_parser.pxd
Mikado/serializers/blast_serializer/btop_parser.pyx
Mikado/serializers/blast_serializer/hit.py
Mikado/serializers/blast_serializer/hsp.py
Mikado/serializers/blast_serializer/query.py
Mikado/serializers/blast_serializer/tab_serialiser.py
Mikado/serializers/blast_serializer/tabular_utils.py
Mikado/serializers/blast_serializer/target.py
Mikado/serializers/blast_serializer/utils.py
Mikado/serializers/blast_serializer/xml_serialiser.py
Mikado/serializers/blast_serializer/xml_utils.py
Mikado/subprograms/__init__.py
Mikado/subprograms/__main__.py
Mikado/subprograms/_utils.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/collapse_compare_stats.py
Mikado/subprograms/util/convert.py
Mikado/subprograms/util/grep.py
Mikado/subprograms/util/metrics.py
Mikado/subprograms/util/stats.py
Mikado/subprograms/util/trim.py
Mikado/tests/Chrysemys_picta_bellii_problematic.gff3
Mikado/tests/Chrysemys_picta_bellii_problematic.list.txt
Mikado/tests/Chrysemys_picta_bellii_problematic.txt
Mikado/tests/ERR588038.R1.fq.gz
Mikado/tests/ERR588038.R2.fq.gz
Mikado/tests/NC_037283.1.fa.gz
Mikado/tests/SRR5037293.pacbio.fastq.gz
Mikado/tests/__init__.py
Mikado/tests/annotation.gff3
Mikado/tests/annotation.gff3.stats
Mikado/tests/assigner_test.py
Mikado/tests/cds_test_1.gtf
Mikado/tests/cds_test_2.gtf
Mikado/tests/check_seed.fa
Mikado/tests/check_seed.gtf
Mikado/tests/check_seed.yaml
Mikado/tests/chr5.fas.gz
Mikado/tests/chr5.fas.gz.fai
Mikado/tests/chr5.fas.gz.gzi
Mikado/tests/chunk-001-proteins.xml.gz
Mikado/tests/complete_padding.bed12
Mikado/tests/configuration.yaml
Mikado/tests/cufflinks.gtf
Mikado/tests/cufflinks.no_transcript.gtf
Mikado/tests/external.yaml
Mikado/tests/genome.fai
Mikado/tests/gtf_check.gtf.gz
Mikado/tests/intervaltree_test.py
Mikado/tests/junctions.bed
Mikado/tests/junctions_duplicates.bed
Mikado/tests/locus_test.py
Mikado/tests/mikado.blast.asn.gz
Mikado/tests/mikado.blast.xml
Mikado/tests/mikado.db
Mikado/tests/mikado_prepared.fasta
Mikado/tests/mikado_prepared.fasta.fai
Mikado/tests/mikado_prepared.gtf
Mikado/tests/neg_pad.bed12
Mikado/tests/neg_pad.fa
Mikado/tests/neg_pad.fa.fai
Mikado/tests/orf_test.py
Mikado/tests/pacbio.bam
Mikado/tests/pad_three_neg.bed12
Mikado/tests/pad_utr.bed12
Mikado/tests/padding_test.bed12
Mikado/tests/padding_test.fa
Mikado/tests/padding_test.fa.fai
Mikado/tests/padding_test.rev_compl.bed12
Mikado/tests/padding_test.rev_compl.fa
Mikado/tests/padding_test.rev_compl.fa.fai
Mikado/tests/parser_test.py
Mikado/tests/phasing_padding.bed12
Mikado/tests/plants.suspicious_requirement.yaml
Mikado/tests/prepare_misc_test.py
Mikado/tests/reference.gff3
Mikado/tests/scoring_only_cds.yaml
Mikado/tests/test.reads.bam
Mikado/tests/test_bed12.py
Mikado/tests/test_blast_inputs.py
Mikado/tests/test_blast_related.py
Mikado/tests/test_clique_methods.py
Mikado/tests/test_compare.py
Mikado/tests/test_configurators.py
Mikado/tests/test_db_utils.py
Mikado/tests/test_external_async.py
Mikado/tests/test_external_scores.py
Mikado/tests/test_gene.py
Mikado/tests/test_invalid_orfs.py
Mikado/tests/test_light.py
Mikado/tests/test_mRNA.bam
Mikado/tests/test_mRNA.bam.bai
Mikado/tests/test_metrics.py
Mikado/tests/test_modifications.py
Mikado/tests/test_scores.py
Mikado/tests/test_serialise_external.py
Mikado/tests/test_serialise_junctions.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/test_transcript_negative.py
Mikado/tests/test_transcript_positive.py
Mikado/tests/test_transcript_single.py
Mikado/tests/test_truncated_cds.fa
Mikado/tests/test_truncated_cds.fa.fai
Mikado/tests/test_truncated_cds.gff3
Mikado/tests/test_utils.py
Mikado/tests/transcripts.fasta.prodigal.gff3
Mikado/tests/trinity.bam
Mikado/tests/trinity.bed12
Mikado/tests/trinity.cDNA_match.gff3
Mikado/tests/trinity.gff3
Mikado/tests/trinity.gtf
Mikado/tests/trinity.ids
Mikado/tests/trinity.match_matchpart.gff3
Mikado/tests/trinity.minimap2.bam
Mikado/tests/trinity.minimap2.bam.bai
Mikado/tests/trinity.no_transcript_feature.gtf
Mikado/tests/trinity_stats.txt
Mikado/tests/trinity_unsorted.gff3
Mikado/tests/trinity_unsorted.gtf
Mikado/tests/uniprot_sprot_plants.fasta.gz
Mikado/tests/uniprot_sprot_plants.fasta.gz.fai
Mikado/tests/uniprot_sprot_plants.fasta.gz.gzi
Mikado/tests/utilities_test.py
Mikado/tests/zom_junctions.bed
Mikado/tests/blast_data/diamond.0.9.30.tsv.gz
Mikado/tests/blast_data/diamond.0.9.30.xml.gz
Mikado/tests/blast_data/transcripts.fasta
Mikado/tests/blast_data/transcripts.fasta.fai
Mikado/tests/blast_input_tests/commands.sh
Mikado/tests/blast_input_tests/queries.fasta
Mikado/tests/blast_input_tests/queries.fasta.fai
Mikado/tests/blast_input_tests/uniprot.fasta
Mikado/tests/blast_input_tests/sanitised/uniprot.fasta
Mikado/tests/blast_input_tests/sanitised/uniprot.fasta.fai
Mikado/tests/blast_input_tests/sanitised/blast/tsv/blast.tsv.gz
Mikado/tests/blast_input_tests/sanitised/blast/xml/blast.xml.gz
Mikado/tests/blast_input_tests/sanitised/blast_parse_seqids/tsv/blast.tsv.gz
Mikado/tests/blast_input_tests/sanitised/blast_parse_seqids/xml/blast.xml.gz
Mikado/tests/blast_input_tests/sanitised/diamond/daa/blast.daa
Mikado/tests/blast_input_tests/sanitised/diamond/tsv/blast.tsv.gz
Mikado/tests/blast_input_tests/sanitised/diamond/xml/blast.xml.gz
Mikado/tests/blast_input_tests/uniprot/uniprot.fasta
Mikado/tests/blast_input_tests/uniprot/uniprot.fasta.fai
Mikado/tests/blast_input_tests/uniprot/blast/tsv/blast.tsv.gz
Mikado/tests/blast_input_tests/uniprot/blast/xml/blast.xml.gz
Mikado/tests/blast_input_tests/uniprot/blast_parse_seqids/tsv/blast.tsv.gz
Mikado/tests/blast_input_tests/uniprot/blast_parse_seqids/xml/blast.xml.gz
Mikado/tests/blast_input_tests/uniprot/diamond/daa/blast.daa
Mikado/tests/blast_input_tests/uniprot/diamond/tsv/blast.tsv.gz
Mikado/tests/blast_input_tests/uniprot/diamond/xml/blast.xml.gz
Mikado/tests/fusion_test/fusion_test_pred.gtf
Mikado/tests/fusion_test/fusion_test_ref.gff3
Mikado/tests/test_external/abundance.h5
Mikado/tests/test_external/abundance.tsv
Mikado/tests/test_external/data.txt
Mikado/tests/test_external/mikado_prepared.fasta
Mikado/tests/test_external/mikado_prepared.fasta.fai
Mikado/tests/test_external/wrong_1.tsv
Mikado/tests/test_external/wrong_2.tsv
Mikado/tests/test_external_aphid/annotation_run1.metrics.testds.txt
Mikado/tests/test_external_aphid/aphid.scoring.yaml
Mikado/tests/test_external_aphid/mikado.configuration.testds.yaml
Mikado/tests/test_external_aphid/mikado_prepared.testds.fasta
Mikado/tests/test_external_aphid/mikado_prepared.testds.fasta.fai
Mikado/transcripts/__init__.py
Mikado/transcripts/pad.py
Mikado/transcripts/reference_gene.py
Mikado/transcripts/transcript.py
Mikado/transcripts/transcriptchecker.py
Mikado/transcripts/transcriptcomputer.py
Mikado/transcripts/transcript_methods/__init__.py
Mikado/transcripts/transcript_methods/retrieval.py
Mikado/transcripts/transcript_methods/splitting.py
Mikado/utilities/__init__.py
Mikado/utilities/dbutils.py
Mikado/utilities/f1.c
Mikado/utilities/f1.pxd
Mikado/utilities/f1.pyx
Mikado/utilities/file_type.py
Mikado/utilities/intervaltree.cpp
Mikado/utilities/intervaltree.pxd
Mikado/utilities/intervaltree.pyx
Mikado/utilities/log_utils.py
Mikado/utilities/namespace.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/extract_test_case.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