.coveragerc
.gitattributes
.gitignore
.pylintrc
CITATION.bib
CITATION.cff
Dockerfile
LICENSE
README.md
appveyor.yml
docker_banner.sh
requirements.txt
setup.cfg
setup.py
.github/workflows/ci.yml
docs/Makefile
docs/make.bat
docs/source/conf.py
docs/source/index.rst
docs/source/installation.rst
docs/source/introduction.rst
docs/source/output.rst
docs/source/_static/docker.gif
docs/source/programs/add_transcripts.rst
docs/source/programs/programs.rst
docs/source/programs/thoraxe.rst
docs/source/programs/transcript_query.rst
tests/test_add_transcripts.py
tests/test_alignment.py
tests/test_ases.py
tests/test_merging.py
tests/test_pir.py
tests/test_subexons.py
tests/test_thoraxe.py
tests/test_transcript_info.py
tests/test_transcript_query.py
tests/data/species_list.txt
tests/data/update_outputs.sh
tests/data/user_transcript.csv
tests/data/CAMK2A/Ensembl/exonstable.tsv
tests/data/CAMK2A/Ensembl/sequences.fasta
tests/data/CAMK2A/Ensembl/tree.nh
tests/data/CAMK2A/Ensembl/tsl.csv
tests/data/GPRIN1/Ensembl/exonstable.tsv
tests/data/GPRIN1/Ensembl/sequences.fasta
tests/data/GPRIN1/Ensembl/tree.nh
tests/data/GPRIN1/Ensembl/tsl.csv
tests/data/KIF1B/Ensembl/ensembl_version.csv
tests/data/KIF1B/Ensembl/exonstable.tsv
tests/data/KIF1B/Ensembl/sequences.fasta
tests/data/KIF1B/Ensembl/tree.nh
tests/data/KIF1B/Ensembl/tsl.csv
tests/data/MAPK8/Ensembl/exonstable.tsv
tests/data/MAPK8/Ensembl/sequences.fasta
tests/data/MAPK8/Ensembl/tree.nh
tests/data/MAPK8/Ensembl/tsl.csv
tests/data/MAPK8_all/Ensembl/ensembl_version.csv
tests/data/MAPK8_all/Ensembl/exonstable.tsv
tests/data/MAPK8_all/Ensembl/sequences.fasta
tests/data/MAPK8_all/Ensembl/tree.nh
tests/data/MAPK8_all/Ensembl/tsl.csv
tests/data/MAPK8_output/thoraxe/ases_table.csv
tests/data/MAPK8_output/thoraxe/path_table.csv
tests/data/MAPK8_output/thoraxe/s_exon_table.csv
tests/data/MAPK8_output/thoraxe/splice_graph.gml
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_1.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_10.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_11.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_12.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_13.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_14.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_15.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_16.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_17.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_18.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_19.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_2.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_21.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_22.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_3.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_4.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_5.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_6.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_7.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_8.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/chimeric_alignment_9.fasta
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_1.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_10.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_11.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_12.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_13.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_14.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_15.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_16.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_17.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_18.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_19.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_2.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_21.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_22.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_3.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_4.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_5.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_6.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_7.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_8.txt
tests/data/MAPK8_output/thoraxe/_intermediate/gene_ids_9.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_1.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_10.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_11.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_12.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_13.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_14.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_15.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_16.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_17.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_18.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_19.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_2.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_21.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_22.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_3.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_4.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_5.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_6.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_7.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_8.txt
tests/data/MAPK8_output/thoraxe/_intermediate/msa_matrix_9.txt
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_1.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_10.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_11.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_12.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_13.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_14.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_15.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_16.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_17.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_18.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_19.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_2.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_21.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_22.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_3.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_4.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_5.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_6.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_7.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_8.csv
tests/data/MAPK8_output/thoraxe/_intermediate/subexon_table_9.csv
tests/data/MAPK8_output/thoraxe/_intermediate/transcript_table.csv
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_10_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_11_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_11_1.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_12_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_13_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_14_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_15_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_16_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_17_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_18_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_19_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_1_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_1_1.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_21_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_21_1.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_22_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_2_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_2_1.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_3_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_3_1.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_4_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_4_1.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_5_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_6_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_6_1.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_6_2.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_7_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_7_1.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_7_2.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_7_3.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_8_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_9_0.fasta
tests/data/MAPK8_output/thoraxe/phylosofs/s_exons.tsv
tests/data/MAPK8_output/thoraxe/phylosofs/transcripts.pir
tests/data/MAPK8_output/thoraxe/phylosofs/transcripts.txt
tests/data/MAPK8_output/thoraxe/phylosofs/tree.nh
tests/data/POLR3B/Ensembl/ensembl_version.csv
tests/data/POLR3B/Ensembl/exonstable.tsv
tests/data/POLR3B/Ensembl/sequences.fasta
tests/data/POLR3B/Ensembl/tree.nh
tests/data/POLR3B/Ensembl/tsl.csv
tests/data/POLR3B_output/thoraxe/ases_table.csv
tests/data/POLR3B_output/thoraxe/path_table.csv
tests/data/POLR3B_output/thoraxe/s_exon_table.csv
tests/data/POLR3B_output/thoraxe/splice_graph.gml
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_1.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_10.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_11.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_12.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_13.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_14.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_15.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_16.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_17.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_18.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_19.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_2.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_20.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_21.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_22.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_23.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_24.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_25.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_26.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_27.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_28.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_29.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_3.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_30.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_31.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_32.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_33.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_34.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_35.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_36.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_37.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_38.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_39.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_4.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_40.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_41.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_42.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_43.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_44.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_45.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_46.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_47.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_48.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_49.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_5.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_50.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_51.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_53.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_54.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_55.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_57.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_6.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_7.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_8.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/chimeric_alignment_9.fasta
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_1.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_10.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_11.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_12.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_13.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_14.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_15.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_16.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_17.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_18.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_19.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_2.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_20.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_21.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_22.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_23.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_24.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_25.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_26.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_27.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_28.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_29.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_3.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_30.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_31.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_32.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_33.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_34.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_35.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_36.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_37.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_38.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_39.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_4.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_40.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_41.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_42.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_43.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_44.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_45.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_46.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_47.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_48.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_49.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_5.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_50.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_51.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_53.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_54.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_55.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_57.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_6.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_7.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_8.txt
tests/data/POLR3B_output/thoraxe/_intermediate/gene_ids_9.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_1.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_10.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_11.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_12.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_13.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_14.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_15.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_16.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_17.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_18.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_19.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_2.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_20.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_21.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_22.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_23.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_24.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_25.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_26.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_27.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_28.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_29.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_3.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_30.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_31.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_32.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_33.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_34.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_35.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_36.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_37.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_38.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_39.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_4.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_40.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_41.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_42.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_43.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_44.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_45.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_46.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_47.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_48.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_49.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_5.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_50.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_51.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_53.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_54.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_55.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_57.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_6.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_7.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_8.txt
tests/data/POLR3B_output/thoraxe/_intermediate/msa_matrix_9.txt
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_1.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_10.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_11.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_12.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_13.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_14.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_15.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_16.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_17.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_18.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_19.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_2.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_20.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_21.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_22.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_23.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_24.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_25.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_26.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_27.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_28.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_29.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_3.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_30.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_31.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_32.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_33.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_34.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_35.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_36.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_37.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_38.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_39.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_4.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_40.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_41.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_42.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_43.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_44.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_45.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_46.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_47.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_48.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_49.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_5.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_50.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_51.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_53.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_54.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_55.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_57.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_6.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_7.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_8.csv
tests/data/POLR3B_output/thoraxe/_intermediate/subexon_table_9.csv
tests/data/POLR3B_output/thoraxe/_intermediate/transcript_table.csv
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_10_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_11_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_12_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_12_1.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_13_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_14_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_15_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_16_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_17_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_17_1.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_18_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_19_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_1_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_20_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_21_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_22_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_23_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_24_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_25_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_25_1.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_25_2.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_26_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_27_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_27_1.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_28_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_29_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_2_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_30_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_31_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_32_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_33_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_34_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_35_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_36_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_37_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_38_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_39_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_3_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_40_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_41_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_42_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_43_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_44_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_45_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_46_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_47_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_48_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_48_1.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_49_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_4_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_50_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_51_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_53_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_54_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_55_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_57_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_5_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_6_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_7_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_7_1.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_7_2.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_7_3.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_8_0.fasta
tests/data/POLR3B_output/thoraxe/msa/msa_s_exon_9_0.fasta
tests/data/POLR3B_output/thoraxe/phylosofs/s_exons.tsv
tests/data/POLR3B_output/thoraxe/phylosofs/transcripts.pir
tests/data/POLR3B_output/thoraxe/phylosofs/transcripts.txt
tests/data/POLR3B_output/thoraxe/phylosofs/tree.nh
thoraxe/__init__.py
thoraxe/thoraxe.py
thoraxe/version.py
thoraxe.egg-info/PKG-INFO
thoraxe.egg-info/SOURCES.txt
thoraxe.egg-info/dependency_links.txt
thoraxe.egg-info/entry_points.txt
thoraxe.egg-info/not-zip-safe
thoraxe.egg-info/requires.txt
thoraxe.egg-info/top_level.txt
thoraxe/add_transcripts/__init__.py
thoraxe/add_transcripts/add_transcripts.py
thoraxe/subexons/__init__.py
thoraxe/subexons/alignment.py
thoraxe/subexons/ases.py
thoraxe/subexons/graph.py
thoraxe/subexons/phylosofs.py
thoraxe/subexons/plot.py
thoraxe/subexons/rescue.py
thoraxe/subexons/subexons.py
thoraxe/subexons/tidy.py
thoraxe/subexons/assets/cluster_plots.html
thoraxe/transcript_info/__init__.py
thoraxe/transcript_info/clusters.py
thoraxe/transcript_info/exon_clustering.py
thoraxe/transcript_info/phases.py
thoraxe/transcript_info/transcript_info.py
thoraxe/transcript_query/__init__.py
thoraxe/transcript_query/transcript_query.py
thoraxe/utils/__init__.py
thoraxe/utils/folders.py
thoraxe/utils/species.py
thoraxe/utils/split.py
thoraxe/utils/windows.py