.coveragerc
.gitattributes
.gitignore
.pylintrc
.travis.yml
Dockerfile
LICENSE
README.md
appveyor.yml
docker_banner.sh
push_docs.sh
setup.cfg
setup.py
docs/Makefile
docs/make.bat
docs/source/conf.py
docs/source/index.rst
docs/source/installation.rst
docs/source/output.rst
docs/source/_static/docker.gif
docs/source/programs/programs.rst
docs/source/programs/thoraxe.rst
docs/source/programs/transcript_query.rst
tests/test_alignment.py
tests/test_ases.py
tests/test_merging.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/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_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_2.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_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_2.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_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_2.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_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_2.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_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_1_0.fasta
tests/data/MAPK8_output/thoraxe/msa/msa_s_exon_1_1.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_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
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/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