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satta pushed a change to branch upstream
in repository ariba.
from eebec95 New upstream version 2.7.2+ds
new 83edd46 New upstream version 2.9.0+ds
new b69312e New upstream version 2.9.0+ds
new a3fddfd New upstream version 2.9.2+ds
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
README.md | 32 +-
ariba/__init__.py | 1 +
ariba/assembly.py | 1 +
ariba/assembly_compare.py | 33 ++
ariba/assembly_variants.py | 23 +-
ariba/cluster.py | 5 +-
ariba/clusters.py | 2 -
ariba/ext/vcfcall_ariba.cpp | 3 +-
ariba/external_progs.py | 7 +
ariba/mapping.py | 4 +
ariba/mic_plotter.py | 651 +++++++++++++++++++++
ariba/ref_genes_getter.py | 53 ++
ariba/summary.py | 38 +-
ariba/summary_cluster.py | 23 +-
ariba/summary_cluster_variant.py | 58 +-
ariba/summary_sample.py | 2 +-
ariba/tasks/__init__.py | 1 +
ariba/tasks/micplot.py | 39 ++
ariba/tasks/summary.py | 10 +-
ariba/tests/assembly_compare_test.py | 31 +
ariba/tests/assembly_variants_test.py | 17 +-
ariba/tests/data/mic_plotter_load_mic_file.tsv | 7 +
ariba/tests/data/mic_plotter_load_summary_file.tsv | 3 +
...oxplot_tsv.antibio1.exclude.no_combinations.tsv | 3 +
...mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv | 2 +
..._to_boxplot_tsv.antibio1.no.no_combinations.tsv | 4 +
.../mic_plotter_to_boxplot_tsv.antibio1.no.tsv | 3 +
...to_boxplot_tsv.antibio1.yes.no_combinations.tsv | 5 +
.../mic_plotter_to_boxplot_tsv.antibio1.yes.tsv | 3 +
...oxplot_tsv.antibio2.exclude.no_combinations.tsv | 4 +
...mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv | 3 +
..._to_boxplot_tsv.antibio2.no.no_combinations.tsv | 4 +
.../mic_plotter_to_boxplot_tsv.antibio2.no.tsv | 3 +
...to_boxplot_tsv.antibio2.yes.no_combinations.tsv | 4 +
.../mic_plotter_to_boxplot_tsv.antibio2.yes.tsv | 3 +
ariba/tests/data/summary_test_load_fofn | 4 +
ariba/tests/data/summary_test_whole_run.out.csv | 6 +-
ariba/tests/mapping_test.py | 3 +
ariba/tests/mic_plotter_test.py | 283 +++++++++
ariba/tests/summary_cluster_test.py | 16 +-
ariba/tests/summary_cluster_variant_test.py | 104 ++--
ariba/tests/summary_sample_test.py | 9 +-
ariba/tests/summary_test.py | 129 ++--
install_dependencies.sh | 10 +-
scripts/ariba | 55 +-
setup.py | 3 +-
46 files changed, 1529 insertions(+), 178 deletions(-)
create mode 100644 ariba/mic_plotter.py
create mode 100644 ariba/tasks/micplot.py
create mode 100644 ariba/tests/data/mic_plotter_load_mic_file.tsv
create mode 100644 ariba/tests/data/mic_plotter_load_summary_file.tsv
create mode 100644
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv
create mode 100644
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv
create mode 100644
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv
create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv
create mode 100644
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv
create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv
create mode 100644
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv
create mode 100644
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv
create mode 100644
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv
create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv
create mode 100644
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv
create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv
create mode 100644 ariba/tests/data/summary_test_load_fofn
create mode 100644 ariba/tests/mic_plotter_test.py
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