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satta pushed a change to branch master
in repository ariba.
from 285b94a Realise that 2.7.2+ds-1 was not yet uploaded - fix
changelog and re-upload to experimental
new 83edd46 New upstream version 2.9.0+ds
new 8d2b3e7 Merge tag 'upstream/2.9.0+ds'
The 2 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 | 10 +-
ariba/__init__.py | 1 +
ariba/assembly_compare.py | 33 ++
ariba/assembly_variants.py | 23 +-
ariba/cluster.py | 4 +-
ariba/ext/vcfcall_ariba.cpp | 3 +-
ariba/mic_plotter.py | 651 +++++++++++++++++++++
ariba/ref_genes_getter.py | 53 ++
ariba/summary.py | 37 +-
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/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 ++--
scripts/ariba | 55 +-
setup.py | 3 +-
40 files changed, 1494 insertions(+), 162 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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