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satta pushed a change to branch upstream
in repository ariba.
from f56815e New upstream version 2.6.1+ds
new 5ee95ba New upstream version 2.7.0+ds
The 1 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
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Summary of changes:
ariba/__init__.py | 2 +
ariba/common.py | 25 +++++
ariba/megares_data_finder.py | 68 ++++++++++++
ariba/megares_zip_parser.py | 119 +++++++++++++++++++++
ariba/ref_genes_getter.py | 38 +++----
.../data/megares_zip_parse_extract_files_ok.zip | Bin 0 -> 1328 bytes
...megares_zip_parse_extract_files_one_missing.zip | Bin 0 -> 1116 bytes
.../data/megares_zip_parser_load_annotations.csv | 3 +
.../megares_zip_parser_load_header_mappings.tsv | 3 +
.../data/megares_zip_parser_write_files.expect.fa | 6 ++
.../data/megares_zip_parser_write_files.expect.tsv | 3 +
.../megares_annotations_v1.01.csv | 4 +
.../megares_database_v1.01.fasta | 6 ++
.../megares_to_external_header_mappings_v1.01.tsv | 4 +
ariba/tests/megares_data_finder_test.py | 36 +++++++
ariba/tests/megares_zip_parser_test.py | 84 +++++++++++++++
scripts/ariba | 2 +-
setup.py | 3 +-
18 files changed, 385 insertions(+), 21 deletions(-)
create mode 100644 ariba/megares_data_finder.py
create mode 100644 ariba/megares_zip_parser.py
create mode 100644 ariba/tests/data/megares_zip_parse_extract_files_ok.zip
create mode 100644
ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip
create mode 100644 ariba/tests/data/megares_zip_parser_load_annotations.csv
create mode 100644 ariba/tests/data/megares_zip_parser_load_header_mappings.tsv
create mode 100644 ariba/tests/data/megares_zip_parser_write_files.expect.fa
create mode 100644 ariba/tests/data/megares_zip_parser_write_files.expect.tsv
create mode 100644
ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv
create mode 100644
ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta
create mode 100644
ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv
create mode 100644 ariba/tests/megares_data_finder_test.py
create mode 100644 ariba/tests/megares_zip_parser_test.py
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