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sascha-guest pushed a change to branch upstream
in repository fastaq.
from e255484 Imported Upstream version 3.2.0
new 08dda22 Imported Upstream version 3.6.1
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
been added to this reference.
Summary of changes:
pyfastaq/common.py | 2 +-
pyfastaq/genetic_codes.py | 31 +++++++++++
pyfastaq/intervals.py | 7 +++
pyfastaq/runners/to_fasta.py | 4 +-
pyfastaq/runners/to_orfs_gff.py | 2 +-
pyfastaq/sequences.py | 24 +++++++--
pyfastaq/tasks.py | 60 +++++++++++++++++++++-
...o_fasta.strip_after_whitespace_non_unique.in.fa | 6 +++
..._fasta.strip_after_whitespace_non_unique.out.fa | 6 +++
...st.to_fasta.strip_after_whitespace_unique.in.fa | 6 +++
...t.to_fasta.strip_after_whitespace_unique.out.fa | 6 +++
pyfastaq/tests/data/tasks_test_to_fastg.fasta | 4 ++
pyfastaq/tests/data/tasks_test_to_fastg.fastg | 8 +++
....ids => tasks_test_to_fastg.ids_to_circularise} | 1 -
pyfastaq/tests/intervals_test.py | 10 ++++
pyfastaq/tests/sequences_test.py | 30 +++++++++++
pyfastaq/tests/tasks_test.py | 45 ++++++++++++++++
setup.py | 13 ++---
18 files changed, 247 insertions(+), 18 deletions(-)
create mode 100644
pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_non_unique.in.fa
create mode 100644
pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_non_unique.out.fa
create mode 100644
pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_unique.in.fa
create mode 100644
pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_unique.out.fa
create mode 100644 pyfastaq/tests/data/tasks_test_to_fastg.fasta
create mode 100644 pyfastaq/tests/data/tasks_test_to_fastg.fastg
copy pyfastaq/tests/data/{sequences_test_filter_by_ids_file.fa.ids =>
tasks_test_to_fastg.ids_to_circularise} (50%)
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