[med-svn] [fastaq] branch upstream updated (e255484 -> 08dda22)

[Sascha Steinbiss]

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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
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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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