[med-svn] [circlator] branch upstream updated (03b0ae8 -> cd94621)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository circlator.

      from  03b0ae8   Imported Upstream version 1.2.1
       new  cd94621   Imported Upstream version 1.3.0

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:
 .travis.yml                                        |   4 -
 circlator/__init__.py                              |   2 +-
 circlator/external_progs.py                        |  45 +-
 circlator/fixstart.py                              |  55 --
 circlator/program.py                               |  55 +-
 circlator/start_fixer.py                           | 337 +++++++++
 circlator/tasks/all.py                             |   5 +-
 circlator/tasks/fixstart.py                        |   6 +-
 circlator/tasks/progcheck.py                       |   6 +-
 ...tart_fixer_find_circular_using_prodigal.ctgs.fa | 109 +++
 ...art_fixer_find_circular_using_promer.contigs.fa | 168 +++++
 .../start_fixer_find_circular_using_promer.refs.fa |  75 ++
 ...t_contigs.fasta => start_fixer_init_contigs.fa} |   0
 circlator/tests/data/start_fixer_init_dnaA.fa      |   2 +
 circlator/tests/data/start_fixer_init_ignore_ids   |   2 +
 .../data/start_fixer_max_length_from_fasta_file.fa |   6 +
 .../data/start_fixer_rearrange_contigs.expect.fa   | 776 +++++++++++++++++++++
 .../data/start_fixer_rearrange_contigs.expect.log  |   8 +
 .../tests/data/start_fixer_rearrange_contigs.in.fa | 776 +++++++++++++++++++++
 .../data/start_fixer_rearrange_contigs.refs.fa     |  50 ++
 .../data/start_fixer_run_bit_of_everything.ctg.fa  | 282 ++++++++
 .../start_fixer_run_bit_of_everything.expect.fa    | 282 ++++++++
 .../data/start_fixer_run_bit_of_everything.ignore  |   1 +
 .../data/start_fixer_run_bit_of_everything.ref.fa  |  25 +
 .../data/start_fixer_run_ignore_all.expect.fa      |   2 +
 circlator/tests/data/start_fixer_run_ignore_all.fa |   2 +
 .../data/start_fixer_run_ignore_all.to_ignore      |   1 +
 .../data/start_fixer_run_none_for_prodigal.ctg.fa  |  91 +++
 .../start_fixer_run_none_for_prodigal.expect.fa    |  91 +++
 .../data/start_fixer_run_none_for_prodigal.ref.fa  |  25 +
 ..._fixer_write_fasta_plus_circularized_ends.in.fa |   8 +
 ...fixer_write_fasta_plus_circularized_ends.out.fa |  12 +
 ...rite_fasta_plus_circularized_ends.out.ignore.fa |   6 +
 .../data/start_fixer_write_renamed_contigs.fa      |   4 +
 circlator/tests/start_fixer_test.py                | 225 ++++++
 circlator/versions.py                              |   7 +-
 install_dependencies.sh                            |   2 +-
 setup.py                                           |   5 +-
 38 files changed, 3447 insertions(+), 111 deletions(-)
 delete mode 100644 circlator/fixstart.py
 create mode 100644 circlator/start_fixer.py
 create mode 100644 circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa
 create mode 100644 circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa
 create mode 100644 circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa
 copy circlator/tests/data/{assembly_test_get_contigs.fasta => start_fixer_init_contigs.fa} (100%)
 create mode 100644 circlator/tests/data/start_fixer_init_dnaA.fa
 create mode 100644 circlator/tests/data/start_fixer_init_ignore_ids
 create mode 100644 circlator/tests/data/start_fixer_max_length_from_fasta_file.fa
 create mode 100644 circlator/tests/data/start_fixer_rearrange_contigs.expect.fa
 create mode 100644 circlator/tests/data/start_fixer_rearrange_contigs.expect.log
 create mode 100644 circlator/tests/data/start_fixer_rearrange_contigs.in.fa
 create mode 100644 circlator/tests/data/start_fixer_rearrange_contigs.refs.fa
 create mode 100644 circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa
 create mode 100644 circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa
 create mode 100644 circlator/tests/data/start_fixer_run_bit_of_everything.ignore
 create mode 100644 circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa
 create mode 100644 circlator/tests/data/start_fixer_run_ignore_all.expect.fa
 create mode 100644 circlator/tests/data/start_fixer_run_ignore_all.fa
 create mode 100644 circlator/tests/data/start_fixer_run_ignore_all.to_ignore
 create mode 100644 circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa
 create mode 100644 circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa
 create mode 100644 circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa
 create mode 100644 circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa
 create mode 100644 circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa
 create mode 100644 circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa
 create mode 100644 circlator/tests/data/start_fixer_write_renamed_contigs.fa
 create mode 100644 circlator/tests/start_fixer_test.py

-- 
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