Fix and perspectives#

Fixes#

#FIXME be aware of multigraph in the input data
- #TODO print error and exit program if multigraph

Output files#

Documentation#

#DOCU Map of regions
- Filename format, c.f. fmt_map_of_regions_filename function
- File format, c.f. write_map_of_regions function (read & write)
#DOCU Contigs of regions
- Filename format, c.f. fmt_contigs_of_regions_filename function
- File format, c.f. write_contigs_of_regions function (read & write)
Debug files
- #DOCU Vertices of regions
  - Filename format, c.f. fmt_vertices_of_regions_filename function
  - File format, c.f. write_vertices_of_regions function (read & write)
- #DOCU Repeated fragments canonicals
  - Filename format, c.f. fmt_repfrag_canonicals_filename function
  - File format, c.f. write_repfrag_canonicals function (read & write)
#DOCU the default directory is UID-like generated
- yyyy-mm-dd_HH-MM-SS_<instance_name>

#DOCU Output a YAML with run information

<generated_output_directory>/io_config.yaml

contig_attributes: <path>
contig_links: <path>
starter_id: C0
multiplicity_upperbound: 4
presence_score_upperbound: 1.0
solver: cbc
output_directory: <path>
instance_name: khloraascaf
debug: true

<generated_output_directory>/solutions.yaml

instance_name: khloraascaf
- ilp_combination:
    - ir
    - sc
  contigs_of_regions: <path>
  map_of_regions: <path>
- ilp_combination:
    - dr
    - sc
  contigs_of_regions: <path>
  map_of_regions: <path>

<generated_output_directory>/debugs.yaml

- ilp_combination:
    - ir
  starter_vertex: <occorc>
  ilp_status: Optimal
  opt_value: 3.0
  vertices_of_regions: <path>
  map_of_regions: <path>
  repfrag: <path>
- ilp_combination:
    - dr
  starter_vertex: <occorc>
  ilp_status: Optimal
  opt_value: 3.0
  vertices_of_regions: <path>
  map_of_regions: <path>
  repfrag: <path>
- ilp_combination:
    - ir
    - sc
  starter_vertex: <occorc>
  ilp_status: Optimal
  opt_value: 129.98000000000002
  vertices_of_regions: <path>
  map_of_regions: <path>
- ilp_combination:
    - dr
    - sc
  starter_vertex: <occorc>
  ilp_status: Optimal
  opt_value: 129.98000000000002
  vertices_of_regions: <path>
  map_of_regions: <path>

Features#

#TODO run_example.sh script that use same data as function example
#TODO function there_is_a_solution() -> bool
#TODO function to extract from stdout the output directory uid
#IDEA implement one class for each metadata type? (io, solutions, all_scaffolding)
- GOOD: use getters instead of constants key on a dict from which the logic is hidden
- GOOD: use class method to retrieve an existing one (if exists, else raising)
- GOOD: init only on creation of a new metadata
- BAD: repeated keys as class constants (e.g. KEY_ILP_COMBINATION)
- GOOD: hide keys
- SOSO: functions bump_* become methods write_to_yaml (note: this is not “bump”…)

Print log: stdout and stderr#

#TODO use logging module
- How to make all the modules follow the same logger configs?
  - See realpython with add_logger in __init__.py ?
#TODO option verbose
#TODO stdout the run directory path
- e.g. [INFO] output_directory="<path>"
#TODO stdout the run metadata file path
- e.g. [INFO] khloraascaf_run_metadata="<path>"
#TODO print errors (e.g. from exceptions raised) in stderr
- e.g. [ERROR] error msg

Next (research world)#

#IDEA think about e.g. several IR & how to adapt these functions bellow?
- If the pulp model want to keep sub-paths with avoiding the previous repeated fragments to be paired, then is it sufficient to read the previous repeated regions given by the result object?

#IDEA should repeat to construct solution until no changes?

.
├── ir
│   ├── ir-ir
│   │   ├── ir-ir-ir
│   │   ├── ir-ir-dr
│   │   └── ir-ir-un
│   └── ir-dr
└── dr
    ├── dr-ir
    └── dr-dr

For now, do just at maximum (ir-dr-un) or (dr-ir-un)