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General Association (GA)

a general (common) association package for two (larger) sorted genome location files

Feature

  1. flexible function (a special class of map-reduce framework)
  2. python paradigm and design pattern applied

Install and Usage

  1. a basic usage (without install):
python3 ga/association.py <test/1.vcf> <test/2.vcf> [associated_output] [left_outer_output] [right_outer_output]

see ga/association.py for details.

  1. install the package
python3 setup.py install [--prefix PATH dir]

then call the command thereafter

ga <test/1.vcf> <test/2.vcf>

Output

[associated_out] (association.out for default) keeps all associated (overlap) records.

[left_outer_output] keeps left non-associated records.

[right_outer_output] keeps right non-associated records.

Extend

In all most cases, you need only add a record keep rule callable (e.g. new_add_compare) for two (associated) under-compared records in particular application.

Then call the iterative_overlap_block function's record_keep_rule parameter with new_add_compare.

For some depth improvements, you would rewrite the record_keep_rule and paired_unit_rules simultaneously for adaptation.