Opened 3 years ago

Closed 7 months ago

#701 closed task (performed)

separate code for PosVarParsimony SAI calculation

Reported by: westram Owned by: westram
Priority: major Milestone: r18q1
Component: ARB_NTREE Version: SVN
Keywords: silva, posvar, pvp Cc: cquast@…

Description (last modified by westram)

Motivation:

  • needed by SILVA pipeline

Goal:

  • code to calculate posvar-SAI shall move into its own library (separated from GUI code and ARB_NTREE)
  • functionality needed in pipeline:
    1. load tree from file
    2. calculate SAI from tree + sequences
    3. delete tree

Proposed interface:

  1. new function
    GB_ERROR TREE_load_to_db(GBDATA *gb_main, 
                             const char *treefile, 
                             const char *treename);
    
  2. new function
    GB_ERROR PVP_calculate(GBDATA *gb_main,
                           const char *ali_name,
                           const char *tree_name,
                           const char *target_SAI_name);
    
  3. to delete a tree from database simply use
    GB_ERROR error = NULL;
    {
      GB_transaction ta(gb_main);
      GBDATA *gb_tree = GBT_find_tree(gb_main, name);
      if (gb_tree) error = GB_delete(gb_tree);
    }
    

Put 1. into SL/TREE_READ and 2. into new library.

Change History (8)

comment:1 Changed 21 months ago by westram

  • Description modified (diff)
  • Milestone set to wishlist

comment:2 Changed 20 months ago by westram

  • Milestone changed from wishlist to r18q1
  • Status changed from new to assigned

comment:3 Changed 12 months ago by westram

  • Status changed from assigned to accepted

comment:4 Changed 7 months ago by westram

  • Status changed from accepted to _started

comment:5 Changed 7 months ago by westram

  • Keywords posvar pvp added

comment:6 Changed 7 months ago by westram

  • Resolution set to "fixed"
  • Status changed from _started to closed

CLI tool added by [16919]:

> bin/arb_calc_pvp --help

arb_calc_pvp -- calculate positional variability SAI
Usage: arb_calc_pvp [switches] <database> <treename> <aliname>

switches:
--savename <dbname>        save database with different name
                           (default is to overwrite input <database>)
--tree-import <treefile>   load tree from <treefile> + store in database as <treename>
                           (default: use tree existing in database)
--tree-delete              delete tree <treename> (before saving database)
--sainame <sai>            use alternate SAI name (default: POS_VAR_BY_PARSIMONY)

comment:7 Changed 7 months ago by westram

  • Resolution "fixed" deleted
  • Status changed from closed to _started

comment:8 Changed 7 months ago by westram

  • Resolution set to performed
  • Status changed from _started to closed
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