new

phylogeny/dissim_full.sh

@@ -0,0 +1,61 @@
+#!/bin/bash --noprofile
+THIS=`dirname $0`
+source $THIS/../bash_common.sh
+if [ $# -ne 2 ]; then
+  echo "Build a distance tree #2/inc/tree using precomputed pairwise dissimilarities"
+  echo "#1: pairwise dissimilarities file where each line has format: object1 object2 dissimilarity. Missing dissimilarities are inf"
+  echo "#2: output directory (to be created)"
+  echo "Requires: object names should have no dashes"
+  exit 1
+fi
+FULL=$1
+DIR=$2
+
+
+mkdir $DIR
+cd $DIR
+
+
+section "list"
+awk '{print $1};' $FULL >  tmp
+awk '{print $2};' $FULL >> tmp
+sort -u tmp > list
+rm tmp
+if grep '-' list; then
+  error "Names should have not contain dashes"
+fi
+wc -l list
+
+section "dissim_full"
+awk '{if ($1 < $2)  printf "%s\t%s\t%s\n", $1, $2, $3};' $FULL >  tmp
+awk '{if ($1 > $2)  printf "%s\t%s\t%s\n", $2, $1, $3};' $FULL >> tmp
+sort -u tmp | sed 's/\t/-/1' > dissim_full
+rm tmp
+
+$THIS/distTree_inc_init_stnd.sh inc $THIS/inc/dissim_full "" "" "" ""
+touch inc/dissim_full
+
+section "inc/dissim"
+sort -R list | head -3000 | sort > list.init
+$THIS/../list2pairs list.init | tr '\t' '-' | sort > dissim_request
+rm list.init
+inc/pairs2dissim.sh dissim_request "" inc/dissim log
+rm dissim_request
+$THIS/distTree_inc_dissim2indiscern.sh inc inc/dissim
+$THIS/../dm/pairs2dm inc/dissim 1 "dissim" 6 -distance > data.dm
+
+section "Initial tree"
+VARIANCE=`cat inc/variance`
+$THIS/makeDistTree  -threads 5  -data data  -dissim_attr "dissim"  -variance $VARIANCE  -optimize  -subgraph_iter_max 10  -output_tree inc/tree  > inc/hist/makeDistTree-complete.1
+rm data.dm
+cp inc/tree inc/hist/tree.1
+
+section "inc/new/"
+$THIS/tree2obj.sh inc/tree > tree.list
+$THIS/../setMinus list tree.list > new.list
+rm tree.list
+$THIS/distTree_inc_new_cmd.sh inc "touch" new.list
+rm new.list
+
+super_section "Incremental tree building"
+$THIS/distTree_inc.sh inc 1 ""

version.inc

@@ -1,6 +1,7 @@
-#define VERSION "1.7.3"
+#define VERSION "1.8.1"
 
 
+// 1.8.1  05/11/2021  inc/dissim_full
 // 1.7.3  04/23/2021  combine_dissims.cpp: weighted combination of all dissimilarities
 //                    str2real() bug in reading nan's
 // 1.7.2  04/19/2021  d_{CDS,PRT}: arithmetic average is used