Shell Programming and Scripting

{

 “tree”: “((A:0.2{0},B:0.09{1}):0.7{2},C:0.5{3}){​4};”,

 “placements”:

 [

  {“p”: [[1, −2578.16, 0.777385, 0.004132, 0.0006], [0, −2580.15, 0.107065, 0.000009, 0.0153]], “n”: [“fragment1”]},

  {“p”: [[3, −2576.46, 1.0, 0.003555, 0.000006]], “n”: [“fragment2”]}
],

 “metadata”:

 {“invocation”:

  “pplacer -c tiny.refpkg frags.fasta”

 },

 “version”: 3,

 “fields”:

 [“edge_num”, “likelihood”, “like_weight_ratio”,

    “distal_length”, “pendant_length”]

}

fragment1 B −2578.16 0.777385 0.004132 0.0006
fragment1 A −2580.15 0.107065 0.000009 0.0153
fragment2 C −2576.46, 1.0, 0.003555, 0.000006

awk '
/tree/ {FS="[\(\),]"; gsub(" ","");
  for (i=1; i<=NF; i++) {
    if ($i ~ /:.*\{/) {
      n=$i; sub(".*[{]","",n); sub("[}].*","",n);
      v=$i; if ($i ~ /.:/) {sub(":.*","",v); l=v; p=v} else {l=p}
      x[n]=v;
    }
  }
}
/fragment/ {FS="[][]" ; a=$(NF-1); gsub("[ .]","",a);
  for (i=1; i<=NF; i++) if ($i ~ /.*,.*,/) {
     s=$i; sub(" *,.*","", s);
     t=$i; sub("^[^,]*, *","", t);
     print a, x[s], t, $i;}
  }
' infile