separate notebook for full (rtt) analysis)

ktmeaton · Jul 16, 2020 · c6e5364 · c6e5364
1 parent 28c45e1
commit c6e5364
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diff --git a/docs/exhibit/exhibit_main.rst b/docs/exhibit/exhibit_main.rst
@@ -247,31 +247,3 @@ Regression Plot
     --clock-filter 3 \
     --keep-root \
     --outdir $project/nextstrain/treetime_clock/ori_subtree/
-
-
-MEGA
-^^^^
-
-**Shell Script**::
-
-  tail -n+2 $project/nextstrain/metadata_nextstrain_geocode_state.tsv | \
-    awk -F "\t" -v nameCol=1 -v dateCol=5 '{
-      if (substr($dateCol,1,1) == "[")
-      {
-        dates=substr($dateCol,2,length($dateCol)-2);
-        split(dates,dateSplit,":");
-        minTime=dateSplit[1];
-        maxTime=dateSplit[2];
-        print "!NodeName=" "\047" $nameCol "\047" " minTime=" minTime " maxTime=" maxTime;
-      }
-      else
-      {
-        print "!Taxa=" "\047" $nameCol "\047" " Time="$dateCol;
-    }}' | sed 's/_/ /g' > $project/nextstrain/metadata_MEGA_raw.txt
-
-  tail -n+2 $project/nextstrain/metadata_nextstrain_geocode_state.tsv | \
-    awk -F "\t" -v nameCol=1 -v dateCol=5 -v project="Assembly_Modern" '{
-      cmd = "grep "$nameCol " " project "/iqtree/iqtree.core-filter0_bootstrap.treefile"
-      print ( cmd | getline result )
-      close(cmd);
-    }'