doc update for new geocode

ktmeaton · Jul 5, 2020 · 407d607 · 407d607
1 parent 34f4953
commit 407d607
Showing 1 changed file with 69 additions and 33 deletions.
diff --git a/docs/exhibit/exhibit_main.rst b/docs/exhibit/exhibit_main.rst
@@ -221,6 +221,27 @@ Extract metadata from the SQLite database.
         $sqliteDB \
         $scriptsDir
 
+Geocode
+^^^^^^^
+
+Use the GeoPy module with Nominatim to geocode global addresses.
+
+**Shell Scripts**::
+
+      $scriptsDir/geocode_NextStrain.py \
+       --in-tsv Assembly_Modern/nextstrain/metadata_nextstrain.tsv \
+       --loc-col BioSampleGeographicLocation \
+       --out-tsv Assembly_Modern/nextstrain/metadata_nextstrain_geocode_state.tsv\
+       --out-lat-lon Assembly_Modern/nextstrain/lat_longs_state.tsv \
+       --div state
+
+      $scriptsDir/geocode_NextStrain.py \
+       --in-tsv Assembly_Modern/nextstrain/metadata_nextstrain.tsv \
+       --loc-col BioSampleGeographicLocation \
+       --out-tsv Assembly_Modern/nextstrain/metadata_nextstrain_geocode_state.tsv\
+       --out-lat-lon Assembly_Modern/nextstrain/lat_longs_state.tsv \
+       --div state
+
 Combine treetime and augur
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -229,19 +250,16 @@ Activate the nextstrain/treetime environment.
 ::
 
     conda activate nextstrain-8.0.0
-    pip install git+git://github.com/ktmeaton/biopython@newickio-comment
-    pip install git+git://github.com/ktmeaton/treetime@comment-concat
 
-::
+Create a time-calibrated phylogeny.
 
-    #conda activate nextstrain-8.0.0
-    conda activate treetime-env
+::
 
-    # What about mods to biopython and treetime?
+    mkdir -p $project/nextstrain/treetime_clock/
 
     treetime \
       --aln $project/snippy_multi/snippy-core.full_CHROM.filter0.fasta \
-      --tree $project/iqtree/iqtree.core-filter0.treefile \
+      --tree $project/iqtree/iqtree.core-filter0_bootstrap.treefile \
       --dates $project/nextstrain/metadata_nextstrain.tsv \
       --clock-filter 3 \
       --keep-root \
@@ -253,43 +271,61 @@ Activate the nextstrain/treetime environment.
       --coalescent skyline \
       --covariation \
       --outdir $project/nextstrain/treetime_clock \
-      --date-column BioSampleCollectionDate
+      --date-column BioSampleCollectionDate \
+      --verbose 6 2>&1 | tee $project/nextstrain/treetime_clock/treetime_clock.log
+
+Run mugration analysis to estimate biovar variable.
+
+::
+
+    mkdir -p $project/nextstrain/treetime_mugration_biovar/
 
     treetime mugration \
-      --tree treetime_clock/timetree.nexus \
-      --attribute region \
-      --states ../data/metadata_treetime.tsv \
+      --tree $project/nextstrain/treetime_clock/timetree.nexus \
+      --attribute BioSampleBiovar \
+      --states $project/nextstrain/metadata_nextstrain.tsv \
       --confidence \
-      --outdir treetime_mugration_region/
+      --outdir $project/nextstrain/treetime_mugration_biovar/ \
+      --verbose 6 2>&1 | tee $project/nextstrain/treetime_mugration_biovar/treetime_mugration_biovar.log
+
+Use augur to create the needed json files for auspice.
 
-    mkdir -p augur/
-    mkdir -p auspice/
+::
+
+    mkdir -p $project/nextstrain/augur/
+    mkdir -p $project/nextstrain/auspice/
 
     augur refine \
-      --alignment ../results/aligned.fasta \
-      --tree treetime_clock/divergence_tree.nexus \
-      --metadata ../data/metadata_treetime.tsv \
-      --output-tree augur/augur-refine.nwk \
-      --output-node-data augur/mutation_length.json \
+      --alignment $project/snippy_multi/snippy-core.full_CHROM.filter0.fasta \
+      --tree $project/nextstrain/treetime_clock/divergence_tree.nexus \
+      --metadata $project/nextstrain/metadata_nextstrain.tsv \
+      --output-tree $project/nextstrain/augur/augur-refine.nwk \
+      --output-node-data $project/nextstrain/augur/mutation_lengths.json \
       --keep-root
 
-    sed -i 's/branch_length/mutation_length/g' augur/mutation_length.json
+    sed -i 's/branch_length/mutation_length/g' $project/nextstrain/augur/mutation_lengths.json
+
+    augur ancestral \
+      --tree $project/nextstrain/treetime_clock/divergence_tree.nexus \
+      --alignment $project/snippy_multi/snippy-core.full_CHROM.filter0.fasta \
+      --output-node-data $project/nextstrain/augur/nt_muts.json
 
     $scriptsDir/treetime_dates_json.py \
-      --time treetime_clock/timetree.nexus \
-      --dates treetime_clock/dates.tsv \
-      --json augur/branch_lengths.json
+      --time $project/nextstrain/treetime_clock/timetree.nexus \
+      --dates $project/nextstrain/treetime_clock/dates.tsv \
+      --json $project/nextstrain/augur/branch_lengths.json
 
     $scriptsDir/treetime_mugration_json.py \
-        --tree treetime_mugration_region/annotated_tree.nexus \
-        --json augur/traits_region.json \
-        --conf treetime_mugration_region/confidence.csv \
-        --trait region
+        --tree $project/nextstrain/treetime_mugration_biovar/annotated_tree.nexus \
+        --json $project/nextstrain/augur/traits_biovar.json \
+        --conf $project/nextstrain/treetime_mugration_biovar/confidence.csv \
+        --trait biovar
+
+    mkdir -p $project/nextstrain/auspice/
 
     augur export v2 \
-        --tree augur/augur-refine.nwk \
-        --metadata ../data/metadata_treetime.tsv \
-        --node-data augur/nt_muts.json augur/mutation_length.json augur/dates.json augur/traits_region.json \
-        --lat-longs ../config/lat_longs.tsv \
-        --auspice-config ../config/auspice_config.json \
-        --output auspice/auspice.json
+        --tree $project/nextstrain/augur/augur-refine.nwk \
+        --metadata $project/nextstrain/metadata_nextstrain_geocode_country.tsv \
+        --node-data $project/nextstrain/augur/mutation_lengths.json $project/nextstrain/augur/branch_lengths.json augur/traits_biovar.json \
+        --output $project/nextstrain/auspice/auspice.json \
+        --lat-long $project/nextstrain/lat_longs_country.tsv