tutorial

docs/PhyscraperRun.md

@@ -0,0 +1,18 @@
+## Details on running using physcraper_run.py
+
+
+## QuickStart
+
+For a simple run you just need the study id and tree id from OpenTree (see more about searching in FindTrees.md),
+and an alignment file that goes with that tree.
+
+    physcraper_run.py -s <study_id> -t <tree_id> -a <alignment_file_path> -as <alignment_schema> -o <output_directory>
+
+
+To update this tree
+https://tree.opentreeoflife.org/curator/study/view/ot_350/?tab=home&tree=Tr53296
+
+(alignment already downloaded from treebase)
+
+
+    physcraper_run.py -s ot_350 -t Tr53297 -a docs/examples/ot_350Tr53297.aln -as nexus -o ot_350_analysis

docs/Tutorial.md

@@ -20,17 +20,27 @@ In order to further assess, lets update the tree!
 
 ### Run the auto update
 
-The blast search part of updating trees take a long time! (hours)
+
+The script `physcraper_run.py` wraps together linking the trees an alignment, blasting, aligning sequences, and 
+inferring an updated tree.  
+The blast search part of updating trees take a long time! (this analysis took around 12 hours)
 
 
     physcraper_run.py -s pg_55 -t tree5864 -tb -r -o pg_55
 
 
 We have put example outputs from this command in docs/examples/pg_55
 
+### Output stucture
+
+The analysis folder has several subdirectories.
+each folder is labelled with a 'tag', whcih is the 
+
+
+
 ### Compare your new tree to existing relationships
 
-    tree_comparison.py -d docs/examples/pg_55/ -og otu376420 otu376439 otu376452 -o tmp_comp
+    tree_comparison.py -d docs/examples/pg_55/ -og otu376420 otu376439 otu376452 -o pg_55_comparison
 
 
 
@@ -40,3 +50,6 @@ We have put example outputs from this command in docs/examples/pg_55
     podarc = treetaxon.generate_TreeTax_from_run('test_podarcis')
     podarc.write_labelled(label='^ot:ottTaxonName', norepeats=False, path='test_podarcis/repeats.tre')
 
+
+
+##Example with Data Dryad chiroptera gene trees???