use local aln

docs/examples/data_scrape_local_aln.py

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+import physcraper
+import dendropy
+import pickle
+import sys
+import os
+import json
+from peyotl.nexson_syntax import (
+    extract_tree,
+    get_subtree_otus,
+    extract_otu_nexson,
+    PhyloSchema,
+)
+import dendropy
+
+configfi = "docs/examples/example.config"
+study_id = "ot_350"
+tree_id = "Tr53297"
+workdir ="scrape_ot_350"
+
+
+# Read in the configuration information
+conf = physcraper.ConfigObj(configfi)
+
+
+#Get an existing tree from the Open Tree of life, and convert it to newick format
+nexson = physcraper.opentree_helpers.get_nexson(study_id, 'api')
+newick = extract_tree(nexson,
+                      tree_id,
+                      PhyloSchema('newick',
+                                   output_nexml2json='1.2.1',
+                                   content="tree",
+                                   tip_label="ot:originalLabel"))
+
+tre = dendropy.Tree.get(data=newick,
+                   schema="newick",
+                   preserve_underscores=True)
+
+
+aln = dendropy.DnaCharacterMatrix.get(file=open("docs/examples/{}{}.aln".format(study_id, tree_id)), schema="nexus", taxon_namespace=tre.taxon_namespace)
+
+tre.write(path="docs/examples/{}{}.tre".format(study_id, tree_id), schema="nexus")
+
+# To preserve taxon labels and relationships, 
+#we will combine the alignement, tree and taxon information into a single data object
+# By using the OpenTree Phylesystem API we can get the orgininal taxon names as well as the taxon mappings
+data_obj = physcraper.generate_ATT_from_phylesystem(aln=aln,
+                                         workdir=workdir,
+                                         config_obj=conf,
+                                         study_id=study_id,
+                                         tree_id=tree_id)
+
+#data_obj.write_files()
+#json.dump(data_obj.otu_dict, open('{}/otu_dict.json'.format(workdir), 'wb'))
+
+sys.stdout.write("{} taxa in alignement and tree\n".format(len(data_obj.aln)))
+
+# We need to create a physcraper ids object to translate between ncbi and OpenTree identifiers.
+ids = physcraper.IdDicts(conf, workdir=workdir)
+
+
+# Create an 'scraper' object to get data from NCBI, align it an
+scraper = physcraper.PhyscraperScrape(data_obj, ids)
+
+#scraper.read_blast_wrapper()
+scraper.est_full_tree()
+scraper.data.write_labelled(label='^ot:ottTaxonName')