command line args

bin/opentree_scrape.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+import argparse
+import sys
+import physcraper
+from physcraper.opentree_helpers import scraper_from_opentree
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-s","--study_id", help="OpenTree study id")
+parser.add_argument("-t","--tree_id", help="tree id")
+parser.add_argument("-a","--alignment", help="path to alignment")
+parser.add_argument("-as","--aln_schema", help="alignment schema (nexus or fasta)")
+parser.add_argument("-o","--output", help="path to output directory")
+
+
+args = parser.parse_args()
+
+
+
+# Create an 'scraper' object to get data from NCBI, align it an
+scraper = scraper_from_opentree(study_id =args.study_id, 
+                                tree_id = args.tree_id, 
+                                alnfile = args.alignment, 
+                                aln_schema = args.aln_schema,
+                                workdir = args.output)
+
+sys.stdout.write("{} taxa in alignment and tree\n".format(len(scraper.data.aln)))
+
+
+#scraper.read_blast_wrapper()
+scraper.est_full_tree()
+scraper.data.write_labelled(label='^ot:ottTaxonName')

setup.py

@@ -11,5 +11,6 @@
       author='Emily Jane McTavish',
       author_email='ejmctavish@gmail.com',
       packages=['physcraper'],
+      scripts=['bin/opentree_scrape.py'],
       install_requires=[]
      )