Merge pull request #63 from McTavishLab/dev

Dev

.travis.yml

@@ -56,7 +56,7 @@ install:
 script:
   - wget 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
   - gunzip  -cd taxdump.tar.gz | (tar xvf - names.dmp nodes.dmp)
-  - mv *.dmp tests/data/
+  - mv *.dmp taxonomy/
   - echo 'no' | python tests/testfilesetup.py
   #- py.test tests/ --setup-only
   - sh tests/run_tests.sh

physcraper/scrape.py

@@ -242,7 +242,7 @@ def run_web_blast_query(self, query, equery, fn_path):
         :return: runs web blast query and writes it to file
         """
         if self.config.url_base:
-            debug("blasting {} using {}".format(self.config.url_base))
+            debug("blasting {} using {}".format(fn_path, self.config.url_base))
             result_handle = AWSWWW.qblast("blastn",
                                           "nt",
                                           query,

setup.py

@@ -8,11 +8,5 @@
       author='Emily Jane McTavish',
       author_email='ejmctavish@gmail.com',
       packages=['physcraper'],
-      install_requires=[
-          'dendropy==4.1.0',
-          'configparser',
-          'biopython',
-          'urllib3',
-          'peyotl',
-      ]
+      install_requires=[]
      )

tests/test_add_all.py

@@ -25,6 +25,6 @@ def test_add_all():
     filteredScrape.seq_filter = ['deleted', 'subsequence,', 'not', "removed", "deleted,"]
     filteredScrape.remove_identical_seqs()
     sp_d = filteredScrape.make_sp_dict(filteredScrape.new_seqs_otu_id)
-    assert len(sp_d) == 7
+    assert len(sp_d) == 5
     for taxon in sp_d:
         assert len(sp_d[taxon]) <= threshold