Merge pull request #35 from phac-nml/sistr_cmd_update_2018

Sistr cmd update 2018
phac-nml · Oct 3, 2019 · 6381483 · 6381483
2 parents 4630fae + 3925340
commit 6381483
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Showing 28 changed files with 379 additions and 105,731 deletions.
diff --git a/.gitignore b/.gitignore
@@ -14,3 +14,8 @@ tmp
 *.b6
 .RData
 .Rhistory
+*.fasta
+*.csv
+*.hdf
+*.txt
+*.msh
diff --git a/setup.py b/setup.py
@@ -1,6 +1,9 @@
 import os
 from distutils.core import setup
 from setuptools import find_packages
+import sys
+sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+from sistr.version import __version__
 
 classifiers = """
 Development Status :: 3 - Alpha
@@ -49,6 +52,8 @@ def read(fname):
         'numpy>=1.11.1',
         'pandas>=0.18.1',
         'tables>=3.3.0',
+        'pycurl>=7.43.0',
+        'scipy>=1.1.0'
     ],
     extras_require={
         'test': ['pytest>=2.9.2',],

diff --git a/sistr/data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv b/sistr/data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv
diff --git a/sistr/data/antigens/fliC.fasta b/sistr/data/antigens/fliC.fasta
diff --git a/sistr/data/antigens/fljB.fasta b/sistr/data/antigens/fljB.fasta
diff --git a/sistr/data/antigens/wzx.fasta b/sistr/data/antigens/wzx.fasta
diff --git a/sistr/data/antigens/wzy.fasta b/sistr/data/antigens/wzy.fasta
diff --git a/sistr/data/cgmlst/README.md b/sistr/data/cgmlst/README.md
diff --git a/sistr/data/cgmlst/cgmlst-centroid.fasta b/sistr/data/cgmlst/cgmlst-centroid.fasta
diff --git a/sistr/data/cgmlst/cgmlst-full.fasta b/sistr/data/cgmlst/cgmlst-full.fasta
diff --git a/sistr/data/cgmlst/cgmlst-profiles.csv b/sistr/data/cgmlst/cgmlst-profiles.csv
diff --git a/sistr/data/cgmlst/cgmlst-profiles.hdf b/sistr/data/cgmlst/cgmlst-profiles.hdf
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,3 +14,8 @@ tmp @@
     *.b6
     .RData
     .Rhistory
+    *.fasta
+    *.csv
+    *.hdf
+    *.txt
+    *.msh