fix framed dependency

cdanielmachado · Oct 1, 2019 · 7eb898a · 7eb898a
1 parent 47de13b
commit 7eb898a
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Showing 4 changed files with 12 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -23,3 +23,4 @@ carveme.egg-info/*
 
 docs/_build/*
 Dockerfile
+.idea/encodings.xml
diff --git a/carveme/reconstruction/ncbi_download.py b/carveme/reconstruction/ncbi_download.py
@@ -11,7 +11,7 @@ def load_ncbi_table(inputfile):
     return table
 
 
-def download_ncbi_genome(accession, refseq_table, prefer_protein=True):
+def download_ncbi_genome(accession, refseq_table, prefer_protein=True, overwrite=False):
 
     if accession not in refseq_table.index:
         print('Invalid accession code')
@@ -27,6 +27,10 @@ def download_ncbi_genome(accession, refseq_table, prefer_protein=True):
 
         outputfile = '{}.faa.gz'.format(accession)
 
+        if os.path.exists(outputfile) and not overwrite:
+            print('File exists, skipping.')
+            return outputfile
+
         _, result = urllib.request.urlretrieve(url, outputfile)
 
         if result.get_content_type() != 'application/x-gzip':
@@ -40,6 +44,10 @@ def download_ncbi_genome(accession, refseq_table, prefer_protein=True):
 
         outputfile = '{}.fna.gz'.format(accession)
 
+        if os.path.exists(outputfile) and not overwrite:
+            print('File exists, skipping.')
+            return outputfile
+
         _, result = urllib.request.urlretrieve(url, outputfile)
 
         if result.get_content_type() != 'application/x-gzip':

diff --git a/requirements_dev.txt b/requirements_dev.txt
@@ -1,4 +1,4 @@
-framed==0.5.1
+framed>=0.5
 pandas>=0.20.0
 requests>=2.18
 

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@
     readme = readme_file.read()
 
 requirements = [
-    "framed==0.5.1",
+    "framed>=0.5",
     "pandas>=0.20.0",
     "requests>=2.18"
 ]