release v1.0.0

Author: fmalmeida

conda.recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
  name: falmeida-py
- version: '0.9'
+ version: '1.0.0'
 
 source:
  path: ..

falmeida_py/bacannot2json.py

@@ -41,29 +41,20 @@
 ##############################
 ### fix keys in dictionary ###
 ##############################
+def convert_dictkey(d):
+ ###change all keys in a dict d
+ return { str(k): convert_dictvalue(v) for k,v in d.items() }
+
+def convert_dictvalue(v):
+ ###if v is a dict do convert_dictkey() for v, else raise v
+ if isinstance(v, dict):
+ return convert_dictkey(v)
+ else:
+ return v
+
 def stringify_keys(d):
  """Convert a dict's keys to strings if they are not."""
- for key in d.keys():
-
- # check inner dict
- if isinstance(d[key], dict):
- value = stringify_keys(d[key])
- else:
- value = d[key]
-
- # convert nonstring to string if needed
- if not isinstance(key, str):
- try:
- d[str(key)] = value
- except Exception:
- try:
- d[repr(key)] = value
- except Exception:
- raise
-
- # delete old key
- del d[key]
- return d
+ return convert_dictkey(d)
 
 ###############################################
 ### based on annotations figure sample name ###

falmeida_py/plasmid_function.py

@@ -82,8 +82,9 @@ def plasmids_stats(bacannot_summary):
  bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['inc_types'] = {}
  bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['identity'] = {}
  bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['accession'] = {}
+ 
  for index, row in results.iterrows():
- contig = row['Contig']
+ contig = str(row['Contig'])
  bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['inc_types'] = row['Plasmid']
  bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['identity'] = row['Identity']
  bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number']

falmeida_py/version.py

@@ -14,7 +14,7 @@
 If not, see <http://www.gnu.org/licenses/>.
 """
 
-__version__ = '0.9'
+__version__ = '1.0.0'
 
 def get_version():
  return __version__