I tried to run OASIS but I had some problems regarding installation.
I got the following error during an initial test:
"/usr/local/lib/python2.7/dist-packages/Bio/ParserSupport.py:30: BiopythonDeprecationWarning: Bio.ParserSupport is now deprecated will be removed in a future release of Biopython.
"future release of Biopython.", BiopythonDeprecationWarning)
/usr/local/lib/python2.7/dist-packages/Bio/Blast/NCBIStandalone.py:41: BiopythonDeprecationWarning: This module has been deprecated. Consider Bio.SearchIO for parsing BLAST output instead.
"parsing BLAST output instead.", BiopythonDeprecationWarning)
Traceback (most recent call last):
File "/usr/local/bin/OASIS", line 98, in
data_folder=data_folder)
File "/usr/local/lib/python2.7/dist-packages/OASIS/AnnotatedGenome.py", line 59, in init
aafile = os.path.join(data_folder, ISFINDER_AA_FILE)
NameError: global name 'ISFINDER_AA_FILE' is not defined"
Apparently, the file 'ISFinder_aa.fasta' is missing. May I ask where could I find this file?
I tried to run OASIS but I had some problems regarding installation. I got the following error during an initial test:
"/usr/local/lib/python2.7/dist-packages/Bio/ParserSupport.py:30: BiopythonDeprecationWarning: Bio.ParserSupport is now deprecated will be removed in a future release of Biopython. "future release of Biopython.", BiopythonDeprecationWarning) /usr/local/lib/python2.7/dist-packages/Bio/Blast/NCBIStandalone.py:41: BiopythonDeprecationWarning: This module has been deprecated. Consider Bio.SearchIO for parsing BLAST output instead. "parsing BLAST output instead.", BiopythonDeprecationWarning) Traceback (most recent call last): File "/usr/local/bin/OASIS", line 98, in
data_folder=data_folder)
File "/usr/local/lib/python2.7/dist-packages/OASIS/AnnotatedGenome.py", line 59, in init
aafile = os.path.join(data_folder, ISFINDER_AA_FILE)
NameError: global name 'ISFINDER_AA_FILE' is not defined"
Apparently, the file 'ISFinder_aa.fasta' is missing. May I ask where could I find this file?