12-Nov-2018 15:40:26 INFO GEOparse - Parsing ./GSE1563.soft.gz:
Traceback (most recent call last):
File "C:/Users/Ciaran/Box Sync/MesiSTRAT/PublicDataSetSearch/ReFormatShittyNCBIOutput.py", line 95, in <module>
gse = GEOparse.get_GEO(filepath="./GSE1563.soft.gz")
File "C:\ProgramData\Anaconda2\lib\site-packages\GEOparse\GEOparse.py", line 84, in get_GEO
return parse_GSE(filepath)
File "C:\ProgramData\Anaconda2\lib\site-packages\GEOparse\GEOparse.py", line 502, in parse_GSE
with utils.smart_open(filepath) as soft:
File "C:\ProgramData\Anaconda2\lib\contextlib.py", line 17, in __enter__
return self.gen.next()
File "C:\ProgramData\Anaconda2\lib\site-packages\GEOparse\utils.py", line 154, in smart_open
fh = fopen(filepath, mode)
File "C:\ProgramData\Anaconda2\lib\gzip.py", line 34, in open
return GzipFile(filename, mode, compresslevel)
File "C:\ProgramData\Anaconda2\lib\gzip.py", line 94, in __init__
fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
ValueError: Invalid mode ('rtb')
Process finished with exit code 1
Hi,
The following code from the first section of the tutorials is broken on my machine. I'm running Anaconda Python 3.6 on windows 10.
Produces the following error