Comments (7)
Carldeboer
commented on August 10, 2024
Any ideas?
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rsharris
commented on August 10, 2024
(I'm not a recently active contributor to this package, where "recent" is at decade resolution)
My best guess at the python3 problem is that the file wasn't opened in binary mode. So file.read thinks it's got a text file and decided to sanity check it for ascii compliance. The default for file.open is text mode. Not clear whether line 91 in aggregateGenomeData.py has "rb" as one of its arguments.
At one time there was no difference between text and binary files on *nix machines. I wonder if that's still true. Looking at https://docs.python.org/3/tutorial/inputoutput.html , the only difference I see mentioned is the usual windows vs *nix line endings.
That's just a guess though. Interested to know if I'm right.
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jxtx
commented on August 10, 2024
We've really not tested on python 3. Should work on 2, I have not had a
chance to try yet.
…On Wed, Dec 21, 2016 at 4:37 PM Bob Harris ***@***.***> wrote:
(I'm not a recently active contributor to this package, where "recent" is
at decade resolution)
My best guess at the python3 problem is that the file wasn't opened in
binary mode. So file.read thinks it's got a text file and decided to sanity
check it for ascii compliance. The default for file.open is text mode. Not
clear whether line 91 in aggregateGenomeData.py has "rb" as one of its
arguments.
At one time there was no difference between text and binary files on *nix
machines. I wonder if that's still true. Looking at
https://docs.python.org/3/tutorial/inputoutput.html , the only difference
I see mentioned is the usual windows vs *nix line endings.
That's just a guess though. Interested to know if I'm right.
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Carldeboer
commented on August 10, 2024
Is there a chance this could be an install issue? A previous version worked, but I was having a problem where data from chr6 was missing and so upgraded. Deleting the newer version seemed to have broken the old. Copying the old version back to the lib dir and deleting the newer versions resulted in a similar error.
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jxtx
commented on August 10, 2024
Seems quite possible since the Travis tests (always a clean install) pass.
Is installing from bioconda an option?
…On Mon, Jan 2, 2017 at 9:54 PM Carl de Boer ***@***.***> wrote:
Is there a chance this could be an install issue? A previous version
worked, but I was having a problem where data from chr6 was missing and so
upgraded. Deleting the newer version seemed to have broken the old. Copying
the old version back to the lib dir and deleting the newer versions
resulted in a similar error.
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Carldeboer
commented on August 10, 2024
Looks like it was indeed a bad install. It works now, but unfortunately the bug I was hoping was fixed in the latest version remains so I will open a new ticket.
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jxtx
commented on August 10, 2024
Thanks Carl.
…-- jt
On Thu, Jan 5, 2017 at 12:42 PM, Carl de Boer ***@***.***> wrote:
Looks like it was indeed a bad install. It works now, but unfortunately
the bug I was hoping was fixed in the latest version remains so I will open
a new ticket.
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