MakeDb.py returns error

[Eric Mukherjee]

I have an IMGT output of 12 sequences I'm trying to make a Db out of, but when I run it, this happens:

C:\Users\Infin\Desktop\HammersSequences>MakeDb.py imgt -i IMGToutput.zip -s SequencesVH.fasta --regions --scores Traceback (most recent call last): File "C:\Users\Infin\Anaconda3\Scripts\MakeDb.py", line 23, in <module> from changeo.IO import countDbFile, extractIMGT, getDbWriter, readRepo File "C:\Users\Infin\Anaconda3\lib\site-packages\changeo\IO.py", line 24, in <module> csv.field_size_limit(sys.maxsize) OverflowError: Python int too large to convert to C long

I'm using Windows 10, Python 3.6.0 as part of Anaconda 4.3.1 64-bit

[Eric Mukherjee]

Seems like the problem is that in Windows, long is always 32-bit. Even if I manually edit IO.py to set the limit to 1000000, the following happens:

C:\Users\Infin\Desktop\HammersSequences>MakeDb.py imgt -i IMGToutput.zip -s SequencesVH.fasta --regions --scores usage: MakeDb.py [-h] [--version] ... MakeDb.py: error: the following arguments are required:

...and no arguments are listed

[Jason Vander Heiden]

Hey @emukherj, I'm investigating this, but I have to setup a Windows/Anaconda environment to do so and that might take day.

In the meantime, I suspect just commenting that line out:

# csv.field_size_limit(sys.maxsize)

Should work. It's not necessary for the vast majority of use cases.

[Jason Vander Heiden]

This should now be fixed as of fd501c1. You can install directly from bitbucket via:

pip install hg+https://bitbucket.org/kleinstein/changeo#default --upgrade --no-deps --force-reinstall

You may have to install mercurial for windows first.

Let me know it still gives you trouble.

[Jason Vander Heiden]

No news is good news.

[Eric Mukherjee]

Hey sorry my laptop is in the shop; ill let you know if it works when i get back