issue about downloading database

[yaober]

Hello, when I tried to download the database from your website(http://www.imgt.org/download/V-QUEST/IMGT_V-QUEST_reference_directory/Homo_sapiens/IG/IGHV.fasta), there was an error. could you kindly help me to check the website? thanks for your assistance

[reccej]

Hmmm, looks like the link changed to only accept https connections. We'll have to update the script with updated links, thanks for the info

[reccej]

For example: https://www.imgt.org/download/V-QUEST/IMGT_V-QUEST_reference_directory/Homo_sapiens/IG/IGHV.fasta works

[reccej]

@Ch-rode @yaober I've just pushed an update to the repository that fixes all of the links in the setup script (as well as another minor bug).

I haven't gotten all of the changes pushed to pip yet but if you git clone this repository and do the local install method the setup script should work now:
git clone https://github.com/crowelab/PyIR cd PyIR/ pip3 install --user .

Let me know if something is wrong

[Ch-rode]

@reccej thanks a lot, everything is working now.
I am sorry to bother again, I was also wondering if you added the isotypes as well. I cloned the repo but i do not find them in the output.
thanks again

[reccej]

I thought I did, the isotype databases are in the source but maybe they're not getting properly compiled to a BLAST library -- I'll have to confer with @myersml5 about it. I've been mostly out of the sequencing game for 3 years and he's my go-to now

[reccej]

If you wanna get funky with it, look in the pyir/data/crowelab_data folder for the files 'human_gl_C.fasta' and 'human_TCR_C.fasta'. They can be used to build a BLAST database which should be able to be fed into PyIR using the --germlineC flag, but it may be a spotty implementation