allow user-specified germlines in ighutil

[psathyrella]

So we need to be able to specify alternative germline files in Connor's ighutil/vdjalign package. Erick volunteered, ha ha, right?

The main package is here

As it says in the readme, you install with

make -C clj pip install ./python # I would add --user

The way it's set up now, it always loads germline versions from files in this directory, and the options such as --j-subset specify the file suffix, e.g. --j-subset adaptive tells it to load ighj-adaptive.fasta. One problem with this is that imgt seems to quite enjoy regularly changing both the name corresponding to a given sequence and the sequence corresponding to a given name.

So ideally I could specify something like --germline-dir, and it always looks for igh[vdj].fasta in that directory.

The code that actually loads the file is here. The farthest I got was figuring out that if I add this line:

return open('/home/dralph/work/partis/data/' + file_name)

in _handle() it properly looks in that directory. But I need to do in on the command line!

I can of course ask Connor as well, or do it myself, but you sounded stoked on it...

[matsen]

Heh, I did volunteer? I don't think I'm the best person to help with this. Would you like some help from Brian?

[psathyrella]

ha ha. Yeah you said to call you over if I had to look into connor's code again. No, I can do it fine.