Parsing auxiliary data paths when running run_igblastn

[chuckzzzz]

Description of the question

Hi! Thanks for developing this wonderful tool!

I am not sure if this is a bug so I will pose it as a question. I noticed that when formatting the command to pass to igblastn, the optional file directory does not have a "/" in front. Is this intentional? This is relevant to line 4503 and 4533 in _preprocessing.py.

Following the changeO igblast setup, the igblast folder has a structure like this:

├── igblast
│   ├── database
│   ├── fasta
│   ├── internal_data
│   ├──optional_file
└──

The command to run is formatted like this

...
igdb + "/database/imgt_" + org + "_" + loci + "_j",
"-auxiliary_data",
igdb + "optional_file/" + org + "_gl.aux",
"-domain_system"
...

So if the structure holds, the optional file will not be located since it's not considered as a folder. Say my path to the igblast folder is ~/test/igblast, then all the optional file will be formatted as ~/test/igblastoptional_file/human_gl.aux while the other vdj files will be something like ~/test/igblast/database/imgt_human_ig_j.

I might be missing something here, but let me know if this is supposed to be the way it is. Thanks!

Minimal example

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Any error message produced by the code above

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[zktuong]

Hi @chuckzzzz thanks for this!

You are correct but it depends on how igdb (which is basically $IGDATA in my installation instructions) is exported/specified. Currently i've written in both the singularity container and the instructions for that to be IGDATA=/share/database/igblast/ so the / is going to be there. It's doesn't seem to mind the double // in e.g. igdb + "/database/imgt_" + org + "_" + loci + "_v" so everything still works.

Ideally i should have just use pathlib to handle this, so then there won't be any potential issues but just need to find the time to implement it properly.

something like:

import os
from pathlib import Path

env = os.environ.copy()
igdb = env["IGDATA"] if "IGDATA" in env else igblast_db
assert(Path(igdb).exists()

org = "human"
loci = "ig"
dbpath = Path(igdb) / "database"
imgt_org_loci = "imgt_" + org + "_" + loci + "_"
vpath = str(dbpath / (imgt_org_loci + "v"))
dpath = str(dbpath / (imgt_org_loci + "d"))
jpath = str(dbpath / (imgt_org_loci + "j"))
auxpath = str(Path(igdb) / "optional_file" / (org + "_gl.aux"))


cmd = [
    "igblastn",
    "-germline_db_V",
    vpath,
    "-germline_db_D",
    dpath,
    "-germline_db_J",
    jpath,
    "-auxiliary_data",
    auxpath,
    ...,
]

[chuckzzzz]

gotcha thanks it makes sense!