Can't load VDJtools file

[f6v]

🐛 Bug

First off, thanks for the package! I'm new to immune repertoire files, but it seems like my data is in VDJtools format:

count freq cdr3nt cdr3aa v d j

1 2.1566179055358223E-6 REDACTED REDACTED TRAV-10,TRAV-10D,TRAV-10N . TRAJ-12

Is that right, or the format is off? Because I'm getting the following error:

== Step 1/3: loading repertoire files... ==

Processing "" ... -- [1/1] Parsing "~/dev/TCR_novaseq/export/vdjtools//Clonotypes-30581-001.1 (paired).txt" -- unsupported format, skipping

== Step 2/3: checking metadata files and merging files... ==

Processing "" ... -- Metadata file not found; creating a dummy metadata... Warning: Unknown or uninitialised column: Sample. Warning: Unknown or uninitialised column: Sample.

== Step 3/3: processing paired chain data... ==

Done!

The code:

imm_data <- repLoad(file.path(data_path, .mode = "single")

[vadimnazarov]

Hi @f6v , thank you for using the package! Could you provide information on what version of VDJtools you are using please? An example of the file would be great too, as we will be able to quickly identify the issues using your file.

[f6v]

@vadimnazarov thanks for getting back to me! It's actually a custom export process to VDJtools format. There's a possibility the said export process is off. I've attached two files: one that can be successfully imported with immunarch, and one that can't. They have different headers, does that matter?

export_errors.txt export_works.txt

[lianggongzifang]

Hi @f6v , thank you for using the package! Could you provide information on what version of VDJtools you are using please? An example of the file would be great too, as we will be able to quickly identify the issues using your file.

Hi @vadimnazarov , I have the same problem. I had loaded VDJtools file successfully using the version 0.6.5, but it failed using the version 0.6.7. The error is as mentioned above, "unsupported format, skipping".

[ElviMagda]

🐛 Bug

First off, thanks for the package! I'm new to immune repertoire files, but it seems like my data is in VDJtools format:

count freq cdr3nt cdr3aa v d j

1 2.1566179055358223E-6 REDACTED REDACTED TRAV-10,TRAV-10D,TRAV-10N . TRAJ-12

Is that right, or the format is off? Because I'm getting the following error:

== Step 1/3: loading repertoire files... == Processing "" ... -- [1/1] Parsing "~/dev/TCR_novaseq/export/vdjtools//Clonotypes-30581-001.1 (paired).txt" -- unsupported format, skipping == Step 2/3: checking metadata files and merging files... == Processing "" ... -- Metadata file not found; creating a dummy metadata... Warning: Unknown or uninitialised column: Sample. Warning: Unknown or uninitialised column: Sample. == Step 3/3: processing paired chain data... == Done!

The code:

imm_data <- repLoad(file.path(data_path, .mode = "single")

Hi,

in case it helps, we changed the "freq" column name for "frequency" and it worked.

Best, Elvira

[Alexander230]

Hi, @f6v, @lianggongzifang and @ElviMagda!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

I've made an experimental fix for the parser, now it correctly detects files with "freq" column instead of "frequency" as vdjtools. Please check it with your data! To install immunarch from branch with this fix, you can use these commands:

install.packages(c("devtools", "pkgload"))
devtools::install_github("immunomind/immunarch", ref="vdjtools-parser-fix")
devtools::reload(pkgload::inst("immunarch"))

When the fix will be finalized, it will be moved to dev branch; after that, to install it, use ref="dev" instead of ref="vdjtools-parser-fix" in these commands.

Best regards, Aleksandr

[lianggongzifang]

ok, it works now! Thank you!

[Alexander230]

Nice, thank you for checking, I'm glad to hear that it's working now! If you have more questions, or the fix doesn't work for anyone else, feel free to reopen the issue.

Best regards, Aleksandr