Bed file additional field error

[SwiftSeal]

Heya,

I'm running the latest devtools install of GENESPACE and ran into an unexpected error. I prefer to write the bed and peptide directories manually with other scripts - in this case the bed files were produced by https://agat.readthedocs.io/en/latest/gff_to_bed.html. A typical entry might look like:

chr01   69219140        69220392        chr01_000440.1  0       +       69219432        69220118        255,0,0 3       310,231,529     0,404,723

Running gpar <- init_genespace(wd = getwd(), path2mcscanx = "/blah/blah/MCScanX") resulted in the following error:

Checking Working Directory ... PASS: `/blah/blah/blah/`
Checking user-defined parameters ...
        Genome IDs & ploidy ... 
                chilense        : 1
                chmielewskii    : 1
                corneliomulleri : 1
                galapagense     : 1
                habrochaites    : 1
                lycopersicoides : 1
                lycopersicum    : 1
                neorickii       : 1
                peruvianum      : 1
                pimpinellifolium: 1
        Outgroup ... NONE
        n. parallel processes ... 16
        collinear block size ... 5
        collinear block search radius ... 25
        n gaps in collinear block ... 5
        synteny buffer size... 100
        only orthogroups hits as anchors ... TRUE
        n secondary hits ... 0
Checking annotation files (.bed and peptide .fa):
Error in bd$id : $ operator is invalid for atomic vectors

I narrowed the issue down to the read_bed function: https://github.com/jtlovell/GENESPACE/blob/1d7b7274bdb142f321b3c46f3af130084b65fa7f/R/utils.R#L297-L313 It seems to be linked to this issue with fread? https://stackoverflow.com/questions/25691637/using-colclasses-and-select-arguments-of-fread-simultaneously

Testing bd <- fread("morethan4columns.bed", select = 1:4, colClasses = c("character", "numeric", "numeric", "character"), header = FALSE, col.names = c("chr", "start", "end", "id")) results in:

Error in fread("morethan4columns.bed",  : 
  colClasses= is an unnamed vector of types, length 4, but there are 12 columns in the input. To specify types for a subset of columns, you can use a named vector, list format, or specify types using select= instead of colClasses=. Please see examples in ?fread.

Removing colClasses or switching to 4 column bed files fixes this - I've opted to just fix my external bed processing, but highlighting in case anyone else encounters this as it seems the read_bed error seems to fail silently! README says other fields should be ignored also.

Cheers! Fantastic software otherwise : - )

[jtlovell]

Ok. Good sleuthing. So, does it run through if you just strip out the other columns so that it is just the first 4? The GENESPACE input specifications is just a 4-column bed file.

[SwiftSeal]

Aye runs fine with 4 columns! Highlighted just in case anyone else encounters a similar issue as the README suggests additional columns are ignored: https://github.com/jtlovell/GENESPACE/blob/893f9022a76b6d8ef99e0b5e43f4d6b0fdf0e200/readme.md?plain=1#L146