Read error on TabulaSapients 10X data

Transferred issue from here: https://github.com/rasmushenningsson/SingleCell10x.jl/issues/5

Hi Rasmus,

Just for fun, I thought I'd try applying SingleCellProjections to a dataset I had on hand, the TabulaSapiens eye .h5ad file. If you want to grab this file yourself, you can find it here: https://figshare.com/articles/dataset/Tabula_Sapiens_release_1_0/14267219?file=34701970.

However, it seems that load_h5ad isn't particularly happy with this file:

(jl_NPMjKi) pkg> st # Julia 1.11.0-rc2
Status `/tmp/jl_NPMjKi/Project.toml`
  [03d38035] SingleCellProjections v0.4.0

julia> counts = load_counts("/data/gene_variants_data/extracted/tabula_sapiens/TS_Eye.h5ad/TS_Eye.h5ad")
ERROR: unexpected character '\x04' after quoted field at row 250 column 1
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] 
    @ DelimitedFiles ~/.julia/packages/DelimitedFiles/aGcsu/src/DelimitedFiles.jl:727
  [3] readdlm_string(sbuff::String, dlm::Char, T::Type, eol::Char, auto::Bool, optsd::Dict{Symbol, Union{…}})
    @ DelimitedFiles ~/.julia/packages/DelimitedFiles/aGcsu/src/DelimitedFiles.jl:461
  [4] readdlm_auto(input::IOStream, dlm::Char, T::Type, eol::Char, auto::Bool; opts::@Kwargs{})
    @ DelimitedFiles ~/.julia/packages/DelimitedFiles/aGcsu/src/DelimitedFiles.jl:231
  [5] readdlm_auto
    @ ~/.julia/packages/DelimitedFiles/aGcsu/src/DelimitedFiles.jl:231 [inlined]
  [6] readdlm
    @ ~/.julia/packages/DelimitedFiles/aGcsu/src/DelimitedFiles.jl:226 [inlined]
  [7] readdlm
    @ ~/.julia/packages/DelimitedFiles/aGcsu/src/DelimitedFiles.jl:86 [inlined]
  [8] _read10x_features(io::IOStream; delim::Char)
    @ SingleCell10x ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:306
  [9] _read10x_features
    @ ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:305 [inlined]
 [10] #19
    @ ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:315 [inlined]
 [11] #1
    @ ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:57 [inlined]
 [12] open(f::SingleCell10x.var"#1#2"{SingleCell10x.var"#19#20"{@Kwargs{delim::Char}}, Bool}, args::String; kwargs::@Kwargs{})
    @ Base ./io.jl:410
 [13] open
    @ ./io.jl:407 [inlined]
 [14] _open(f::SingleCell10x.var"#19#20"{@Kwargs{delim::Char}}, filename::String)
    @ SingleCell10x ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:55
 [15] #_read10x_features#18
    @ ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:314 [inlined]
 [16] _read10x_features_triplet(filename::String; guess::Function, kwargs::@Kwargs{})
    @ SingleCell10x ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:329
 [17] _read10x_features_triplet
    @ ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:327 [inlined]
 [18] #_read10x_features_autodetect#22
    @ ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:324 [inlined]
 [19] _read10x_features_autodetect
    @ ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:320 [inlined]
 [20] read10x_features(io::String, featuretype::Type; kwargs::@Kwargs{})
    @ SingleCell10x ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:357
 [21] read10x_features
    @ ~/.julia/packages/SingleCell10x/XLhW5/src/fileio.jl:356 [inlined]
 [22] _load10x_metadata
    @ ~/.julia/packages/SingleCellProjections/0yZXZ/src/load.jl:96 [inlined]
 [23] load10x(filename::String; lazy::Bool, var_id::Nothing, var_id_delim::Char, kwargs::@Kwargs{})
    @ SingleCellProjections ~/.julia/packages/SingleCellProjections/0yZXZ/src/load.jl:135
 [24] load10x
    @ ~/.julia/packages/SingleCellProjections/0yZXZ/src/load.jl:130 [inlined]
 [25] #29
    @ ./broadcast.jl:1306 [inlined]
 [26] _broadcast_getindex_evalf
    @ ./broadcast.jl:673 [inlined]
 [27] _broadcast_getindex
    @ ./broadcast.jl:646 [inlined]
 [28] getindex
    @ ./broadcast.jl:605 [inlined]
 [29] copy
    @ ./broadcast.jl:906 [inlined]
 [30] materialize
    @ ./broadcast.jl:867 [inlined]
 [31] load_counts(loadfun::typeof(load10x), filenames::String; sample_names::Nothing, sample_name_col::Nothing, lazy::Bool, lazy_merge::Bool, obs_id_col::String, obs_id_delim::Char, obs_id_prefixes::Nothing, extra_var_id_cols::Symbol, duplicate_var::Nothing, duplicate_obs::Nothing, callback::Nothing, kwargs::@Kwargs{})
    @ SingleCellProjections ~/.julia/packages/SingleCellProjections/0yZXZ/src/load.jl:221
 [32] load_counts
    @ ~/.julia/packages/SingleCellProjections/0yZXZ/src/load.jl:199 [inlined]
 [33] load_counts(filenames::String)
    @ SingleCellProjections ~/.julia/packages/SingleCellProjections/0yZXZ/src/load.jl:227
 [34] top-level scope
    @ REPL[8]:1
Some type information was truncated. Use `show(err)` to see complete types.

Locally modifying _read10x_features to get the first 200 bytes of the IO that readdlm was called on, this is what I find:

\x89HDF\r\n\x1a\n\0\0\0\0\0\b\b\0\x04\0\x10\0\0\0\0\0\0\0\0\0\0\0\0\0\xff\xff\xff\xff\xff\xff\xff\xff\$\x84\xd5F\0\0\0\0\xff\xff\xff\xff\xff\xff\xff\xff\0\0\0\0\0\0\0\0`\0\0\0\0\0\0\0\x01\0\0\0\0\0\0\0\x88\0\0\0\0\0\0\0\xa8\x02\0\0\0\0\0\0\x01\0\x01\0\x01\0\0\0\x18\0\0\0\0\0\0\0\x11\0\x10\0\0\0\0\0\x88\0\0\0\0\0\0\0\xa8\x02\0\0\0\0\0\0TREE\0\0\x01\0\xff\xff\xff\xff\xff\xff\xff\xff\xff\xff\xff\xff\xff\xff\xff\xff\0\0\0\0\0\0\0\0\xe0\x05\0\0\0\0\0\0 \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0...

BioJulia / SingleCellProjections.jl

Read error on TabulaSapients 10X data #22