tree + h5ls

h5tree.sh

#!/bin/bash

usage () {
    cat <<HELP_USAGE
usage: h5tree [OPTIONS] file[/OBJECT]

  OPTIONS
   -h, -?, --help              Print a usage message and exit
   -L level, -P pattern, etc   Any flag accepted by \`tree\`

  file/OBJECT
    Each object consists of an HDF5 file name optionally followed by a
    slash and an object name within the file (if no object is specified
    within the file then the contents of the root group are displayed).
    The file name may include a printf(3C) integer format such as
    "%05d" to open a file family.
HELP_USAGE
}

# 0. print usage IFF no args or --help flag
(( ! $# )) || [[ " $@ " =~ " --help "|" -h "|" -? " ]] && { usage; exit 0; }

# 1. parse arg/s
_H5="${@:$#}"       # last arg
FLAGS="${*%${!#}}"  # rest of args (`tree` flags)
                                                                                                                
# H5="$( echo $_H5 | sed -E 's/(\.h5[^/]*).*$/\1/' )" # .h5* file (e.g. includes .h5ad)                                                                 
# H5="$( echo $_H5 | sed -E 's/(\.[^/]*).*$/\1/' )"   # <-- allow file with any .suffix
H5="${_H5/.h5\/*/.h5}" # .h5 file  
H5PATH="${_H5/$H5/}"   # (optional) path/within/h5

[[ -f "$H5" ]] && {
    _HASHED=$( sha1sum "$H5" | awk '{print $1}' )
    DIR="/tmp/$_HASHED"
}

# 2. walk $H5 & mirror structure
# (skip if already processed <--> hashed $DIR exists)
[[ ! -d "$DIR" ]] && h5ls -r "$H5" 2>/dev/null | sed -n 's/Dataset //p' | sed 's/\/Inf/+/g' |
    while read -r line; do
        mkdir -p "$DIR/$line"
    done

# 3. tree the shadow directory
# (after asserting $H5 is valid hdf5 & $H5PATH is valid path/to/object)
MAYBE_ERROR=$( h5ls "$H5$H5PATH" 2>&1 | grep -e "\*\*NOT FOUND\*\*" -e "unable to open file" )
[[ $MAYBE_ERROR ]] && {
    echo $MAYBE_ERROR
    exit 1
}                  || {
    # replace 1st line (/tmp/dir) with actual filename.h5, & skip junk at end
    echo "$( basename $H5 )$H5PATH"
    tree $FLAGS "$DIR$H5PATH" | tail -n +2 | head -n -2
}