Open *.gz (or other compressed files)

[prairie-guy]

I am new to nushell. There is much I really like!

I’m trying to customize it for my own use cases, one of which is working with large compressed files, most frequently compressed with .gz but also tar.gz Within nushell, it would be great to overload open so that I could have .gz files be recognized and opened natively. Here is what I do now:

gunzip -c ratio_converted_uniq_5mC164/B1.tsv.gz | from tsv

This works well, but I have other file types I would like to open with other files types as well:

def "open gz" [file] {gunzip -c $file} 

I’m sorry in advance if this question has been addressed in nushell documentation, within these discussions or online. I’ve looked . . .

[sholderbach]

Under the hood open will look for from ... commands which match the file ending. so open file.tsv is doing the file opening and then invokes from tsv with the default arguments. Since #10593 you can define a from tsv.gz that will decompress the stream and dispatch to from tsv in turn.

def "from tsv.gz" [] {
  zcat | from tsv
}

[prairie-guy]

This is great. I defined my own “open gz”, but def “from tsv.gz” is better. Many thanks!

[sholderbach]

Defining from gz is still a useful idea, otherwise you have to define from fastq.gz, from txt.gz, ... but you can still specialize with a custom from like for from bed.gz

def "from gz" [] {
  zcat
}

def "from bed.gz" [] {
  zcat | from tsv --noheaders
}

open IMR-90_18_hg38.bed.gz | first 10
╭─#─┬column1┬column2─┬column3─┬───column4───╮
│ 0 │ chr1  │  10000 │  10600 │ 12_ZNF/Rpts │
│ 1 │ chr1  │  10600 │  13000 │ 6_TxWk      │
│ 2 │ chr1  │  13000 │  13200 │ 11_EnhWk    │
│ 3 │ chr1  │  13200 │  16000 │ 6_TxWk      │
│ 4 │ chr1  │  16000 │  17000 │ 5_Tx        │
│ 5 │ chr1  │  17000 │  19200 │ 6_TxWk      │
│ 6 │ chr1  │  19200 │  79000 │ 18_Quies    │
│ 7 │ chr1  │  79000 │  93600 │ 17_ReprPCWk │
│ 8 │ chr1  │ 605020 │ 605420 │ 1_TssA      │
│ 9 │ chr1  │ 605420 │ 725620 │ 18_Quies    │
╰───┴───────┴────────┴────────┴─────────────╯