finder – Easy methods to take away a file named “.”?

Overview

Incorrect specification of an argument in a commandline device (particulars beneath) has led to the creation of a file actually named “.”. I’ve already came upon that immediately attempting to delete in Finder will set off deletion of all content material within the containing folder (fortuitously this can be a non permanent folder), however nonetheless not the “.” file itself. Furthermore, no folders containing this file might be efficiently deleted, neither with Finder nor from bash/zsh shell.

Makes an attempt to delete from zsh

For instance:

mytmp % ls -hal
complete 65
drwx------  1 person  employees    16K Aug 21 11:20 .
-rwx------  1 person  employees     0B Aug 21 09:51 .
drwx------  1 person  employees    16K Aug 16 16:30 ..

mytmp % ls -aB
.   .   ..

mytmp % rm -rf '.'                   
rm: "." and ".." might not be eliminated

mytmp % cd ..

scratch % rm -rf mytmp
rm: mytmp: Permission denied

scratch % sudo rm -rf mytmp
rm: mytmp: Permission denied

I’ve additionally tried variations with out -r, since actually it’s the non-directory model that’s to be deleted.

I moreover tried the suggestion of @bmike to use the inode. Whereas we are able to determine the inode, the deletion doesn’t seem to work:

scratch % ls -ila mytmp
complete 65
8056451580272514705 drwx------  1 person  employees  16384 Aug 21 11:20 .
8652239633868421122 -rwx------  1 person  employees      0 Aug 21 09:51 .
                  2 drwx------  1 person  employees  16384 Aug 21 11:43 ..

scratch % discover mytmp -inum 8652239633868421122 -delete

## no change
scratch % ls -ila mytmp
complete 65
8056451580272514705 drwx------  1 person  employees  16384 Aug 21 11:20 .
8652239633868421122 -rwx------  1 person  employees      0 Aug 21 09:51 .
                  2 drwx------  1 person  employees  16384 Aug 21 11:43 ..

How can one really delete (or rename) such a file?

Further Background

The device that resulted on this was haplogrep, a Java-based CLI. One can set up it via Conda by way of

conda set up -c conda-forge -c bioconda haplogrep

The subcommand used was haplogrep classify, which has the next choices:

mytmp % haplogrep classify

mtDNA Haplogroup Classifiction v2.4.0
https://github.com/seppinho/haplogrep-cmd
(c) Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer, Dominic Pacher
[email protected]

[classify]
Lacking required choices: '--input=<in>', '--output=<out>', '--format=<format>'
Utilization: haplogrep classify [--chip] [--extend-report] [--rsrs]
                          [--skip-alignment-rules] [--write-fasta]
                          [--write-fasta-msa] --format=<format>
                          [--hetLevel=<hetLevel>] [--hits=<hits>] --in=<in>
                          [--lineage=<lineage>] [--metric=<metric>] --out=<out>
                          [--phylotree=<tree>]
      --chip                VCF information from a genotype chip
                              Default: false
      --extend-report       Add flag for a prolonged last output
                              Default: false
      --format=<format>     Specify enter file format: vcf, fasta or hsd
      --hetLevel=<hetLevel> Add heteroplasmies with a stage > X from the VCF
                              file to the profile (default: 0.9)
      --hits=<hits>         Calculate greatest n hits
      --in, --input=<in>    Enter VCF, fasta or hsd file
      --lineage=<lineage>   Export lineage info as dot file, n0=no
                              tree, 1=with SNPs, 2=solely construction, no SNPs
      --metric=<metric>     Specifiy different metrics (hamming or jaccard) than
                              default (kulczynski)
      --out, --output=<out> Output file location
      --phylotree=<tree>    Specify phylotree model
      --rsrs                Use RSRS Model
                              Default: false
      --skip-alignment-rules
                            Skip mtDNA nomenclature fixes primarily based on guidelines for
                              FASTA import
                              Default: false
      --write-fasta         Write leads to fasta format
                              Default: false
      --write-fasta-msa     Write a number of sequence alignment (_MSA.fasta)
                              Default: false

I misinterpreted the “Output file location” description of the --out argument as asking for a path, main me to make use of --out . and thus leading to making a file named “.”.

Renaming

The file itself can’t be renamed in Finder or with mv, nonetheless, the containing folder might be renamed.