Update cheatsheets

tldr/linux/compseq

@@ -0,0 +1,41 @@
+---
+syntax: markdown
+tags: [tldr, linux]
+source: https://github.com/tldr-pages/tldr.git
+---
+# compseq
+
+> Calculate the composition of unique words in sequences.
+> More information: <https://www.bioinformatics.nl/cgi-bin/emboss/help/compseq/>.
+
+- Count observed frequencies of words in a FASTA file, providing parameter values with interactive prompt:
+
+`compseq {{path/to/file.fasta}}`
+
+- Count observed frequencies of amino acid pairs from a FASTA file, save output to a text file:
+
+`compseq {{path/to/input_protein.fasta}} -word 2 {{path/to/output_file.comp}}`
+
+- Count observed frequencies of hexanucleotides from a FASTA file, save output to a text file and ignore zero counts:
+
+`compseq {{path/to/input_dna.fasta}} -word 6 {{path/to/output_file.comp}} -nozero`
+
+- Count observed frequencies of codons in a particular reading frame; ignoring any overlapping counts (i.e. move window across by word-length 3):
+
+`compseq -sequence {{path/to/input_rna.fasta}} -word 3 {{path/to/output_file.comp}} -nozero -frame {{1}}`
+
+- Count observed frequencies of codons frame-shifted by 3 positions; ignoring any overlapping counts (should report all codons except the first one):
+
+`compseq -sequence {{path/to/input_rna.fasta}} -word 3 {{path/to/output_file.comp}} -nozero -frame 3`
+
+- Count amino acid triplets in a FASTA file and compare to a previous run of `compseq` to calculate expected and normalised frequency values:
+
+`compseq -sequence {{path/to/human_proteome.fasta}} -word 3 {{path/to/output_file1.comp}} -nozero -infile {{path/to/output_file2.comp}}`
+
+- Approximate the above command without a previously prepared file, by calculating expected frequencies using the single base/residue frequencies in the supplied input sequence(s):
+
+`compseq -sequence {{path/to/human_proteome.fasta}} -word 3 {{path/to/output_file.comp}} -nozero -calcfreq`
+
+- Display help (use `-help -verbose` for more information on associated and general qualifiers):
+
+`compseq -help`

tldr/lsar

@@ -0,0 +1,34 @@
+---
+syntax: markdown
+tags: [tldr, common]
+source: https://github.com/tldr-pages/tldr.git
+---
+# lsar
+
+> List an archive file's contents.
+> See also: `unar`, `ar`.
+> More information: <https://manned.org/lsar>.
+
+- List an archive file's contents:
+
+`lsar {{path/to/archive}}`
+
+- List a password protected archive file's contents:
+
+`lsar {{path/to/archive}} --password {{password}}`
+
+- Print al[L] available information about each file in the archive (it's very long):
+
+`lsar {{-L|--verylong}} {{path/to/archive}}`
+
+- Test the integrity of the files in the archive (if possible):
+
+`lsar --test {{path/to/archive}}`
+
+- List the archive file's contents in JSON format:
+
+`lsar --json {{path/to/archive}}`
+
+- Display help:
+
+`lsar --help`

tldr/touch

@@ -20,6 +20,6 @@ source: https://github.com/tldr-pages/tldr.git
 
 `touch -c -t {{YYYYMMDDHHMM.SS}} {{path/to/file1 path/to/file2 ...}}`
 
-- Set the file time of a specific file to the time of anothe[r] file and don't [c]reate file if it doesn't exist:
+- Set the files' timestamp to the [r]eference file's timestamp, and do not [c]reate the file if it does not exist:
 
-`touch -c -r {{~/.emacs}} {{path/to/file1 path/to/file2 ...}}`
+`touch -c -r {{path/to/reference_file}} {{path/to/file1 path/to/file2 ...}}`

tldr/unar

@@ -10,20 +10,20 @@ source: https://github.com/tldr-pages/tldr.git
 
 - Extract an archive to the current directory:
 
-`unar {{archive}}`
+`unar {{path/to/archive}}`
 
 - Extract an archive to the specified directory:
 
-`unar -o {{path/to/directory}} {{archive}}`
+`unar -o {{path/to/directory}} {{path/to/archive}}`
 
 - Force overwrite if files to be unpacked already exist:
 
-`unar -f {{archive}}`
+`unar -f {{path/to/archive}}`
 
 - Force rename if files to be unpacked already exist:
 
-`unar -r {{archive}}`
+`unar -r {{path/to/archive}}`
 
 - Force skip if files to be unpacked already exist:
 
-`unar -s {{archive}}`
+`unar -s {{path/to/archive}}`