diff --git a/tldr/linux/compseq b/tldr/linux/compseq new file mode 100644 index 00000000..a2327a12 --- /dev/null +++ b/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: . + +- 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` diff --git a/tldr/lsar b/tldr/lsar new file mode 100644 index 00000000..d18c46f9 --- /dev/null +++ b/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: . + +- 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` diff --git a/tldr/touch b/tldr/touch index 4fc2971e..a62cd0ff 100644 --- a/tldr/touch +++ b/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 ...}}` diff --git a/tldr/unar b/tldr/unar index 5170c283..f16cf70b 100644 --- a/tldr/unar +++ b/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}}`