Useful_one_liners

A place to keep one-line pieces of code that might come in handy

Bash

1. Find files of a certain type and copy to another location:

find . -name \*.xls -exec cp {} newDir \;

From: https://stackoverflow.com/questions/15617016/copy-all-files-with-a-certain-extension-from-all-subdirectories

2. Find files of a certain type and copy to a new location retaining file structure:

find top_level_folder/ -name '*.tsv' | cpio -pdm new_folder_name/

3. Find files of a certain name and copy them to a new folder using the name of the folder they are in as the name of the file (useful for examples such as the one below where a pipeline puts out a generic name, say for a fasta file)

find . -type f -name "contigs.fa" -printf "/%P\n" | while read FILE ; do DIR=$(dirname "$FILE" );\cp ."$FILE" "../fastas_for_emmtyper""$DIR".fa;done

Note also in this example, you can test it by adding echo immediately before cp.

From: https://askubuntu.com/questions/746860/rename-a-file-to-parent-directorys-name-in-terminal

4. Generate a input tsv from a list of files of a given type (.fa used here) and their paths in multiple subdirectories:

find $PWD -name '*.fa' -type f -print0 | while IFS= read -r -d '' file; do echo -e "$(basename "$file" .fa)\t$file"; done > input.tab

Note, you can modify this as necessary to change the type of file or the amount of the file name removed to form the sample name in the first column

Scripts

The below scripts may be of use:

Script	Comment	Source
Fasta parser	Python script to parse a multi fasta file and report composition as well as produce file listing entries that contain non-ATGC bases	made by Co-pilot

Nextflow

General bioinformatics packages

Seqkit