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noc => (BOOL) to ignore case in matching inv => (BOOL) to extract what DOES NOT match The only ones that are taken care of are: | /. Special characters in names or descriptions will be an issue regex => (BOOL) to look for containing the word and not an exact match both => (BOOL) to look into both headers and description desc => (BOOL) to look for match in the description and not the header (extracting line that matches + 3 lines after the match)Īlso, this makes irrelevant the use of these options: Will be extracted using grep -A 3 for each word set with -m
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Only relevant if -fq is set as well, because the sequences grep => (BOOL) Chose this with -fq to use grep instead of using BioSeq fq => (BOOL) if input file is in fastq format output will also be fastq out => (STRING) to set the name of the output file (default = ) file => (BOOL) chose this if -m corresponds to a file descriptions only (spaces allowed) if -desc is set
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PERL SCRIPT TO FIND WORD IN FILE FULL
full fasta headers (use -both to match both, otherwise only ID is looked at) If the \">\" or is kept with the ID, then all lines need to have it (unless -grep) (ii) a file: it can be a fasta/fastq file, or simply a file with a list of IDs (one column) Note that there can't be spaces in the command line, or they have to be escaped with \ (i) in command line: you can set several words using, (comma) as a separator. m => (STRING) provide (i) a word or a list of words, or (ii) a path to a file Perl fasta_ -in fastafile.fa -m list.txt -both -v To extract all sequences that have their full header listed in a file Perl fasta_ -in fastafile.fa -m list.txt -v To extract all sequences that have their ID listed in a file Perl fasta_ -in fastafile.fa -m virus -both -inv -v To extract all sequences that don't have the word \"virus\" in the description or in the ID Perl fasta_ -in fastafile.fa -m ERV,LTR -regex -v To extract all sequences containing ERV or LTR in IDs only: matching ID (from command line or using another fasta file or a file containing a list of IDs using -file) The ID corresponds to anything before the first space, description is anything that's after (even if spaces) the complement of that (meaning, extract when it does not match), option -inv (inverse match) containing a word in the ID or in the description (-desc), or in both (-both) matching ID (from command line or from a file containing a list of IDs using -file) That’s It! If you know any other command-line trick to find string or word in files, do share with us or ask any questions regarding this topic, use the comment form below.This script allows to extract fasta sequences from a file. $ grep -Rinw ~/bin/ -e 'check_root' -e 'netstat'
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In addition, it is possible to search for more than one pattern, using the following command. $ grep -Rnw -include=\*.sh ~/bin/ -e 'check_root' This example instructs grep to only look through all. $ grep -Rinw ~/bin/ -e 'check_root'Īssuming there are several types of files in a directory you wish to search in, you can also specify the type of files to be searched for instance, by their extension using the -include option. If you want to know the exact line where the string of text exist, include the -n option. To ignore case distinctions employ the -i option as shown: $ grep -Riw ~/bin/ -e 'check_root' You should use the sudo command when searching certain directories or files that require root permissions (unless you are managing your system with the root account). Where the -R option tells grep to read all files under each directory, recursively, following symbolic links only if they are on the command line and option -w instructs it to select only those lines containing matches that form whole words, and -e is used to specify the string (pattern) to be searched. The command below will list all files containing a line with the text “ check_root”, by recursively and aggressively searching the ~/bin directory. Read Also: 11 Advanced Linux ‘Grep’ Commands on Character Classes and Bracket Expressions
PERL SCRIPT TO FIND WORD IN FILE HOW TO
This article will guide you on how to do that, you will learn how to recursively dig through directories to find and list all files that contain a given string of text.Ī simple way to work this out is by using grep pattern searching tool, is a powerful, efficient, reliable and most popular command-line utility for finding patterns and words from files or directories on Unix-like systems. Do you want to find all files that contain a particular word or string of text on your entire Linux system or a given directory.