Results for "Oneliner"
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Fancy Oneliner for Bioinformatics !!
This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You ca...2856 days ago
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- To remove all line ends (\n) from a Unix text file: sed ':a;N;$!ba;s/\n//g' filename.txt > newfilename_oneline.txt To get average for a column of numbers (here the...
2214 days ago
Wire posts
Bio-Scripts
Bash oneliner to extract all ids from a multifasta file
#List of ids - one per line in allIds.txt $ awk 'BEGIN{while((getline0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa # You can play with this f=!l[$1 ] if wanted to extract or not extract the ids1535 days ago
Reformat the multifasta for sequence length !
#awk oneliner to reformat the multifasta sequences awk '!/^>/ {printf "%s", $0; n = "\n"} /^>/ {print n $0; n = ""}' file.fasta | fold -w 1001389 days ago
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Perl one-liner for beginners !
I often use the following arguments to perl: -e Makes the line of code be executed instead of a script -n Forces your line to be called in a loop. Allows you to take lines from the diamond operator (or stdin) -p Forces your line to be called in a loop. Prints $_ at the end This ...Tags: perl, oneliner, linux, handy, script, codes
1378 days ago
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- How about this oneliner ;) perl -ne 'chomp;if( />(.*)/){$head = $1; $i=0; next};@a=split("",$_); foreach(@a){$i++;if($_ eq "N" && $s ==0 ){print "$head\t$i"; $s =1}elsif($s==1 && $_ ne "N"){print "\t$i\n";$s=0}}' infile.fa
2687 days ago
Comment on "Perl one-liner for bioinformatician !!!"
Nice collection of Perl oneliner. Thank you for the useful list. You can also track other perl onliner posted on wire at http://bioinformaticsonline.com/thewire/tag/Oneliner3625 days ago
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