BOL: Results for "Oneliner"

Results for "Oneliner"

- Poonam Mahapatra@poonam
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...
2842 days ago

- Rahul Nayak@rahul
Bioinformatics OneLiner
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...
2201 days ago

- Jit@jit.aber
Remove the blank space from a fasta file. perl -nlwe 'tr/ //d; print if length' fileName #Delete #Space #Fasta #Perl #Oneliner
3605 days ago
- Neelam Jha@neelam
zcat input_file.fastq.gz | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa #fastaQ2fasta #fastaq #fasta #Oneliner
3629 days ago
+16 more Wire posts

- biogeek@biogeek
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 ids
1521 days ago
- BioStar@biostar
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 100
1375 days ago
+2 more Bio-Scripts

- Bulbul@bulbul
Comment on "BioGeek Fun"
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
2673 days ago
- Jitendra Narayan@admin
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/Oneliner
3611 days ago
+1 more Comments