one-liner

Here’s the matrix that we’ll be using: $ paste <(seq 1 5) <(seq 12 16) 1 12 2 13 3 14 4 15 5 16 Now, let’s use a perl one-liner with nested maps to transpose the matrix:

Let’s assume you have an array of numbers and you want to extract intervals from this array. For example, from such an array: 2,3,4,5,8,9,10,11,12,15,18,19,20 you should be getting (2-5), (8-12), (18-20) as intervals.

More bioinformatic case: Let’s assume you ran samtools pileup format and want to extract intervals from the genomic coordinates that has at least one hit.

Soon after SAM/BAM format became standard for short-read alignment softwares, high caliber tools have been emerging that can process the widely accepted format. bedtools is one of them and it’s easy to use and flexible.

In this post, I’ll demonstrate how to use gnuplot in a one-liner. We’ll use the pipe but unfortunately you cannot pipe raw data to gnuplot directly (as far as I know).

In an earlier [post]({{ ref “post/perl-one-liner-to-process-sequence-files-in-stream.md” }}) we learned how to use Bio::SeqIO module to process fasta files with one-liner. Let’s do more with this capability. What about selecting random sequences from a fasta file?

perl5i project explains itself as “Perl 5 has a lot of warts, fix as much of it as possible in one pragma”. You can run your scripts with it by including perl5i (ie, use perl5i;).

Most of the “most used commands” approaches does not consider pipes and other complexities. This approach considers pipes, process substitution by backticks or $() and multiple commands separated by ;

Let’s assume we have a file with five columns where first column is text and rest of the columns are numeric. How can we calculate the standard deviation (or other statistical functions) with a perl one-liner?

Need a practical way to process fasta files with Bio::SeqIO module ? Below code will print sequence id and sequence length with tab per line. perl -MBio::SeqIO -e '$seq=Bio::SeqIO->new(-fh=>\text{*}STDIN);while($myseq=$seq->next_seq){print $myseq->id,"\text{t}",$myseq->length,"\n";}' < filename OR

Very nice perl one-liner using map, sort and array range to show top ten occurrences Taken from Tech@Sakana blog perl -ane '$c{$F[0]}++; END {print map {${}_{.}"\text{t}->\text{t}".$c{$_} .