Results for "one liner"
Blogs
Perl one-liner for beginners !
...file, split line at each space and print words one per line. perl -ne ...abs.txt > justSecondColumn.txt One-Liner: Sort lines by their length...gth $b} <>' textFile One-Liner: Print second column, unless...1381 days ago
Bookmarks
Download mutliple fasta file from NCBI in one GO!!
if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta seque...t you already have a list of GIs or accession IDs . Alternatively, use one liner perl script: perl -ne 'if(/^...3910 days ago
Pages
- ...doc perlrun), but I'm just going to cover the ones you'll commonly need to debu...means you can't use single-quotes within the one liner code. If you're using Windo...nd often test them at the command line with a one liner to see what they contain. For...
3269 days ago
Top-level pages
Most Commonly used Awk by Bioinformatician
...emory, and it's much faster to do it all with one. This is ideal for something...ng on the fly. You can use awk to make a neat one-liner for some quick job in the t...re.com/Unix/Awk.html A famous list of useful one-liners - though they're short, many...3912 days ago
Perl one-liner for bioinformatician !!!
...nowing a little bit of Perl onliner is extremely helpful. Perl one-liners are small and awesome Perl...once, and many more. Perl one-liners will make you the shell warr...le spaces, delete all leaving one(make the file a single spaced f...spot.in/2010/11/some-unixperl-oneliners-for.html http://genomespot....3628 days ago
Wire posts
Bio-Scripts
- bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam
1833 days ago
Samtools commands for bioinformatician !
...positions samtools depth -a sorted_dupremoved.bam > depth.txt ### one liner to count mean depth samtoo...epth -a sorted_dupremoved.bam | awk '{c++;s+=$3}END{print s/c}' ### one liner to count coverage breadth sa...1602 days ago
- +3 more Bio-Scripts
Groups
Awk is widely used these days for extraction and manipulation of large scale biological data in Unix/Linux.Most of the awk code is single liner. Useful Weblinks: http://ww...3919 days ago
Tags
- Awk is widely used these days for extraction and manipulation of large scale biological data in Unix/Linux.Most of the awk code is single liner. Useful Weblinks: http://www.grymoire.com/Unix/Awk.html http://www.hcs.harvard.edu/~dholland/computers/awk.html http://www.pement.org/awk/awk1line.tx...
Tags: awk, gawk, nawk, sed, data, sequencing, one liner
3919 days ago
Comments
Comment on "How to install Perl modules manually, using CPAN command, and other quick ways"
Check the perl module Test if dependencies are met by running this perl one-liner: perl -e "use JSON::XS;"1234 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Some of the commonly used bioinformatics one-liner by Stephen Turner @ https://github.com/stephenturner/oneliners3810 days ago
