BOL: Wire posts tagged with 'count'

Wire post by LEGE

LEGE — Thu, 02 Sep 2021 06:41:33 -0500

Count number of fasta sequence $ awk '/^>/ { f = !a[$0]++ } f' aaaa.fa > bbbb.fa #count #fasta #oneliner

Wire post by Rahul Nayak

Rahul Nayak — Thu, 20 Dec 2018 13:18:03 -0600

Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

Wire post by Aaryan Lokwani

Aaryan Lokwani — Fri, 22 Jun 2018 04:41:13 -0500

Count the contigs length in index fasta file with samtools. $ awk '{s+=$2}END{print s}' scaffolds.fasta.fai #Fasta #Index #Length #Count #Size #Samtools

Wire post by Jit

Jit — Wed, 08 Nov 2017 12:05:57 -0600

Get the reads in fastq file: awk '{s++}END{print s/4}' file.fastq #reads #count #ngs #fastq

Wire post by Rahul Nayak

Rahul Nayak — Fri, 23 Jun 2017 05:06:43 -0500

Count the number of bases in fasta file. grep -v ">" file.fasta | wc | awk '{print $3-$1}' #Fasta #Count #Bases

Wire post by Rahul Nayak

Rahul Nayak — Wed, 09 Sep 2015 16:17:11 -0500

Count the number of sequences in fastaq file. grep -c '^@' sample1.fq #Fastaq #Count #Number #Grep #Dirty #Oneliner #NGS

Wire post by Jit

Jit — Mon, 21 Jul 2014 06:37:42 -0500

To count number of fasta entries, I use: grep -c '^>' mySequences.fasta #Perl #Count #Number #Fasta #Linux #Grep

Wire post by Jit

Jit — Wed, 11 Jun 2014 03:54:53 -0500

Count the number of occurrence of pattern in a file using Perl. perl -e '$_ = <>; print scalar ( () = m/needle/g ), "\n"' #Perl #Perloneliner #Count #Occurrence

Wire post by Jit

Jit — Wed, 11 Jun 2014 03:04:58 -0500

Count the number of "pattern" occurrence in a file grep -o 'pattern' anc.annots.gff | wc -l #Linux #grep #Count #Number #Occurrence

Wire post by Jit

Jit — Tue, 10 Jun 2014 05:34:41 -0500

Count the total number of lines in a file. my $total=@{[]}; #Perl #Count #Number #Total #File

Wire post by Rahul Nayak

Rahul Nayak — Sun, 11 May 2014 10:16:51 -0500

perl -nle '$count += () = /XY[0-9]+/g; END {print $count}' inputfile #Count #Perl #Perloneliner