BOL: Wire posts tagged with 'Extract'

Wire post by Rahul Nayak

Rahul Nayak — Wed, 09 Sep 2015 16:01:53 -0500

Extract sequences by their ID from a fasta file. perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.txt sample1.fa #Extract #Sequences #IDs #Fasta #Perl #Trick #Oneliner

Wire post by Jit

Jit — Fri, 06 Jun 2014 02:38:28 -0500

perl -nle 'if (/^>/) { $sl = 0; print; next } next if ($sl >= 200); $_ = substr($_, 0, 200-$sl) if ($sl + length($_) > 200); $sl += length($_); print;' file.fa >new.fa #Perl #Extract #Fasta

Wire post by Jit

Jit — Fri, 23 May 2014 10:11:28 -0500

Extract list of read ID from bam file: samtools view mbi.sorted.bam |perl -ne '/ID/ && print' > extractedID.sam #Extract #Ids #SAM #BAM #NGS