BOL: Wire posts tagged with 'ids'

Wire post by Jit

Jit — Tue, 18 Dec 2018 04:18:32 -0600

Extract sequence by ids $ xargs samtools faidx Adineta_vaga.v2.pep.fa < AlienIds > allAlienSeq.fa #Extract #Ids #Sequences

Wire post by Manisha Mishra

Manisha Mishra — Tue, 17 Apr 2018 17:43:19 -0500

Remove the sequence by fasta ids. awk 'BEGIN{while((getline<"ids.txt")>0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa #Remove #Delete #ids #fasta

Wire post by Manisha Mishra

Manisha Mishra — Tue, 17 Apr 2018 16:37:42 -0500

Extract fasta with Ids. $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #extract #fasta #sequence #ids

Wire post by Poonam Mahapatra

Poonam Mahapatra — Mon, 11 Dec 2017 04:22:59 -0600

Remove duplicate fasta ids: awk '/^>/{f=!d[$1];d[$1]=1}f' in.fa > out.fa #duplicate #fasta #ids

Wire post by Radha Agarkar

Radha Agarkar — Fri, 16 Sep 2016 03:00:15 -0500

Extract sequence by using Ids file (assuming one ids in a line): perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.file fasta.file #PerlTricks #PerlOneliner #Perl #Extract #Ids #

Wire post by Radha Agarkar

Radha Agarkar — Fri, 16 Sep 2016 02:57:36 -0500

Extract fasta sequence by Ids: perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #Perl #PerlOneliner #PerlTrick #Extract #Ids #Fasta

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, 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