BOL: Wire posts tagged with 'Remove'

Wire post by Jit

Jit — Mon, 25 May 2020 09:46:18 -0500

Remove conda environment completely $ conda env remove -n env_name #Remove #Conda #Environment

Wire post by BioStar

BioStar — Sat, 22 Sep 2018 07:03:57 -0500

Remove empty line from fasta. $ sed -i '/^$/d' standard_output.final.scaffolds_online.fasta #Empty #Fasta #Remove

Wire post by Jit

Jit — Thu, 02 Aug 2018 07:58:14 -0500

#Remove #smartbell from #pacbio #removesmartbell.sh https://github.com/BioInfoTools/BBMap/blob/master/sh/removesmartbell.sh

Wire post by Jit

Jit — Sat, 23 Jun 2018 16:13:15 -0500

perl -pe 's/[^AGTC\n]/N/gi unless m/>/;' /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta > /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds_corrected.fasta #Remove #Non-ATCG

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 Jit

Jit — Thu, 14 Dec 2017 04:55:21 -0600

#Remove a #sequence by id from multifasta: cat vaga.fa | awk '{if (substr($0,1) == ">scaffold_1 1087316 bp") censor=1; else if (substr($0,1,1) == ">") censor=0; if (censor==0) print $0}' > fixed.fasta

Wire post by Jit

Jit — Thu, 14 Dec 2017 04:00:38 -0600

awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} {if ($2) print ">"$0}' all_p_ctg.fa > all_p_ctg_CORRECTED.fa #remove #empty #clean #fasta

Wire post by Surabhi Chaudhary

Surabhi Chaudhary — Sun, 03 Dec 2017 17:47:00 -0600

Remove the unwanted characters from Fasta file: sed -e '/^[^>]/s/[^ATGCatgc]/N/g' infile.fa #sed #unwanted #illegal #remove #correct #fasta #linux

Wire post by Radha Agarkar

Radha Agarkar — Sun, 03 Dec 2017 15:39:46 -0600

Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas #fasta #remove

Wire post by Jit

Jit — Thu, 10 Aug 2017 04:21:16 -0500

Remove duplicated lines from text file. $ awk '!seen[$0]++' allIds #duplicate #lines #remove #awk

Wire post by Jit

Jit — Mon, 31 Jul 2017 03:50:54 -0500

Remove unwanted character from fasta file. $ sed -e '/^[^>]/s/[^ATGCatgc]/N/g' file.fa #IUPAC #Special #Character #Remove

Wire post by Jit

Jit — Sun, 25 Jun 2017 15:15:33 -0500

Remove four beginning characters from each line of the file. $ sed 's/^....//' genbank.txt #Remove #Sed #Text

Wire post by Jit

Jit — Mon, 13 Mar 2017 11:46:36 -0500

#Remove all line that start with # file: $ sed '/^#/ d' filename #line #sed #linux

Wire post by Rahul Nayak

Rahul Nayak — Wed, 09 Sep 2015 16:05:55 -0500

Remove the fasta description and just keep the identifier. perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #Perl #Oneliner #Trick #Tips #Fasta #Identifier #Remove

Wire post by Jit

Jit — Thu, 14 Aug 2014 19:41:47 -0500

The syntax to remove last character from line or word is as follows: x="foo bar" echo "${x%?}" #Remove #Last #Bash #Linux