BOL: Wire posts tagged with 'header'

Wire post by BioStar

BioStar — Mon, 22 Jan 2024 03:25:18 -0600

Delete all the headers from multifasta file $ awk 'BEGIN {print ">"ARGV[1]};!/^>/{print}' test.fa #fasta #delete #header #multifasta

Wire post by Neel

Neel — Fri, 29 Nov 2019 22:14:54 -0600

Perl onliner to add string to each of the fasta header. $ perl -p -e 's/^(>.*)$/$1-origin/g' in.fasta > out.fasta #String #Header #Fasta

Wire post by Neel

Neel — Fri, 15 Nov 2019 23:13:24 -0600

#Rename the #fasta #header and #keep first $ perl -ne 'if (/^(>\S+)/){print "$1\n";}else{print $_;}' realTestDATA.fa > realTestDATA_headerCorrected.fa #Perl

Wire post by Rahul Nayak

Rahul Nayak — Mon, 11 Feb 2019 06:11:41 -0600

One liner to remove the description information from a fasta file and just keep the identifier $ perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #clean #header #fasta

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 Jit

Jit — Fri, 02 Nov 2018 09:23:44 -0500

Rename the fasta header perl -ane 'if(/\>/){$a++;print ">LR$a\n"}else{print;}' allPacBio_clean.fa > allPacBio_clean_shortName.fa
#fasta #header #rename

Wire post by Rahul Nayak

Rahul Nayak — Wed, 19 Jul 2017 08:26:23 -0500

Remove "|" from fasta header. $ sed 's,|,_,g' -i file.fa #fasta #header #sed

Wire post by Rahul Nayak

Rahul Nayak — Wed, 19 Jul 2017 08:22:57 -0500

Remove unwanted character from fasta file. sed -e '/^[^>]/s/[^ATGCatgc]/N/g' file.fa #fasta #file #header #charater

Wire post by Jit

Jit — Thu, 06 Jul 2017 14:35:32 -0500

Remove the unnecessary #fasta #header. $ sed 's/\s.*$//' Adineta_vaga_v2.0.scaffolds.fa > new_file.fasta

Wire post by Jit

Jit — Fri, 21 Apr 2017 08:28:28 -0500

To clean up a fasta file so only first column of the header is outputted:$ awk '{print $1}' file.fa > output.fa #Sed #Clean #Header #Fasta