BOL: Wire posts tagged with 'Sed'

Wire post by Jit

Jit — Sun, 27 Mar 2022 21:46:27 -0500

sed -i 's/2019/2020/g' test.txt test2.txt test3.txt #Find #Replace #sed

BioStar — Sat, 22 Aug 2020 04:55:28 -0500

Enter newline at the end of the file $ sed -i -e '$a\' file #NewLine #Sed #Line #New

Aaryan Lokwani — Fri, 22 Jun 2018 05:53:37 -0500

Sed illegal charters from fasta. $ sed '/^[^>]/ s/[^AGTC]/N/gi' < seq.fa #fasta #otherthanATGC #replace #sed #Linux #illegal

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

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

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

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

Jit — Sun, 18 Jun 2017 14:14:13 -0500

Append the string to fasta header. $ sed 's/>.*/&_Bacteria/' foo.in > out.fasta #Sed #Fasta #String #Append

Jit — Tue, 30 May 2017 05:17:21 -0500

Filter #blank #lines from a #fasta file using sed. $ sed '/^$/d' finalSample.fa > finalSample_filtered.fa #Linux #Filter #FASTA #SED

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

Jit — Tue, 28 Mar 2017 17:25:07 -0500

Add ">" in front of ids. sed -e 's/^/prefix/' file #Sed #Add #>

Jit — Mon, 13 Mar 2017 11:46:36 -0500

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