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The Wire
#FASTA
Wire posts tagged with 'FASTA'
Neelam Jha
@neelam
Thread
By
Neelam Jha
2979 days ago
Delete space from FASTA header: perl -pe 's/>\S+\K.+//' < file.fasta > new_file.fasta
#PerlOneLiner
#Trick
#Perl
#Space
#Fasta
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3160 days ago
Remove the fasta description and just keep the identifier. perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa
#Perl
#Oneliner
#Trick
#Tips
#Fasta
#Identifier
#Remove
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3160 days ago
Extract sequences by their ID from a fasta file. perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if
@ARGV
' ids.txt sample1.fa
#Extract
#Sequences
#IDs
#Fasta
#Perl
#Trick
#Oneliner
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3188 days ago
Sort FASTA sequence by length: cat f1.fasta| awk '{if($0 ~ /^>/){printf "%st", $0}else{print length($0)"t"$0}}'| sort -k2n,2| awk '{print $1"n"$3}' > sequence.fasta
#Sort
#Fasta
#Trick
#Onliner
Jit
@jit.aber
Thread
By
Jit
3576 days ago
To count number of fasta entries, I use: grep -c '^>' mySequences.fasta
#Perl
#Count
#Number
#Fasta
#Linux
#Grep
Jit
@jit.aber
Thread
By
Jit
3621 days ago
Remove the blank space from a fasta file. perl -nlwe 'tr/ //d; print if length' fileName
#Delete
#Space
#Fasta
#Perl
#Oneliner
Jit
@jit.aber
Thread
By
Jit
3621 days ago
Remove N from a fasta file. Go to vi editor, type :%s/N\{25,\}//g and press enter.
#Vim
#vi
#N
#Replace
#Fasta
Jit
@jit.aber
Thread
By
Jit
3621 days ago
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
Jitendra Narayan
@admin
Thread
By
Jitendra Narayan
3628 days ago
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
https:/
/
github.com/
lh3/
seqtk
#FASTA
#FASTAQ
#NGS
Jit
@jit.aber
Thread
By
Jit
3635 days ago
FastaQ 2 Fasta Oneliner: paste - - - -< totalRNA_placental_1.fastq | perl -pale'$_="
@F
[0..1]"'|tr "\^@" "\>" | perl -pale 's/\s/\n/g'
#Oneliner
#NGS
#FastaQ
#Fasta
Neelam Jha
@neelam
Thread
By
Neelam Jha
3646 days ago
zcat input_file.fastq.gz | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa
#fastaQ2fasta
#fastaq
#fasta
#Oneliner
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3868 days ago
GenBank to FASTA format conversion, Written By Junguk HUR
http:/
/
tinyurl.com/
ntp7w5v
#Perl
#FASTA
#Genbank
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